https://launchpad.net/ubuntu/+source/python-cogent/2023.2.12a1+dfsg-1/+build/25612566 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-ppc64el-002 5.4.0-139-generic #156-Ubuntu SMP Fri Jan 20 17:27:42 UTC 2023 ppc64le Buildd toolchain package versions: launchpad-buildd_230~623~ubuntu20.04.1 python3-lpbuildd_230~623~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.10 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 22 Feb 17:13:30 ntpdate[2128]: adjust time server 10.211.37.1 offset -0.001039 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=lunar --arch=ppc64el PACKAGEBUILD-25612566 --image-type chroot /home/buildd/filecache-default/7984b9498478de1d58b749dc057a3cf5e3226d68 Creating target for build PACKAGEBUILD-25612566 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=lunar --arch=ppc64el PACKAGEBUILD-25612566 Starting target for build PACKAGEBUILD-25612566 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=lunar --arch=ppc64el PACKAGEBUILD-25612566 'deb http://ftpmaster.internal/ubuntu lunar main universe' 'deb http://ftpmaster.internal/ubuntu lunar-security main universe' 'deb http://ftpmaster.internal/ubuntu lunar-updates main universe' 'deb http://ftpmaster.internal/ubuntu lunar-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-25612566 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=lunar --arch=ppc64el PACKAGEBUILD-25612566 Updating target for build PACKAGEBUILD-25612566 Get:1 http://ftpmaster.internal/ubuntu lunar InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main ppc64el Packages [1338 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main Translation-en [510 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/universe ppc64el Packages [14.8 MB] Get:8 http://ftpmaster.internal/ubuntu lunar/universe Translation-en [5931 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el Packages [271 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main Translation-en [106 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/universe ppc64el Packages [789 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/universe Translation-en [385 kB] Fetched 24.7 MB in 6s (3943 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-13-base libproc2-0 The following packages will be upgraded: adduser advancecomp apt bash binutils binutils-common binutils-powerpc64le-linux-gnu coreutils cpp cpp-12 dash debconf diffutils dpkg dpkg-dev e2fsprogs fakeroot g++ g++-12 gcc gcc-12 gcc-12-base gpg gpg-agent gpgconf gpgv grep hostname libacl1 libapt-pkg6.0 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdpkg-perl libext2fs2 libfakeroot libgcc-12-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libitm1 libkmod2 liblsan0 liblzma5 libmpfr6 libncurses6 libncursesw6 libp11-kit0 libpcre2-8-0 libperl5.36 libquadmath0 libreadline8 libselinux1 libsemanage-common libsemanage2 libsqlite3-0 libss2 libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libtsan2 libubsan1 libudev1 libzstd1 linux-libc-dev logsave lsb-base lto-disabled-list ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.36 pkgbinarymangler procps readline-common sed sensible-utils systemd systemd-sysv sysvinit-utils tzdata xz-utils zlib1g 106 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 103 MB of archives. After this operation, 9447 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu lunar/main ppc64el bash ppc64el 5.2.15-2ubuntu1 [956 kB] Get:2 http://ftpmaster.internal/ubuntu lunar/main ppc64el coreutils ppc64el 9.1-1ubuntu2 [1508 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libc-bin ppc64el 2.37-0ubuntu1 [736 kB] Get:4 http://ftpmaster.internal/ubuntu lunar/main ppc64el libcrypt-dev ppc64el 1:4.4.33-2 [143 kB] Get:5 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libc6-dev ppc64el 2.37-0ubuntu1 [2057 kB] Get:6 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libc-dev-bin ppc64el 2.37-0ubuntu1 [20.9 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/main ppc64el libcrypt1 ppc64el 1:4.4.33-2 [106 kB] Get:8 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el linux-libc-dev ppc64el 6.1.0-14.14 [1461 kB] Get:9 http://ftpmaster.internal/ubuntu lunar/main ppc64el gcc-13-base ppc64el 13-20230215-1ubuntu2 [18.7 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgcc-s1 ppc64el 13-20230215-1ubuntu2 [38.5 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libc6 ppc64el 2.37-0ubuntu1 [3178 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el liblzma5 ppc64el 5.4.1-0.2 [154 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgcrypt20 ppc64el 1.10.1-3ubuntu1 [718 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main ppc64el libstdc++6 ppc64el 13-20230215-1ubuntu2 [870 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main ppc64el libacl1 ppc64el 2.3.1-3 [20.4 kB] Get:16 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libaudit-common all 1:3.0.9-1 [5142 B] Get:17 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libaudit1 ppc64el 1:3.0.9-1 [51.2 kB] Get:18 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libcap2 ppc64el 1:2.66-3ubuntu2 [33.2 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main ppc64el libperl5.36 ppc64el 5.36.0-7 [4848 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main ppc64el perl ppc64el 5.36.0-7 [235 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main ppc64el perl-base ppc64el 5.36.0-7 [1855 kB] Get:22 http://ftpmaster.internal/ubuntu lunar/main ppc64el perl-modules-5.36 all 5.36.0-7 [2984 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdb5.3 ppc64el 5.3.28+dfsg2-1 [847 kB] Get:24 http://ftpmaster.internal/ubuntu lunar/main ppc64el zlib1g ppc64el 1:1.2.13.dfsg-1ubuntu4 [70.1 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main ppc64el debconf all 1.5.82 [125 kB] Get:26 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libssl3 ppc64el 3.0.8-1ubuntu1 [2140 kB] Get:27 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libzstd1 ppc64el 1.5.4+dfsg2-3 [373 kB] Get:28 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libkmod2 ppc64el 30+20221128-1ubuntu1 [59.8 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main ppc64el libpcre2-8-0 ppc64el 10.42-1 [256 kB] Get:30 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libselinux1 ppc64el 3.4-1build3 [96.4 kB] Get:31 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el systemd-sysv ppc64el 252.5-2ubuntu1 [11.5 kB] Get:32 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el systemd ppc64el 252.5-2ubuntu1 [3198 kB] Get:33 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libsystemd-shared ppc64el 252.5-2ubuntu1 [1964 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main ppc64el libcryptsetup12 ppc64el 2:2.6.1-1ubuntu1 [329 kB] Get:35 http://ftpmaster.internal/ubuntu lunar/main ppc64el libp11-kit0 ppc64el 0.24.1-2ubuntu1 [258 kB] Get:36 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libsystemd0 ppc64el 252.5-2ubuntu1 [405 kB] Get:37 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libudev1 ppc64el 252.5-2ubuntu1 [110 kB] Get:38 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libapt-pkg6.0 ppc64el 2.5.6 [1016 kB] Get:39 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el dpkg ppc64el 1.21.20ubuntu2 [1470 kB] Get:40 http://ftpmaster.internal/ubuntu lunar/main ppc64el dash ppc64el 0.5.12-2ubuntu1 [105 kB] Get:41 http://ftpmaster.internal/ubuntu lunar/main ppc64el diffutils ppc64el 1:3.8-4 [196 kB] Get:42 http://ftpmaster.internal/ubuntu lunar/main ppc64el grep ppc64el 3.8-5 [170 kB] Get:43 http://ftpmaster.internal/ubuntu lunar/main ppc64el hostname ppc64el 3.23+nmu1ubuntu1 [11.1 kB] Get:44 http://ftpmaster.internal/ubuntu lunar/main ppc64el ncurses-bin ppc64el 6.4-2 [196 kB] Get:45 http://ftpmaster.internal/ubuntu lunar/main ppc64el sed ppc64el 4.9-1 [208 kB] Get:46 http://ftpmaster.internal/ubuntu lunar/main ppc64el ncurses-base all 6.4-2 [21.3 kB] Get:47 http://ftpmaster.internal/ubuntu lunar/main ppc64el sysvinit-utils ppc64el 3.05-7ubuntu2 [28.5 kB] Get:48 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el lsb-base all 11.6 [4606 B] Get:49 http://ftpmaster.internal/ubuntu lunar/main ppc64el adduser all 3.129ubuntu1 [59.0 kB] Get:50 http://ftpmaster.internal/ubuntu lunar/main ppc64el gpgv ppc64el 2.2.40-1ubuntu2 [171 kB] Get:51 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libgnutls30 ppc64el 3.7.8-5ubuntu1 [1038 kB] Get:52 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el apt ppc64el 2.5.6 [1420 kB] Get:53 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el logsave ppc64el 1.47.0-1ubuntu1 [14.7 kB] Get:54 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libext2fs2 ppc64el 1.47.0-1ubuntu1 [255 kB] Get:55 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el e2fsprogs ppc64el 1.47.0-1ubuntu1 [652 kB] Get:56 http://ftpmaster.internal/ubuntu lunar/main ppc64el libattr1 ppc64el 1:2.5.1-4 [13.2 kB] Get:57 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libdebconfclient0 ppc64el 0.267ubuntu1 [7796 B] Get:58 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libsemanage-common all 3.4-1build3 [9808 B] Get:59 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libsemanage2 ppc64el 3.4-1build3 [113 kB] Get:60 http://ftpmaster.internal/ubuntu lunar/main ppc64el libncurses6 ppc64el 6.4-2 [144 kB] Get:61 http://ftpmaster.internal/ubuntu lunar/main ppc64el libncursesw6 ppc64el 6.4-2 [179 kB] Get:62 http://ftpmaster.internal/ubuntu lunar/main ppc64el libtinfo6 ppc64el 6.4-2 [124 kB] Get:63 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgomp1 ppc64el 13-20230215-1ubuntu2 [154 kB] Get:64 http://ftpmaster.internal/ubuntu lunar/main ppc64el libitm1 ppc64el 13-20230215-1ubuntu2 [32.6 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main ppc64el libatomic1 ppc64el 13-20230215-1ubuntu2 [10.6 kB] Get:66 http://ftpmaster.internal/ubuntu lunar/main ppc64el libasan8 ppc64el 13-20230215-1ubuntu2 [2823 kB] Get:67 http://ftpmaster.internal/ubuntu lunar/main ppc64el liblsan0 ppc64el 13-20230215-1ubuntu2 [1227 kB] Get:68 http://ftpmaster.internal/ubuntu lunar/main ppc64el g++-12 ppc64el 12.2.0-14ubuntu2 [11.4 MB] Get:69 http://ftpmaster.internal/ubuntu lunar/main ppc64el gcc-12 ppc64el 12.2.0-14ubuntu2 [19.8 MB] Get:70 http://ftpmaster.internal/ubuntu lunar/main ppc64el libstdc++-12-dev ppc64el 12.2.0-14ubuntu2 [2288 kB] Get:71 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgcc-12-dev ppc64el 12.2.0-14ubuntu2 [1512 kB] Get:72 http://ftpmaster.internal/ubuntu lunar/main ppc64el libtsan2 ppc64el 13-20230215-1ubuntu2 [2641 kB] Get:73 http://ftpmaster.internal/ubuntu lunar/main ppc64el libubsan1 ppc64el 13-20230215-1ubuntu2 [1129 kB] Get:74 http://ftpmaster.internal/ubuntu lunar/main ppc64el libquadmath0 ppc64el 13-20230215-1ubuntu2 [156 kB] Get:75 http://ftpmaster.internal/ubuntu lunar/main ppc64el libmpfr6 ppc64el 4.2.0-1 [343 kB] Get:76 http://ftpmaster.internal/ubuntu lunar/main ppc64el libcc1-0 ppc64el 13-20230215-1ubuntu2 [48.9 kB] Get:77 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libctf0 ppc64el 2.40-2ubuntu2 [110 kB] Get:78 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libctf-nobfd0 ppc64el 2.40-2ubuntu2 [109 kB] Get:79 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.40-2ubuntu2 [2445 kB] Get:80 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libbinutils ppc64el 2.40-2ubuntu2 [728 kB] Get:81 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el binutils ppc64el 2.40-2ubuntu2 [3070 B] Get:82 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el binutils-common ppc64el 2.40-2ubuntu2 [226 kB] Get:83 http://ftpmaster.internal/ubuntu lunar/main ppc64el cpp-12 ppc64el 12.2.0-14ubuntu2 [10.0 MB] Get:84 http://ftpmaster.internal/ubuntu lunar/main ppc64el gcc-12-base ppc64el 12.2.0-14ubuntu2 [19.6 kB] Get:85 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libcom-err2 ppc64el 1.47.0-1ubuntu1 [14.6 kB] Get:86 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libss2 ppc64el 1.47.0-1ubuntu1 [17.5 kB] Get:87 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libproc2-0 ppc64el 2:4.0.3-1ubuntu1 [62.1 kB] Get:88 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el procps ppc64el 2:4.0.3-1ubuntu1 [632 kB] Get:89 http://ftpmaster.internal/ubuntu lunar/main ppc64el sensible-utils all 0.0.17+nmu1 [19.3 kB] Get:90 http://ftpmaster.internal/ubuntu lunar/main ppc64el readline-common all 8.2-1.3 [55.7 kB] Get:91 http://ftpmaster.internal/ubuntu lunar/main ppc64el libreadline8 ppc64el 8.2-1.3 [175 kB] Get:92 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsqlite3-0 ppc64el 3.40.1-1 [749 kB] Get:93 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el openssl ppc64el 3.0.8-1ubuntu1 [1196 kB] Get:94 http://ftpmaster.internal/ubuntu lunar/main ppc64el tzdata all 2022g-2ubuntu1 [397 kB] Get:95 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el xz-utils ppc64el 5.4.1-0.2 [277 kB] Get:96 http://ftpmaster.internal/ubuntu lunar/main ppc64el advancecomp ppc64el 2.5-1 [235 kB] Get:97 http://ftpmaster.internal/ubuntu lunar/main ppc64el g++ ppc64el 4:12.2.0-3ubuntu1 [1116 B] Get:98 http://ftpmaster.internal/ubuntu lunar/main ppc64el gcc ppc64el 4:12.2.0-3ubuntu1 [5194 B] Get:99 http://ftpmaster.internal/ubuntu lunar/main ppc64el cpp ppc64el 4:12.2.0-3ubuntu1 [27.8 kB] Get:100 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el dpkg-dev all 1.21.20ubuntu2 [1117 kB] Get:101 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libdpkg-perl all 1.21.20ubuntu2 [247 kB] Get:102 http://ftpmaster.internal/ubuntu lunar/main ppc64el lto-disabled-list all 38 [12.3 kB] Get:103 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libfakeroot ppc64el 1.31-1ubuntu1 [32.9 kB] Get:104 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el fakeroot ppc64el 1.31-1ubuntu1 [62.1 kB] Get:105 http://ftpmaster.internal/ubuntu lunar/main ppc64el gpg ppc64el 2.2.40-1ubuntu2 [646 kB] Get:106 http://ftpmaster.internal/ubuntu lunar/main ppc64el gpgconf ppc64el 2.2.40-1ubuntu2 [103 kB] Get:107 http://ftpmaster.internal/ubuntu lunar/main ppc64el gpg-agent ppc64el 2.2.40-1ubuntu2 [253 kB] Get:108 http://ftpmaster.internal/ubuntu lunar/main ppc64el pkgbinarymangler all 152 [16.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 103 MB in 7s (13.8 MB/s) (Reading database ... 13031 files and directories currently installed.) Preparing to unpack .../bash_5.2.15-2ubuntu1_ppc64el.deb ... Unpacking bash (5.2.15-2ubuntu1) over (5.2-1ubuntu2) ... Setting up bash (5.2.15-2ubuntu1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 13031 files and directories currently installed.) Preparing to unpack .../coreutils_9.1-1ubuntu2_ppc64el.deb ... Unpacking coreutils (9.1-1ubuntu2) over (8.32-4.1ubuntu1) ... Setting up coreutils (9.1-1ubuntu2) ... (Reading database ... 13031 files and directories currently installed.) Preparing to unpack .../libc-bin_2.37-0ubuntu1_ppc64el.deb ... Unpacking libc-bin (2.37-0ubuntu1) over (2.36-0ubuntu4) ... Setting up libc-bin (2.37-0ubuntu1) ... (Reading database ... 13031 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.33-2_ppc64el.deb ... Unpacking libcrypt-dev:ppc64el (1:4.4.33-2) over (1:4.4.33-1) ... Preparing to unpack .../libc6-dev_2.37-0ubuntu1_ppc64el.deb ... Unpacking libc6-dev:ppc64el (2.37-0ubuntu1) over (2.36-0ubuntu4) ... Preparing to unpack .../libc-dev-bin_2.37-0ubuntu1_ppc64el.deb ... Unpacking libc-dev-bin (2.37-0ubuntu1) over (2.36-0ubuntu4) ... Preparing to unpack .../libcrypt1_1%3a4.4.33-2_ppc64el.deb ... Unpacking libcrypt1:ppc64el (1:4.4.33-2) over (1:4.4.33-1) ... Setting up libcrypt1:ppc64el (1:4.4.33-2) ... (Reading database ... 13031 files and directories currently installed.) Preparing to unpack .../linux-libc-dev_6.1.0-14.14_ppc64el.deb ... Unpacking linux-libc-dev:ppc64el (6.1.0-14.14) over (5.19.0-21.21) ... Selecting previously unselected package gcc-13-base:ppc64el. Preparing to unpack .../gcc-13-base_13-20230215-1ubuntu2_ppc64el.deb ... Unpacking gcc-13-base:ppc64el (13-20230215-1ubuntu2) ... Setting up gcc-13-base:ppc64el (13-20230215-1ubuntu2) ... (Reading database ... 15036 files and directories currently installed.) Preparing to unpack .../libgcc-s1_13-20230215-1ubuntu2_ppc64el.deb ... Unpacking libgcc-s1:ppc64el (13-20230215-1ubuntu2) over (12.2.0-10ubuntu1) ... Setting up libgcc-s1:ppc64el (13-20230215-1ubuntu2) ... (Reading database ... 15036 files and directories currently installed.) Preparing to unpack .../libc6_2.37-0ubuntu1_ppc64el.deb ... Unpacking libc6:ppc64el (2.37-0ubuntu1) over (2.36-0ubuntu4) ... Setting up libc6:ppc64el (2.37-0ubuntu1) ... (Reading database ... 15036 files and directories currently installed.) Preparing to unpack .../liblzma5_5.4.1-0.2_ppc64el.deb ... Unpacking liblzma5:ppc64el (5.4.1-0.2) over (5.2.9-0.0) ... Setting up liblzma5:ppc64el (5.4.1-0.2) ... (Reading database ... 15036 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.10.1-3ubuntu1_ppc64el.deb ... Unpacking libgcrypt20:ppc64el (1.10.1-3ubuntu1) over (1.10.1-2ubuntu1) ... Setting up libgcrypt20:ppc64el (1.10.1-3ubuntu1) ... (Reading database ... 15036 files and directories currently installed.) Preparing to unpack .../libstdc++6_13-20230215-1ubuntu2_ppc64el.deb ... Unpacking libstdc++6:ppc64el (13-20230215-1ubuntu2) over (12.2.0-10ubuntu1) ... Setting up libstdc++6:ppc64el (13-20230215-1ubuntu2) ... (Reading database ... 15036 files and directories currently installed.) Preparing to unpack .../libacl1_2.3.1-3_ppc64el.deb ... Unpacking libacl1:ppc64el (2.3.1-3) over (2.3.1-2) ... Setting up libacl1:ppc64el (2.3.1-3) ... (Reading database ... 15036 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a3.0.9-1_all.deb ... Unpacking libaudit-common (1:3.0.9-1) over (1:3.0.7-1ubuntu3) ... Setting up libaudit-common (1:3.0.9-1) ... (Reading database ... 15036 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.0.9-1_ppc64el.deb ... Unpacking libaudit1:ppc64el (1:3.0.9-1) over (1:3.0.7-1ubuntu3) ... Setting up libaudit1:ppc64el (1:3.0.9-1) ... (Reading database ... 15036 files and directories currently installed.) Preparing to unpack .../libcap2_1%3a2.66-3ubuntu2_ppc64el.deb ... Unpacking libcap2:ppc64el (1:2.66-3ubuntu2) over (1:2.44-1build3) ... Setting up libcap2:ppc64el (1:2.66-3ubuntu2) ... (Reading database ... 15038 files and directories currently installed.) Preparing to unpack .../libperl5.36_5.36.0-7_ppc64el.deb ... Unpacking libperl5.36:ppc64el (5.36.0-7) over (5.36.0-4ubuntu2) ... Preparing to unpack .../perl_5.36.0-7_ppc64el.deb ... Unpacking perl (5.36.0-7) over (5.36.0-4ubuntu2) ... Preparing to unpack .../perl-base_5.36.0-7_ppc64el.deb ... Unpacking perl-base (5.36.0-7) over (5.36.0-4ubuntu2) ... Setting up perl-base (5.36.0-7) ... (Reading database ... 15038 files and directories currently installed.) Preparing to unpack .../perl-modules-5.36_5.36.0-7_all.deb ... Unpacking perl-modules-5.36 (5.36.0-7) over (5.36.0-4ubuntu2) ... Preparing to unpack .../libdb5.3_5.3.28+dfsg2-1_ppc64el.deb ... Unpacking libdb5.3:ppc64el (5.3.28+dfsg2-1) over (5.3.28+dfsg1-0.10) ... Setting up libdb5.3:ppc64el (5.3.28+dfsg2-1) ... (Reading database ... 15038 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.2.13.dfsg-1ubuntu4_ppc64el.deb ... Unpacking zlib1g:ppc64el (1:1.2.13.dfsg-1ubuntu4) over (1:1.2.11.dfsg-4.1ubuntu1) ... Setting up zlib1g:ppc64el (1:1.2.13.dfsg-1ubuntu4) ... (Reading database ... 15038 files and directories currently installed.) Preparing to unpack .../debconf_1.5.82_all.deb ... Unpacking debconf (1.5.82) over (1.5.79ubuntu1) ... Setting up debconf (1.5.82) ... (Reading database ... 15038 files and directories currently installed.) Preparing to unpack .../libssl3_3.0.8-1ubuntu1_ppc64el.deb ... Unpacking libssl3:ppc64el (3.0.8-1ubuntu1) over (3.0.5-2ubuntu2) ... Preparing to unpack .../libzstd1_1.5.4+dfsg2-3_ppc64el.deb ... Unpacking libzstd1:ppc64el (1.5.4+dfsg2-3) over (1.5.2+dfsg-1) ... Setting up libzstd1:ppc64el (1.5.4+dfsg2-3) ... (Reading database ... 15038 files and directories currently installed.) Preparing to unpack .../libkmod2_30+20221128-1ubuntu1_ppc64el.deb ... Unpacking libkmod2:ppc64el (30+20221128-1ubuntu1) over (30+20220905-1ubuntu1) ... Preparing to unpack .../libpcre2-8-0_10.42-1_ppc64el.deb ... Unpacking libpcre2-8-0:ppc64el (10.42-1) over (10.40-1ubuntu1) ... Setting up libpcre2-8-0:ppc64el (10.42-1) ... (Reading database ... 15038 files and directories currently installed.) Preparing to unpack .../libselinux1_3.4-1build3_ppc64el.deb ... Unpacking libselinux1:ppc64el (3.4-1build3) over (3.4-1build1) ... Setting up libselinux1:ppc64el (3.4-1build3) ... (Reading database ... 15038 files and directories currently installed.) Preparing to unpack .../systemd-sysv_252.5-2ubuntu1_ppc64el.deb ... Unpacking systemd-sysv (252.5-2ubuntu1) over (251.4-1ubuntu7) ... Setting up libssl3:ppc64el (3.0.8-1ubuntu1) ... (Reading database ... 15039 files and directories currently installed.) Preparing to unpack .../systemd_252.5-2ubuntu1_ppc64el.deb ... Unpacking systemd (252.5-2ubuntu1) over (251.4-1ubuntu7) ... Preparing to unpack .../libsystemd-shared_252.5-2ubuntu1_ppc64el.deb ... Unpacking libsystemd-shared:ppc64el (252.5-2ubuntu1) over (251.4-1ubuntu7) ... Preparing to unpack .../libcryptsetup12_2%3a2.6.1-1ubuntu1_ppc64el.deb ... Unpacking libcryptsetup12:ppc64el (2:2.6.1-1ubuntu1) over (2:2.5.0-6ubuntu3) ... Preparing to unpack .../libp11-kit0_0.24.1-2ubuntu1_ppc64el.deb ... Unpacking libp11-kit0:ppc64el (0.24.1-2ubuntu1) over (0.24.1-1ubuntu2) ... Setting up libp11-kit0:ppc64el (0.24.1-2ubuntu1) ... (Reading database ... 15051 files and directories currently installed.) Preparing to unpack .../libsystemd0_252.5-2ubuntu1_ppc64el.deb ... Unpacking libsystemd0:ppc64el (252.5-2ubuntu1) over (251.4-1ubuntu7) ... Setting up libsystemd0:ppc64el (252.5-2ubuntu1) ... (Reading database ... 15052 files and directories currently installed.) Preparing to unpack .../libudev1_252.5-2ubuntu1_ppc64el.deb ... Unpacking libudev1:ppc64el (252.5-2ubuntu1) over (251.4-1ubuntu7) ... Setting up libudev1:ppc64el (252.5-2ubuntu1) ... (Reading database ... 15053 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.5.6_ppc64el.deb ... Unpacking libapt-pkg6.0:ppc64el (2.5.6) over (2.5.4) ... Setting up libapt-pkg6.0:ppc64el (2.5.6) ... (Reading database ... 15053 files and directories currently installed.) Preparing to unpack .../dpkg_1.21.20ubuntu2_ppc64el.deb ... Unpacking dpkg (1.21.20ubuntu2) over (1.21.11ubuntu2) ... Setting up dpkg (1.21.20ubuntu2) ... (Reading database ... 15056 files and directories currently installed.) Preparing to unpack .../dash_0.5.12-2ubuntu1_ppc64el.deb ... Unpacking dash (0.5.12-2ubuntu1) over (0.5.11+git20210903+057cd650a4ed-9ubuntu1) ... Setting up dash (0.5.12-2ubuntu1) ... (Reading database ... 15056 files and directories currently installed.) Preparing to unpack .../diffutils_1%3a3.8-4_ppc64el.deb ... Unpacking diffutils (1:3.8-4) over (1:3.8-1) ... Setting up diffutils (1:3.8-4) ... (Reading database ... 15056 files and directories currently installed.) Preparing to unpack .../grep_3.8-5_ppc64el.deb ... Unpacking grep (3.8-5) over (3.8-3) ... Setting up grep (3.8-5) ... (Reading database ... 15056 files and directories currently installed.) Preparing to unpack .../hostname_3.23+nmu1ubuntu1_ppc64el.deb ... Unpacking hostname (3.23+nmu1ubuntu1) over (3.23ubuntu2) ... Setting up hostname (3.23+nmu1ubuntu1) ... (Reading database ... 15056 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.4-2_ppc64el.deb ... Unpacking ncurses-bin (6.4-2) over (6.3+20220423-2) ... Setting up ncurses-bin (6.4-2) ... (Reading database ... 15056 files and directories currently installed.) Preparing to unpack .../archives/sed_4.9-1_ppc64el.deb ... Unpacking sed (4.9-1) over (4.8-1ubuntu2) ... Setting up sed (4.9-1) ... (Reading database ... 15056 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.4-2_all.deb ... Unpacking ncurses-base (6.4-2) over (6.3+20220423-2) ... Setting up ncurses-base (6.4-2) ... (Reading database ... 15056 files and directories currently installed.) Preparing to unpack .../archives/lsb-base_11.6_all.deb ... Unpacking lsb-base (11.6) over (11.2ubuntu1) ... Preparing to unpack .../sysvinit-utils_3.05-7ubuntu2_ppc64el.deb ... Unpacking sysvinit-utils (3.05-7ubuntu2) over (3.04-1ubuntu1) ... Setting up sysvinit-utils (3.05-7ubuntu2) ... (Reading database ... 15056 files and directories currently installed.) Preparing to unpack .../adduser_3.129ubuntu1_all.deb ... moving unchanged adduser.conf to adduser.conf.update-old. New dpkg-conffile will come from the package. Unpacking adduser (3.129ubuntu1) over (3.121ubuntu1) ... Setting up adduser (3.129ubuntu1) ... Installing new version of config file /etc/deluser.conf ... (Reading database ... 15023 files and directories currently installed.) Preparing to unpack .../gpgv_2.2.40-1ubuntu2_ppc64el.deb ... Unpacking gpgv (2.2.40-1ubuntu2) over (2.2.40-1ubuntu1) ... Setting up gpgv (2.2.40-1ubuntu2) ... (Reading database ... 15023 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.8-5ubuntu1_ppc64el.deb ... Unpacking libgnutls30:ppc64el (3.7.8-5ubuntu1) over (3.7.7-2ubuntu2) ... Setting up libgnutls30:ppc64el (3.7.8-5ubuntu1) ... (Reading database ... 15023 files and directories currently installed.) Preparing to unpack .../archives/apt_2.5.6_ppc64el.deb ... Unpacking apt (2.5.6) over (2.5.4) ... Setting up apt (2.5.6) ... Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... (Reading database ... 15023 files and directories currently installed.) Preparing to unpack .../logsave_1.47.0-1ubuntu1_ppc64el.deb ... Unpacking logsave (1.47.0-1ubuntu1) over (1.46.6~rc1-1ubuntu1) ... Preparing to unpack .../libext2fs2_1.47.0-1ubuntu1_ppc64el.deb ... Unpacking libext2fs2:ppc64el (1.47.0-1ubuntu1) over (1.46.6~rc1-1ubuntu1) ... Setting up libext2fs2:ppc64el (1.47.0-1ubuntu1) ... (Reading database ... 15023 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.47.0-1ubuntu1_ppc64el.deb ... Unpacking e2fsprogs (1.47.0-1ubuntu1) over (1.46.6~rc1-1ubuntu1) ... Preparing to unpack .../libattr1_1%3a2.5.1-4_ppc64el.deb ... Unpacking libattr1:ppc64el (1:2.5.1-4) over (1:2.5.1-3) ... Setting up libattr1:ppc64el (1:2.5.1-4) ... (Reading database ... 15023 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.267ubuntu1_ppc64el.deb ... Unpacking libdebconfclient0:ppc64el (0.267ubuntu1) over (0.264ubuntu1) ... Setting up libdebconfclient0:ppc64el (0.267ubuntu1) ... (Reading database ... 15023 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.4-1build3_all.deb ... Unpacking libsemanage-common (3.4-1build3) over (3.4-1build1) ... Setting up libsemanage-common (3.4-1build3) ... (Reading database ... 15023 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.4-1build3_ppc64el.deb ... Unpacking libsemanage2:ppc64el (3.4-1build3) over (3.4-1build1) ... Setting up libsemanage2:ppc64el (3.4-1build3) ... (Reading database ... 15023 files and directories currently installed.) Preparing to unpack .../libncurses6_6.4-2_ppc64el.deb ... Unpacking libncurses6:ppc64el (6.4-2) over (6.3+20220423-2) ... Preparing to unpack .../libncursesw6_6.4-2_ppc64el.deb ... Unpacking libncursesw6:ppc64el (6.4-2) over (6.3+20220423-2) ... Preparing to unpack .../libtinfo6_6.4-2_ppc64el.deb ... Unpacking libtinfo6:ppc64el (6.4-2) over (6.3+20220423-2) ... Setting up libtinfo6:ppc64el (6.4-2) ... (Reading database ... 15023 files and directories currently installed.) Preparing to unpack .../00-libgomp1_13-20230215-1ubuntu2_ppc64el.deb ... Unpacking libgomp1:ppc64el (13-20230215-1ubuntu2) over (12.2.0-10ubuntu1) ... Preparing to unpack .../01-libitm1_13-20230215-1ubuntu2_ppc64el.deb ... Unpacking libitm1:ppc64el (13-20230215-1ubuntu2) over (12.2.0-10ubuntu1) ... Preparing to unpack .../02-libatomic1_13-20230215-1ubuntu2_ppc64el.deb ... Unpacking libatomic1:ppc64el (13-20230215-1ubuntu2) over (12.2.0-10ubuntu1) ... Preparing to unpack .../03-libasan8_13-20230215-1ubuntu2_ppc64el.deb ... Unpacking libasan8:ppc64el (13-20230215-1ubuntu2) over (12.2.0-10ubuntu1) ... Preparing to unpack .../04-liblsan0_13-20230215-1ubuntu2_ppc64el.deb ... Unpacking liblsan0:ppc64el (13-20230215-1ubuntu2) over (12.2.0-10ubuntu1) ... Preparing to unpack .../05-g++-12_12.2.0-14ubuntu2_ppc64el.deb ... Unpacking g++-12 (12.2.0-14ubuntu2) over (12.2.0-10ubuntu1) ... Preparing to unpack .../06-gcc-12_12.2.0-14ubuntu2_ppc64el.deb ... Unpacking gcc-12 (12.2.0-14ubuntu2) over (12.2.0-10ubuntu1) ... Preparing to unpack .../07-libstdc++-12-dev_12.2.0-14ubuntu2_ppc64el.deb ... Unpacking libstdc++-12-dev:ppc64el (12.2.0-14ubuntu2) over (12.2.0-10ubuntu1) ... Preparing to unpack .../08-libgcc-12-dev_12.2.0-14ubuntu2_ppc64el.deb ... Unpacking libgcc-12-dev:ppc64el (12.2.0-14ubuntu2) over (12.2.0-10ubuntu1) ... Preparing to unpack .../09-libtsan2_13-20230215-1ubuntu2_ppc64el.deb ... Unpacking libtsan2:ppc64el (13-20230215-1ubuntu2) over (12.2.0-10ubuntu1) ... Preparing to unpack .../10-libubsan1_13-20230215-1ubuntu2_ppc64el.deb ... Unpacking libubsan1:ppc64el (13-20230215-1ubuntu2) over (12.2.0-10ubuntu1) ... Preparing to unpack .../11-libquadmath0_13-20230215-1ubuntu2_ppc64el.deb ... Unpacking libquadmath0:ppc64el (13-20230215-1ubuntu2) over (12.2.0-10ubuntu1) ... Preparing to unpack .../12-libmpfr6_4.2.0-1_ppc64el.deb ... Unpacking libmpfr6:ppc64el (4.2.0-1) over (4.1.0-3build3) ... Preparing to unpack .../13-libcc1-0_13-20230215-1ubuntu2_ppc64el.deb ... Unpacking libcc1-0:ppc64el (13-20230215-1ubuntu2) over (12.2.0-10ubuntu1) ... Preparing to unpack .../14-libctf0_2.40-2ubuntu2_ppc64el.deb ... Unpacking libctf0:ppc64el (2.40-2ubuntu2) over (2.39.50.20221224-1ubuntu1) ... Preparing to unpack .../15-libctf-nobfd0_2.40-2ubuntu2_ppc64el.deb ... Unpacking libctf-nobfd0:ppc64el (2.40-2ubuntu2) over (2.39.50.20221224-1ubuntu1) ... Preparing to unpack .../16-binutils-powerpc64le-linux-gnu_2.40-2ubuntu2_ppc64el.deb ... Unpacking binutils-powerpc64le-linux-gnu (2.40-2ubuntu2) over (2.39.50.20221224-1ubuntu1) ... Preparing to unpack .../17-libbinutils_2.40-2ubuntu2_ppc64el.deb ... Unpacking libbinutils:ppc64el (2.40-2ubuntu2) over (2.39.50.20221224-1ubuntu1) ... Preparing to unpack .../18-binutils_2.40-2ubuntu2_ppc64el.deb ... Unpacking binutils (2.40-2ubuntu2) over (2.39.50.20221224-1ubuntu1) ... Preparing to unpack .../19-binutils-common_2.40-2ubuntu2_ppc64el.deb ... Unpacking binutils-common:ppc64el (2.40-2ubuntu2) over (2.39.50.20221224-1ubuntu1) ... Preparing to unpack .../20-cpp-12_12.2.0-14ubuntu2_ppc64el.deb ... Unpacking cpp-12 (12.2.0-14ubuntu2) over (12.2.0-10ubuntu1) ... Preparing to unpack .../21-gcc-12-base_12.2.0-14ubuntu2_ppc64el.deb ... Unpacking gcc-12-base:ppc64el (12.2.0-14ubuntu2) over (12.2.0-10ubuntu1) ... Preparing to unpack .../22-libcom-err2_1.47.0-1ubuntu1_ppc64el.deb ... Unpacking libcom-err2:ppc64el (1.47.0-1ubuntu1) over (1.46.6~rc1-1ubuntu1) ... Preparing to unpack .../23-libss2_1.47.0-1ubuntu1_ppc64el.deb ... Unpacking libss2:ppc64el (1.47.0-1ubuntu1) over (1.46.6~rc1-1ubuntu1) ... Selecting previously unselected package libproc2-0:ppc64el. Preparing to unpack .../24-libproc2-0_2%3a4.0.3-1ubuntu1_ppc64el.deb ... Unpacking libproc2-0:ppc64el (2:4.0.3-1ubuntu1) ... Preparing to unpack .../25-procps_2%3a4.0.3-1ubuntu1_ppc64el.deb ... Unpacking procps (2:4.0.3-1ubuntu1) over (2:3.3.17-7ubuntu1) ... Preparing to unpack .../26-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) over (0.0.17) ... Preparing to unpack .../27-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) over (8.2-1.2) ... Preparing to unpack .../28-libreadline8_8.2-1.3_ppc64el.deb ... Unpacking libreadline8:ppc64el (8.2-1.3) over (8.2-1.2) ... Preparing to unpack .../29-libsqlite3-0_3.40.1-1_ppc64el.deb ... Unpacking libsqlite3-0:ppc64el (3.40.1-1) over (3.40.0-1) ... Preparing to unpack .../30-openssl_3.0.8-1ubuntu1_ppc64el.deb ... Unpacking openssl (3.0.8-1ubuntu1) over (3.0.5-2ubuntu2) ... Preparing to unpack .../31-tzdata_2022g-2ubuntu1_all.deb ... Unpacking tzdata (2022g-2ubuntu1) over (2022g-1ubuntu1) ... Preparing to unpack .../32-xz-utils_5.4.1-0.2_ppc64el.deb ... Unpacking xz-utils (5.4.1-0.2) over (5.2.9-0.0) ... Preparing to unpack .../33-advancecomp_2.5-1_ppc64el.deb ... Unpacking advancecomp (2.5-1) over (2.4-1) ... Preparing to unpack .../34-g++_4%3a12.2.0-3ubuntu1_ppc64el.deb ... Unpacking g++ (4:12.2.0-3ubuntu1) over (4:12.2.0-1ubuntu1) ... Preparing to unpack .../35-gcc_4%3a12.2.0-3ubuntu1_ppc64el.deb ... Unpacking gcc (4:12.2.0-3ubuntu1) over (4:12.2.0-1ubuntu1) ... Preparing to unpack .../36-cpp_4%3a12.2.0-3ubuntu1_ppc64el.deb ... Unpacking cpp (4:12.2.0-3ubuntu1) over (4:12.2.0-1ubuntu1) ... Preparing to unpack .../37-dpkg-dev_1.21.20ubuntu2_all.deb ... Unpacking dpkg-dev (1.21.20ubuntu2) over (1.21.11ubuntu2) ... Preparing to unpack .../38-libdpkg-perl_1.21.20ubuntu2_all.deb ... Unpacking libdpkg-perl (1.21.20ubuntu2) over (1.21.11ubuntu2) ... Preparing to unpack .../39-lto-disabled-list_38_all.deb ... Unpacking lto-disabled-list (38) over (37) ... Preparing to unpack .../40-libfakeroot_1.31-1ubuntu1_ppc64el.deb ... Unpacking libfakeroot:ppc64el (1.31-1ubuntu1) over (1.30.1-1ubuntu1) ... Preparing to unpack .../41-fakeroot_1.31-1ubuntu1_ppc64el.deb ... Unpacking fakeroot (1.31-1ubuntu1) over (1.30.1-1ubuntu1) ... Preparing to unpack .../42-gpg_2.2.40-1ubuntu2_ppc64el.deb ... Unpacking gpg (2.2.40-1ubuntu2) over (2.2.40-1ubuntu1) ... Preparing to unpack .../43-gpgconf_2.2.40-1ubuntu2_ppc64el.deb ... Unpacking gpgconf (2.2.40-1ubuntu2) over (2.2.40-1ubuntu1) ... Preparing to unpack .../44-gpg-agent_2.2.40-1ubuntu2_ppc64el.deb ... Unpacking gpg-agent (2.2.40-1ubuntu2) over (2.2.40-1ubuntu1) ... Preparing to unpack .../45-pkgbinarymangler_152_all.deb ... Unpacking pkgbinarymangler (152) over (149) ... Setting up lsb-base (11.6) ... Setting up lto-disabled-list (38) ... Setting up libsqlite3-0:ppc64el (3.40.1-1) ... Setting up binutils-common:ppc64el (2.40-2ubuntu2) ... Setting up linux-libc-dev:ppc64el (6.1.0-14.14) ... Setting up libctf-nobfd0:ppc64el (2.40-2ubuntu2) ... Setting up libcom-err2:ppc64el (1.47.0-1ubuntu1) ... Setting up libgomp1:ppc64el (13-20230215-1ubuntu2) ... Setting up libfakeroot:ppc64el (1.31-1ubuntu1) ... Setting up gcc-12-base:ppc64el (12.2.0-14ubuntu2) ... Setting up tzdata (2022g-2ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Feb 22 17:14:01 UTC 2023. Universal Time is now: Wed Feb 22 17:14:01 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.31-1ubuntu1) ... Setting up perl-modules-5.36 (5.36.0-7) ... Setting up libmpfr6:ppc64el (4.2.0-1) ... Setting up libncurses6:ppc64el (6.4-2) ... Setting up xz-utils (5.4.1-0.2) ... Setting up libquadmath0:ppc64el (13-20230215-1ubuntu2) ... Setting up libproc2-0:ppc64el (2:4.0.3-1ubuntu1) ... Setting up libatomic1:ppc64el (13-20230215-1ubuntu2) ... Setting up libss2:ppc64el (1.47.0-1ubuntu1) ... Setting up libncursesw6:ppc64el (6.4-2) ... Setting up logsave (1.47.0-1ubuntu1) ... Setting up libubsan1:ppc64el (13-20230215-1ubuntu2) ... Setting up advancecomp (2.5-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libcrypt-dev:ppc64el (1:4.4.33-2) ... Setting up libasan8:ppc64el (13-20230215-1ubuntu2) ... Setting up procps (2:4.0.3-1ubuntu1) ... Setting up libcryptsetup12:ppc64el (2:2.6.1-1ubuntu1) ... Setting up libtsan2:ppc64el (13-20230215-1ubuntu2) ... Setting up libbinutils:ppc64el (2.40-2ubuntu2) ... Setting up libc-dev-bin (2.37-0ubuntu1) ... Setting up openssl (3.0.8-1ubuntu1) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up readline-common (8.2-1.3) ... Setting up libcc1-0:ppc64el (13-20230215-1ubuntu2) ... Setting up libperl5.36:ppc64el (5.36.0-7) ... Setting up liblsan0:ppc64el (13-20230215-1ubuntu2) ... Setting up libitm1:ppc64el (13-20230215-1ubuntu2) ... Setting up libkmod2:ppc64el (30+20221128-1ubuntu1) ... Setting up libctf0:ppc64el (2.40-2ubuntu2) ... Setting up cpp-12 (12.2.0-14ubuntu2) ... Setting up pkgbinarymangler (152) ... Setting up libreadline8:ppc64el (8.2-1.3) ... Setting up e2fsprogs (1.47.0-1ubuntu1) ... Installing new version of config file /etc/mke2fs.conf ... Setting up perl (5.36.0-7) ... Setting up libgcc-12-dev:ppc64el (12.2.0-14ubuntu2) ... Setting up libsystemd-shared:ppc64el (252.5-2ubuntu1) ... Setting up libdpkg-perl (1.21.20ubuntu2) ... Setting up cpp (4:12.2.0-3ubuntu1) ... Setting up gpgconf (2.2.40-1ubuntu2) ... Setting up libc6-dev:ppc64el (2.37-0ubuntu1) ... Setting up binutils-powerpc64le-linux-gnu (2.40-2ubuntu2) ... Setting up gpg (2.2.40-1ubuntu2) ... Setting up gpg-agent (2.2.40-1ubuntu2) ... Setting up libstdc++-12-dev:ppc64el (12.2.0-14ubuntu2) ... Setting up systemd (252.5-2ubuntu1) ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up binutils (2.40-2ubuntu2) ... Setting up dpkg-dev (1.21.20ubuntu2) ... Setting up gcc-12 (12.2.0-14ubuntu2) ... Setting up g++-12 (12.2.0-14ubuntu2) ... Setting up systemd-sysv (252.5-2ubuntu1) ... Setting up gcc (4:12.2.0-3ubuntu1) ... Setting up g++ (4:12.2.0-3ubuntu1) ... Processing triggers for libc-bin (2.37-0ubuntu1) ... Processing triggers for debianutils (5.7-0.4) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-25612566 ppc64el lunar-proposed -c chroot:build-PACKAGEBUILD-25612566 --arch=ppc64el --dist=lunar-proposed --nolog python-cogent_2023.2.12a1+dfsg-1.dsc Initiating build PACKAGEBUILD-25612566 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-139-generic #156-Ubuntu SMP Fri Jan 20 17:27:42 UTC 2023 ppc64le sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-ppc64el-002.buildd +==============================================================================+ | python-cogent 2023.2.12a1+dfsg-1 (ppc64el) Wed, 22 Feb 2023 17:14:03 +0000 | +==============================================================================+ Package: python-cogent Version: 2023.2.12a1+dfsg-1 Source Version: 2023.2.12a1+dfsg-1 Distribution: lunar-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-25612566/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/python-cogent-TxxDfm/resolver-nM4Ck4' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-cogent_2023.2.12a1+dfsg-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/python-cogent-TxxDfm/python-cogent-2023.2.12a1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/python-cogent-TxxDfm' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, flit, cython3, pandoc, pybuild-plugin-pyproject, python3-all-dev, python3-matplotlib, python3-numba, python3-numpy, python3-pandas, python3-scitrack, python3-tqdm, python3-tinydb, python3-sphinx, python3-numpydoc, python3-nbsphinx, python3-sphinx-bootstrap-theme, python3-sphinx-gallery, python3-pytest, python3-pytest-cov, python3-pytest-xdist, python3-plotly, python3-typing-extensions, python3-isort, python3-scipy, python3-chardet, python3-jupyterlab-server, python3-jupyter-sphinx-theme, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-python, flit, cython3, pandoc, pybuild-plugin-pyproject, python3-all-dev, python3-matplotlib, python3-numba, python3-numpy, python3-pandas, python3-scitrack, python3-tqdm, python3-tinydb, python3-sphinx, python3-numpydoc, python3-nbsphinx, python3-sphinx-bootstrap-theme, python3-sphinx-gallery, python3-pytest, python3-pytest-cov, python3-pytest-xdist, python3-plotly, python3-typing-extensions, python3-isort, python3-scipy, python3-chardet, python3-jupyterlab-server, python3-jupyter-sphinx-theme, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [564 B] Get:5 copy:/<>/apt_archive ./ Packages [641 B] Fetched 2168 B in 0s (207 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev blt bsdextrautils cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file flit fontconfig-config fonts-dejavu-core fonts-glyphicons-halflings fonts-lyx gettext gettext-base groff-base intltool-debian jupyter-sphinx-theme-common libarchive-zip-perl libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libcurl4 libdebhelper-perl libdeflate0 libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu72 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap libjs-bootswatch libjs-jquery libjs-jquery-hotkeys libjs-jquery-isonscreen libjs-jquery-metadata libjs-jquery-tablesorter libjs-jquery-throttle-debounce libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl liblapack3 liblbfgsb0 liblcms2-2 libldap2 liblerc4 libllvm14 liblua5.3-0 libmagic-mgc libmagic1 libmpdec3 libnghttp2-14 libnorm1 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenjp2-7 libpfm4 libpgm-5.3-0 libpipeline1 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libraqm0 librtmp1 libsasl2-2 libsasl2-modules-db libsodium23 libssh-4 libsub-override-perl libtcl8.6 libtiff6 libtk8.6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxsimd-dev libxslt1.1 libxss1 libyaml-0-2 libzmq5 llvm-14 llvm-14-linker-tools llvm-14-runtime m4 man-db media-types pandoc pandoc-data po-debconf pybuild-plugin-pyproject python-babel-localedata python-matplotlib-data python-tinycss2-common python3 python3-alabaster python3-all python3-all-dev python3-anyio python3-appdirs python3-argon2 python3-attr python3-babel python3-beniget python3-bleach python3-brotli python3-bs4 python3-build python3-certifi python3-cffi-backend python3-chardet python3-commonmark python3-coverage python3-cycler python3-dateutil python3-decorator python3-defusedxml python3-dev python3-distutils python3-docutils python3-entrypoints python3-execnet python3-fastjsonschema python3-fonttools python3-fs python3-gast python3-html5lib python3-idna python3-imagesize python3-importlib-metadata python3-iniconfig python3-installer python3-isort python3-jinja2 python3-json5 python3-jsonschema python3-jupyter-client python3-jupyter-core python3-jupyter-server python3-jupyter-sphinx-theme python3-jupyterlab-pygments python3-jupyterlab-server python3-kiwisolver python3-lib2to3 python3-llvmlite python3-lxml python3-lz4 python3-markupsafe python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-nbclient python3-nbconvert python3-nbformat python3-nbsphinx python3-nest-asyncio python3-numba python3-numpy python3-numpydoc python3-packaging python3-pandas python3-pandas-lib python3-pandocfilters python3-pbr python3-pep517 python3-pil python3-pil.imagetk python3-pkg-resources python3-plotly python3-pluggy python3-ply python3-prometheus-client python3-ptyprocess python3-py python3-pygments python3-pyparsing python3-pyrsistent python3-pytest python3-pytest-cov python3-pytest-xdist python3-pythran python3-recommonmark python3-requests python3-roman python3-scipy python3-scitrack python3-send2trash python3-setuptools python3-six python3-sniffio python3-snowballstemmer python3-soupsieve python3-sphinx python3-sphinx-bootstrap-theme python3-sphinx-gallery python3-sympy python3-tenacity python3-terminado python3-tinycss2 python3-tinydb python3-tk python3-toml python3-tomli python3-tomli-w python3-tornado python3-tqdm python3-traitlets python3-typing-extensions python3-tz python3-ufolib2 python3-urllib3 python3-webencodings python3-websocket python3-wheel python3-zipp python3-zmq python3.10 python3.10-minimal python3.11 python3.11-dev python3.11-minimal sgml-base sphinx-common tk8.6-blt2.5 unicode-data x11-common xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc blt-demo cython-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libboost-doc libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-regex1.74-dev libboost-serialization1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev low-memory-monitor libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk libxsimd-doc llvm-14-doc m4-doc apparmor less www-browser texlive-latex-recommended texlive-xetex texlive-luatex pandoc-citeproc texlive-latex-extra context wkhtmltopdf librsvg2-bin ghc nodejs php python ruby r-base-core libjs-mathjax libjs-katex citation-style-language-styles libmail-box-perl python3-doc python3-venv python-argon2-doc python-attr-doc python-bleach-doc python3-pip python-coverage-doc python-cycler-doc docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french texlive-latex-base execnet-doc python-fastjsonschema-doc python3-genshi python-installer-doc python-jinja2-doc python-jsonschema-doc python3-json-pointer python3-rfc3987 python3-uritemplate python3-webcolors jupyter-sphinx-theme-doc llvmlite-doc python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip texlive-extra-utils python-mpmath-doc python3-gmpy2 python-nbconvert-doc texlive-fonts-recommended texlive-plain-generic python-nbsphinx-doc nvidia-cuda-toolkit gfortran python-pandas-doc python3-statsmodels python-pil-doc python3-ipykernel python-ply-doc subversion python-pygments-doc ttf-bitstream-vera python-pyparsing-doc python3-cryptography python3-openssl python3-socks python-requests-doc python-scipy-doc python-setuptools-doc python3-stemmer fonts-freefont-otf imagemagick-6.q16 latexmk python3-sphinx-rtd-theme sphinx-doc tex-gyre python-sphinx-gallery-doc python3-seaborn texlive-fonts-extra python-sympy-doc python-tenacity-doc python-terminado-doc python-tinycss2-doc tix python3-tk-dbg python3-pycurl python-tornado-doc python3-twisted python3.10-venv python3.10-doc binfmt-support python3.11-venv python3.11-doc sgml-base-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common libjson-xs-perl libldap-common publicsuffix libsasl2-modules libltdl-dev llvm-14-dev libmail-sendmail-perl libpaper-utils python3-sphinxcontrib.bibtex numba-doc python3-pip python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-tables python3-olefile python3-gi isympy-common The following NEW packages will be installed: autoconf automake autopoint autotools-dev blt bsdextrautils cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file flit fontconfig-config fonts-dejavu-core fonts-glyphicons-halflings fonts-lyx gettext gettext-base groff-base intltool-debian jupyter-sphinx-theme-common libarchive-zip-perl libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libcurl4 libdebhelper-perl libdeflate0 libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu72 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap libjs-bootswatch libjs-jquery libjs-jquery-hotkeys libjs-jquery-isonscreen libjs-jquery-metadata libjs-jquery-tablesorter libjs-jquery-throttle-debounce libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl liblapack3 liblbfgsb0 liblcms2-2 libldap2 liblerc4 libllvm14 liblua5.3-0 libmagic-mgc libmagic1 libmpdec3 libnghttp2-14 libnorm1 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenjp2-7 libpfm4 libpgm-5.3-0 libpipeline1 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libraqm0 librtmp1 libsasl2-2 libsasl2-modules-db libsodium23 libssh-4 libsub-override-perl libtcl8.6 libtiff6 libtk8.6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxsimd-dev libxslt1.1 libxss1 libyaml-0-2 libzmq5 llvm-14 llvm-14-linker-tools llvm-14-runtime m4 man-db media-types pandoc pandoc-data po-debconf pybuild-plugin-pyproject python-babel-localedata python-matplotlib-data python-tinycss2-common python3 python3-alabaster python3-all python3-all-dev python3-anyio python3-appdirs python3-argon2 python3-attr python3-babel python3-beniget python3-bleach python3-brotli python3-bs4 python3-build python3-certifi python3-cffi-backend python3-chardet python3-commonmark python3-coverage python3-cycler python3-dateutil python3-decorator python3-defusedxml python3-dev python3-distutils python3-docutils python3-entrypoints python3-execnet python3-fastjsonschema python3-fonttools python3-fs python3-gast python3-html5lib python3-idna python3-imagesize python3-importlib-metadata python3-iniconfig python3-installer python3-isort python3-jinja2 python3-json5 python3-jsonschema python3-jupyter-client python3-jupyter-core python3-jupyter-server python3-jupyter-sphinx-theme python3-jupyterlab-pygments python3-jupyterlab-server python3-kiwisolver python3-lib2to3 python3-llvmlite python3-lxml python3-lz4 python3-markupsafe python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-nbclient python3-nbconvert python3-nbformat python3-nbsphinx python3-nest-asyncio python3-numba python3-numpy python3-numpydoc python3-packaging python3-pandas python3-pandas-lib python3-pandocfilters python3-pbr python3-pep517 python3-pil python3-pil.imagetk python3-pkg-resources python3-plotly python3-pluggy python3-ply python3-prometheus-client python3-ptyprocess python3-py python3-pygments python3-pyparsing python3-pyrsistent python3-pytest python3-pytest-cov python3-pytest-xdist python3-pythran python3-recommonmark python3-requests python3-roman python3-scipy python3-scitrack python3-send2trash python3-setuptools python3-six python3-sniffio python3-snowballstemmer python3-soupsieve python3-sphinx python3-sphinx-bootstrap-theme python3-sphinx-gallery python3-sympy python3-tenacity python3-terminado python3-tinycss2 python3-tinydb python3-tk python3-toml python3-tomli python3-tomli-w python3-tornado python3-tqdm python3-traitlets python3-typing-extensions python3-tz python3-ufolib2 python3-urllib3 python3-webencodings python3-websocket python3-wheel python3-zipp python3-zmq python3.10 python3.10-minimal python3.11 python3.11-dev python3.11-minimal sbuild-build-depends-main-dummy sgml-base sphinx-common tk8.6-blt2.5 unicode-data x11-common xml-core zlib1g-dev 0 upgraded, 273 newly installed, 0 to remove and 0 not upgraded. Need to get 230 MB of archives. After this operation, 1323 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [856 B] Get:2 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libpython3.11-minimal ppc64el 3.11.2-4 [831 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main ppc64el libexpat1 ppc64el 2.5.0-1 [95.3 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el python3.11-minimal ppc64el 3.11.2-4 [2368 kB] Get:5 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el python3-minimal ppc64el 3.11.2-1 [24.6 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main ppc64el media-types all 10.0.0 [25.8 kB] Get:7 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libpython3.11-stdlib ppc64el 3.11.2-4 [1938 kB] Get:8 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el python3.11 ppc64el 3.11.2-4 [565 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libpython3-stdlib ppc64el 3.11.2-1 [7232 B] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el python3 ppc64el 3.11.2-1 [22.9 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main ppc64el libpython3.10-minimal ppc64el 3.10.9-1 [802 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3.10-minimal ppc64el 3.10.9-1 [2208 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main ppc64el sgml-base all 1.31 [11.4 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libjs-jquery-hotkeys all 0~20130707+git2d51e3a9+dfsg-2ubuntu1 [11.4 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main ppc64el libbsd0 ppc64el 0.11.7-2 [60.1 kB] Get:17 http://ftpmaster.internal/ubuntu lunar/main ppc64el libelf1 ppc64el 0.188-2.1 [63.2 kB] Get:18 http://ftpmaster.internal/ubuntu lunar/main ppc64el libfribidi0 ppc64el 1.0.8-2.1ubuntu1 [27.3 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main ppc64el libglib2.0-0 ppc64el 2.74.5-1 [1650 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main ppc64el libmpdec3 ppc64el 2.5.1-2build2 [116 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main ppc64el libpython3.10-stdlib ppc64el 3.10.9-1 [1800 kB] Get:22 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libicu72 ppc64el 72.1-3ubuntu1 [11.1 MB] Get:23 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libxml2 ppc64el 2.9.14+dfsg-1.1build1 [820 kB] Get:24 http://ftpmaster.internal/ubuntu lunar/main ppc64el libyaml-0-2 ppc64el 0.2.5-1 [63.9 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-pkg-resources all 66.1.1-1 [225 kB] Get:26 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3.10 ppc64el 3.10.9-1 [503 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main ppc64el bsdextrautils ppc64el 2.38.1-4ubuntu1 [76.4 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main ppc64el libmagic-mgc ppc64el 1:5.44-3 [293 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main ppc64el libmagic1 ppc64el 1:5.44-3 [104 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main ppc64el file ppc64el 1:5.44-3 [22.4 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main ppc64el gettext-base ppc64el 0.21-11 [40.7 kB] Get:32 http://ftpmaster.internal/ubuntu lunar/main ppc64el libuchardet0 ppc64el 0.0.7-1build2 [80.4 kB] Get:33 http://ftpmaster.internal/ubuntu lunar/main ppc64el groff-base ppc64el 1.22.4-9 [1004 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main ppc64el libedit2 ppc64el 3.1-20221030-2 [122 kB] Get:35 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libnghttp2-14 ppc64el 1.52.0-1 [87.0 kB] Get:36 http://ftpmaster.internal/ubuntu lunar/main ppc64el libpipeline1 ppc64el 1.5.7-1 [25.8 kB] Get:37 http://ftpmaster.internal/ubuntu lunar/main ppc64el libpsl5 ppc64el 0.21.2-1 [60.6 kB] Get:38 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxau6 ppc64el 1:1.0.9-1build5 [8028 B] Get:39 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxdmcp6 ppc64el 1:1.1.3-0ubuntu5 [12.3 kB] Get:40 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxcb1 ppc64el 1.15-1 [55.5 kB] Get:41 http://ftpmaster.internal/ubuntu lunar/main ppc64el libx11-data all 2:1.8.3-3 [118 kB] Get:42 http://ftpmaster.internal/ubuntu lunar/main ppc64el libx11-6 ppc64el 2:1.8.3-3 [737 kB] Get:43 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxext6 ppc64el 2:1.3.4-1build1 [40.0 kB] Get:44 http://ftpmaster.internal/ubuntu lunar/main ppc64el man-db ppc64el 2.11.2-1 [1256 kB] Get:45 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el m4 ppc64el 1.4.19-3 [275 kB] Get:46 http://ftpmaster.internal/ubuntu lunar/main ppc64el autoconf all 2.71-3 [339 kB] Get:47 http://ftpmaster.internal/ubuntu lunar/main ppc64el autotools-dev all 20220109.1 [44.9 kB] Get:48 http://ftpmaster.internal/ubuntu lunar/main ppc64el automake all 1:1.16.5-1.3 [558 kB] Get:49 http://ftpmaster.internal/ubuntu lunar/main ppc64el autopoint all 0.21-11 [420 kB] Get:50 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libtcl8.6 ppc64el 8.6.13+dfsg-2 [1179 kB] Get:51 http://ftpmaster.internal/ubuntu lunar/main ppc64el libbrotli1 ppc64el 1.0.9-2build7 [369 kB] Get:52 http://ftpmaster.internal/ubuntu lunar/main ppc64el libfreetype6 ppc64el 2.12.1+dfsg-4 [521 kB] Get:53 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el fonts-dejavu-core all 2.37-4 [1137 kB] Get:54 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el fontconfig-config ppc64el 2.14.1-3ubuntu2 [32.6 kB] Get:55 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libfontconfig1 ppc64el 2.14.1-3ubuntu2 [182 kB] Get:56 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1 [23.3 kB] Get:57 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxft2 ppc64el 2.3.6-1 [59.8 kB] Get:58 http://ftpmaster.internal/ubuntu lunar/main ppc64el x11-common all 1:7.7+23ubuntu2 [23.4 kB] Get:59 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxss1 ppc64el 1:1.2.3-1build2 [8982 B] Get:60 http://ftpmaster.internal/ubuntu lunar/main ppc64el libtk8.6 ppc64el 8.6.13-2 [916 kB] Get:61 http://ftpmaster.internal/ubuntu lunar/main ppc64el tk8.6-blt2.5 ppc64el 2.5.3+dfsg-4.1build2 [777 kB] Get:62 http://ftpmaster.internal/ubuntu lunar/main ppc64el blt ppc64el 2.5.3+dfsg-4.1build2 [4838 B] Get:63 http://ftpmaster.internal/ubuntu lunar/universe ppc64el cython3 ppc64el 0.29.32-2ubuntu1 [1871 kB] Get:64 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdebhelper-perl all 13.11.4ubuntu3 [66.1 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main ppc64el libtool all 2.4.7-5 [166 kB] Get:66 http://ftpmaster.internal/ubuntu lunar/main ppc64el dh-autoreconf all 20 [16.1 kB] Get:67 http://ftpmaster.internal/ubuntu lunar/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] Get:68 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsub-override-perl all 0.09-4 [8706 B] Get:69 http://ftpmaster.internal/ubuntu lunar/main ppc64el libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:70 http://ftpmaster.internal/ubuntu lunar/main ppc64el dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:71 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdw1 ppc64el 0.188-2.1 [284 kB] Get:72 http://ftpmaster.internal/ubuntu lunar/main ppc64el debugedit ppc64el 1:5.0-5 [51.1 kB] Get:73 http://ftpmaster.internal/ubuntu lunar/main ppc64el dwz ppc64el 0.15-1 [139 kB] Get:74 http://ftpmaster.internal/ubuntu lunar/main ppc64el gettext ppc64el 0.21-11 [970 kB] Get:75 http://ftpmaster.internal/ubuntu lunar/main ppc64el intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:76 http://ftpmaster.internal/ubuntu lunar/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB] Get:77 http://ftpmaster.internal/ubuntu lunar/main ppc64el debhelper all 13.11.4ubuntu3 [925 kB] Get:78 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el python3-lib2to3 all 3.11.2-2 [75.9 kB] Get:79 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el python3-distutils all 3.11.2-2 [130 kB] Get:80 http://ftpmaster.internal/ubuntu lunar/universe ppc64el dh-python all 5.20230130 [101 kB] Get:81 http://ftpmaster.internal/ubuntu lunar/main ppc64el xml-core all 0.18+nmu1 [21.6 kB] Get:82 http://ftpmaster.internal/ubuntu lunar/main ppc64el docutils-common all 0.19+dfsg-6 [129 kB] Get:83 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-tomli all 2.0.1-2 [16.5 kB] Get:84 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-roman all 3.3-3 [9632 B] Get:85 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-docutils all 0.19+dfsg-6 [386 kB] Get:86 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-certifi all 2022.9.24-1 [155 kB] Get:87 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-chardet all 5.1.0+dfsg-2 [119 kB] Get:88 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-idna all 3.3-1 [49.3 kB] Get:89 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-six all 1.16.0-4 [12.4 kB] Get:90 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-urllib3 all 1.26.12-1 [99.7 kB] Get:91 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-requests all 2.28.1+dfsg-1ubuntu1 [49.9 kB] Get:92 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-tomli-w all 1.0.0-2 [7368 B] Get:93 http://ftpmaster.internal/ubuntu lunar/universe ppc64el flit all 3.8.0-3 [89.3 kB] Get:94 http://ftpmaster.internal/ubuntu lunar/universe ppc64el fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] Get:95 http://ftpmaster.internal/ubuntu lunar/universe ppc64el fonts-lyx all 2.3.7-1 [167 kB] Get:96 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] Get:97 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libjs-bootswatch all 3.3.7+dfsg2-1.1 [133 kB] Get:98 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-sphinx-bootstrap-theme all 0.8.1-1 [430 kB] Get:99 http://ftpmaster.internal/ubuntu lunar/universe ppc64el jupyter-sphinx-theme-common all 0.0.6+ds1-11 [13.6 kB] Get:100 http://ftpmaster.internal/ubuntu lunar/main ppc64el libblas3 ppc64el 3.11.0-2 [209 kB] Get:101 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libboost1.74-dev ppc64el 1.74.0-18.1ubuntu3 [9588 kB] Get:102 http://ftpmaster.internal/ubuntu lunar/main ppc64el libboost-dev ppc64el 1.74.0.3ubuntu7 [3490 B] Get:103 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsasl2-modules-db ppc64el 2.1.28+dfsg-10 [22.7 kB] Get:104 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsasl2-2 ppc64el 2.1.28+dfsg-10 [69.2 kB] Get:105 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libldap2 ppc64el 2.6.3+dfsg-1~exp1ubuntu2 [217 kB] Get:106 http://ftpmaster.internal/ubuntu lunar/main ppc64el librtmp1 ppc64el 2.4+20151223.gitfa8646d.1-2build4 [65.5 kB] Get:107 http://ftpmaster.internal/ubuntu lunar/main ppc64el libssh-4 ppc64el 0.10.4-2 [235 kB] Get:108 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libcurl4 ppc64el 7.87.0-2ubuntu2 [360 kB] Get:109 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdeflate0 ppc64el 1.15-1 [53.0 kB] Get:110 http://ftpmaster.internal/ubuntu lunar/main ppc64el libexpat1-dev ppc64el 2.5.0-1 [145 kB] Get:111 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgfortran5 ppc64el 13-20230215-1ubuntu2 [554 kB] Get:112 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgraphite2-3 ppc64el 1.3.14-1build2 [85.9 kB] Get:113 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libharfbuzz0b ppc64el 6.0.0+dfsg-3build1 [515 kB] Get:114 http://ftpmaster.internal/ubuntu lunar/main ppc64el libimagequant0 ppc64el 2.17.0-1 [40.2 kB] Get:115 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] Get:116 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] Get:117 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libjs-jquery-metadata all 12-4 [6582 B] Get:118 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libjs-jquery-tablesorter all 1:2.31.3+dfsg1-3 [193 kB] Get:119 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.5 kB] Get:120 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] Get:121 http://ftpmaster.internal/ubuntu lunar/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] Get:122 http://ftpmaster.internal/ubuntu lunar/main ppc64el libjs-sphinxdoc all 5.3.0-3 [129 kB] Get:123 http://ftpmaster.internal/ubuntu lunar/main ppc64el libjson-perl all 4.10000-1 [81.9 kB] Get:124 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libopenblas0-pthread ppc64el 0.3.21+ds-4 [7289 kB] Get:125 http://ftpmaster.internal/ubuntu lunar/main ppc64el liblapack3 ppc64el 3.11.0-2 [2599 kB] Get:126 http://ftpmaster.internal/ubuntu lunar/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.3-11 [31.3 kB] Get:127 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el liblcms2-2 ppc64el 2.14-2 [243 kB] Get:128 http://ftpmaster.internal/ubuntu lunar/main ppc64el liblerc4 ppc64el 4.0.0+ds-2ubuntu2 [268 kB] Get:129 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libllvm14 ppc64el 1:14.0.6-12 [24.7 MB] Get:130 http://ftpmaster.internal/ubuntu lunar/main ppc64el liblua5.3-0 ppc64el 5.3.6-2 [191 kB] Get:131 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libnorm1 ppc64el 1.5.9+dfsg-2 [252 kB] Get:132 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libopenblas0 ppc64el 0.3.21+ds-4 [6098 B] Get:133 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libopenblas-pthread-dev ppc64el 0.3.21+ds-4 [5117 kB] Get:134 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libopenblas-dev ppc64el 0.3.21+ds-4 [18.7 kB] Get:135 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libpgm-5.3-0 ppc64el 5.3.128~dfsg-2 [168 kB] Get:136 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libpython3.11 ppc64el 3.11.2-4 [2400 kB] Get:137 http://ftpmaster.internal/ubuntu lunar/main ppc64el zlib1g-dev ppc64el 1:1.2.13.dfsg-1ubuntu4 [901 kB] Get:138 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libpython3.11-dev ppc64el 3.11.2-4 [5712 kB] Get:139 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libpython3-dev ppc64el 3.11.2-1 [7486 B] Get:140 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libpython3-all-dev ppc64el 3.11.2-1 [906 B] Get:141 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libqhull-r8.0 ppc64el 2020.2-5 [220 kB] Get:142 http://ftpmaster.internal/ubuntu lunar/main ppc64el libraqm0 ppc64el 0.7.0-4.1 [13.3 kB] Get:143 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsodium23 ppc64el 1.0.18-1build2 [151 kB] Get:144 http://ftpmaster.internal/ubuntu lunar/main ppc64el libjbig0 ppc64el 2.1-6ubuntu1 [34.4 kB] Get:145 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libwebp7 ppc64el 1.2.4-0.1build1 [291 kB] Get:146 http://ftpmaster.internal/ubuntu lunar/main ppc64el libtiff6 ppc64el 4.5.0-4ubuntu1 [253 kB] Get:147 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libwebpdemux2 ppc64el 1.2.4-0.1build1 [11.2 kB] Get:148 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libwebpmux3 ppc64el 1.2.4-0.1build1 [25.2 kB] Get:149 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libxsimd-dev ppc64el 8.1.0-7 [90.7 kB] Get:150 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxslt1.1 ppc64el 1.1.35-1 [185 kB] Get:151 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libzmq5 ppc64el 4.3.4-6 [290 kB] Get:152 http://ftpmaster.internal/ubuntu lunar-proposed/universe ppc64el llvm-14-runtime ppc64el 1:14.0.6-12 [510 kB] Get:153 http://ftpmaster.internal/ubuntu lunar-proposed/universe ppc64el llvm-14-linker-tools ppc64el 1:14.0.6-12 [1412 kB] Get:154 http://ftpmaster.internal/ubuntu lunar-proposed/universe ppc64el libpfm4 ppc64el 4.12.1+git12-g678bca9-1 [188 kB] Get:155 http://ftpmaster.internal/ubuntu lunar-proposed/universe ppc64el llvm-14 ppc64el 1:14.0.6-12 [12.7 MB] Get:156 http://ftpmaster.internal/ubuntu lunar/universe ppc64el pandoc-data all 2.17.1.1-1.1ubuntu1 [80.7 kB] Get:157 http://ftpmaster.internal/ubuntu lunar/universe ppc64el pandoc ppc64el 2.17.1.1-1.1ubuntu1 [29.2 MB] Get:158 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-typing-extensions all 4.4.0-1 [44.0 kB] Get:159 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-more-itertools all 8.10.0-2 [47.9 kB] Get:160 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-zipp all 1.0.0-6 [6090 B] Get:161 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-importlib-metadata all 4.12.0-1 [17.8 kB] Get:162 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-packaging all 23.0-1 [32.7 kB] Get:163 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-pep517 all 0.13.0-2 [16.8 kB] Get:164 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-toml all 0.10.2-1 [16.5 kB] Get:165 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-wheel all 0.38.4-1 [31.2 kB] Get:166 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-build all 0.9.0-1 [17.2 kB] Get:167 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-installer all 0.6.0+dfsg1-1 [17.2 kB] Get:168 http://ftpmaster.internal/ubuntu lunar/universe ppc64el pybuild-plugin-pyproject all 5.20230130 [1714 B] Get:169 http://ftpmaster.internal/ubuntu lunar/main ppc64el python-babel-localedata all 2.10.3-1 [6357 kB] Get:170 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python-matplotlib-data all 3.5.2-4 [2917 kB] Get:171 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python-tinycss2-common all 1.2.1-2 [33.9 kB] Get:172 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el python3-all ppc64el 3.11.2-1 [898 B] Get:173 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el python3.11-dev ppc64el 3.11.2-4 [620 kB] Get:174 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el python3-dev ppc64el 3.11.2-1 [26.8 kB] Get:175 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el python3-all-dev ppc64el 3.11.2-1 [900 B] Get:176 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-sniffio all 1.2.0-1 [6438 B] Get:177 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-anyio all 3.6.2-1 [54.2 kB] Get:178 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-appdirs all 1.4.4-3 [10.8 kB] Get:179 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-cffi-backend ppc64el 1.15.1-5 [107 kB] Get:180 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-argon2 ppc64el 21.1.0-2 [21.5 kB] Get:181 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-attr all 22.2.0-1 [49.6 kB] Get:182 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-tz all 2022.7.1-1 [32.5 kB] Get:183 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-babel all 2.10.3-1 [87.5 kB] Get:184 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-gast all 0.5.2-2 [9394 B] Get:185 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-beniget all 0.4.1-3 [10.0 kB] Get:186 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-webencodings all 0.5.1-5 [11.5 kB] Get:187 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-html5lib all 1.1-3 [87.0 kB] Get:188 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-bleach all 5.0.1-2 [41.9 kB] Get:189 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-brotli ppc64el 1.0.9-2build7 [369 kB] Get:190 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el python3-soupsieve all 2.4-1 [33.4 kB] Get:191 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el python3-bs4 all 4.11.2-2 [98.4 kB] Get:192 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-commonmark all 0.9.1-4 [45.8 kB] Get:193 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-coverage ppc64el 6.5.0+dfsg1-2 [138 kB] Get:194 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-cycler all 0.11.0-1 [8156 B] Get:195 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-dateutil all 2.8.2-1 [79.1 kB] Get:196 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-decorator all 5.1.1-3 [9938 B] Get:197 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-defusedxml all 0.7.1-2 [42.0 kB] Get:198 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-entrypoints all 0.4-2 [7146 B] Get:199 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-execnet all 1.9.0-1 [33.5 kB] Get:200 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-fastjsonschema all 2.16.2-1 [19.9 kB] Get:201 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el python3-numpy ppc64el 1:1.24.2-1 [6761 kB] Get:202 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-ply all 3.11-5 [47.5 kB] Get:203 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-pythran ppc64el 0.11.0+ds-7 [427 kB] Get:204 http://ftpmaster.internal/ubuntu lunar-proposed/universe ppc64el python3-scipy ppc64el 1.10.0-12 [17.1 MB] Get:205 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-ufolib2 all 0.14.0+dfsg1-1 [34.4 kB] Get:206 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-mpmath all 1.2.1-2 [419 kB] Get:207 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-sympy all 1.11.1-1 [4449 kB] Get:208 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-fs all 2.4.16-2 [91.0 kB] Get:209 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-lxml ppc64el 4.9.2-1 [1890 kB] Get:210 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-lz4 ppc64el 4.0.2+dfsg-1 [27.6 kB] Get:211 http://ftpmaster.internal/ubuntu lunar/universe ppc64el unicode-data all 15.0.0-1 [8262 kB] Get:212 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-fonttools ppc64el 4.38.0-1 [1184 kB] Get:213 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-imagesize all 1.4.1-1 [6844 B] Get:214 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] Get:215 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-isort all 5.6.4-1 [63.1 kB] Get:216 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-markupsafe ppc64el 2.1.2-1 [13.9 kB] Get:217 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-jinja2 all 3.0.3-2 [107 kB] Get:218 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-json5 all 0.9.10-1 [15.7 kB] Get:219 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-setuptools all 66.1.1-1 [453 kB] Get:220 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-pyrsistent ppc64el 0.18.1-1build2 [58.6 kB] Get:221 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-jsonschema all 4.6.0-3ubuntu1 [63.6 kB] Get:222 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-traitlets all 5.5.0-1 [86.1 kB] Get:223 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-jupyter-core all 4.12.0-1 [23.7 kB] Get:224 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-nest-asyncio all 1.5.4-1 [6256 B] Get:225 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-tornado ppc64el 6.2.0-3 [290 kB] Get:226 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-py all 1.11.0-1 [73.2 kB] Get:227 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-zmq ppc64el 24.0.1-4 [399 kB] Get:228 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-jupyter-client all 7.4.9-2 [92.3 kB] Get:229 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-pygments all 2.14.0+dfsg-1 [785 kB] Get:230 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-jupyterlab-pygments all 0.2.2-3 [6054 B] Get:231 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-nbformat all 5.5.0-1 [40.1 kB] Get:232 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-nbclient all 0.7.2-1 [54.9 kB] Get:233 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-pandocfilters all 1.5.0-1 [24.0 kB] Get:234 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-tinycss2 all 1.2.1-2 [19.6 kB] Get:235 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-nbconvert all 6.5.3-3 [151 kB] Get:236 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el python3-prometheus-client all 0.16.0-0.1 [45.7 kB] Get:237 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-send2trash all 1.8.1~b0-2 [15.3 kB] Get:238 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-ptyprocess all 0.7.0-5 [15.1 kB] Get:239 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-terminado all 0.17.0-1 [15.4 kB] Get:240 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-websocket all 1.2.3-1 [34.7 kB] Get:241 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-jupyter-server all 1.23.3-1 [149 kB] Get:242 http://ftpmaster.internal/ubuntu lunar/main ppc64el sphinx-common all 5.3.0-3 [691 kB] Get:243 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-alabaster all 0.7.12-1 [17.8 kB] Get:244 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-snowballstemmer all 2.2.0-2 [59.6 kB] Get:245 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-sphinx all 5.3.0-3 [556 kB] Get:246 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-nbsphinx all 0.8.11+ds-1 [36.9 kB] Get:247 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-recommonmark all 0.7.1+ds-5 [16.9 kB] Get:248 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-jupyter-sphinx-theme all 0.0.6+ds1-11 [2812 B] Get:249 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-jupyterlab-server all 2.16.5-1 [40.8 kB] Get:250 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-kiwisolver ppc64el 1.4.4-1 [59.9 kB] Get:251 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-llvmlite ppc64el 0.39.1-2 [135 kB] Get:252 http://ftpmaster.internal/ubuntu lunar/main ppc64el libopenjp2-7 ppc64el 2.5.0-1build1 [234 kB] Get:253 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el python3-pil ppc64el 9.4.0-1.1build1 [463 kB] Get:254 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el python3-tk ppc64el 3.11.2-2 [103 kB] Get:255 http://ftpmaster.internal/ubuntu lunar-proposed/universe ppc64el python3-pil.imagetk ppc64el 9.4.0-1.1build1 [9778 B] Get:256 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-pyparsing all 3.0.9-1 [83.1 kB] Get:257 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-matplotlib ppc64el 3.5.2-4 [6846 kB] Get:258 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-numba ppc64el 0.56.4+dfsg-2 [1665 kB] Get:259 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-numpydoc all 1.5.0-1 [43.7 kB] Get:260 http://ftpmaster.internal/ubuntu lunar-proposed/universe ppc64el python3-pandas-lib ppc64el 1.5.3+dfsg-2 [4132 kB] Get:261 http://ftpmaster.internal/ubuntu lunar-proposed/universe ppc64el python3-pandas all 1.5.3+dfsg-2 [2912 kB] Get:262 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-pbr all 5.11.0-0ubuntu1 [65.8 kB] Get:263 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el python3-tenacity all 8.2.1-1 [14.1 kB] Get:264 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-plotly all 5.4.1+dfsg-1 [2639 kB] Get:265 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-pluggy all 1.0.0+repack-1 [15.1 kB] Get:266 http://ftpmaster.internal/ubuntu lunar-proposed/universe ppc64el python3-pytest all 7.2.1-2 [237 kB] Get:267 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libjs-jquery-isonscreen all 1.2.0-1.1 [3244 B] Get:268 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-pytest-cov all 4.0.0-1 [21.0 kB] Get:269 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-pytest-xdist all 3.1.0-1 [30.1 kB] Get:270 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-scitrack all 2021.5.3-3 [9424 B] Get:271 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-sphinx-gallery all 0.10.1-3 [94.9 kB] Get:272 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-tinydb all 3.15.2-4 [16.6 kB] Get:273 http://ftpmaster.internal/ubuntu lunar/universe ppc64el python3-tqdm all 4.64.1-1 [98.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 230 MB in 1min 16s (3017 kB/s) Selecting previously unselected package libpython3.11-minimal:ppc64el. (Reading database ... 15179 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-4_ppc64el.deb ... Unpacking libpython3.11-minimal:ppc64el (3.11.2-4) ... Selecting previously unselected package libexpat1:ppc64el. Preparing to unpack .../libexpat1_2.5.0-1_ppc64el.deb ... Unpacking libexpat1:ppc64el (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-4_ppc64el.deb ... Unpacking python3.11-minimal (3.11.2-4) ... Setting up libpython3.11-minimal:ppc64el (3.11.2-4) ... Setting up libexpat1:ppc64el (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-4) ... Selecting previously unselected package python3-minimal. (Reading database ... 15493 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.11.2-1_ppc64el.deb ... Unpacking python3-minimal (3.11.2-1) ... Selecting previously unselected package media-types. Preparing to unpack .../media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package libpython3.11-stdlib:ppc64el. Preparing to unpack .../libpython3.11-stdlib_3.11.2-4_ppc64el.deb ... Unpacking libpython3.11-stdlib:ppc64el (3.11.2-4) ... Selecting previously unselected package python3.11. Preparing to unpack .../python3.11_3.11.2-4_ppc64el.deb ... Unpacking python3.11 (3.11.2-4) ... Selecting previously unselected package libpython3-stdlib:ppc64el. Preparing to unpack .../libpython3-stdlib_3.11.2-1_ppc64el.deb ... Unpacking libpython3-stdlib:ppc64el (3.11.2-1) ... Setting up python3-minimal (3.11.2-1) ... Selecting previously unselected package python3. (Reading database ... 15901 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1_ppc64el.deb ... Unpacking python3 (3.11.2-1) ... Selecting previously unselected package libpython3.10-minimal:ppc64el. Preparing to unpack .../001-libpython3.10-minimal_3.10.9-1_ppc64el.deb ... Unpacking libpython3.10-minimal:ppc64el (3.10.9-1) ... Selecting previously unselected package python3.10-minimal. Preparing to unpack .../002-python3.10-minimal_3.10.9-1_ppc64el.deb ... Unpacking python3.10-minimal (3.10.9-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../003-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../004-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-jquery-hotkeys. Preparing to unpack .../005-libjs-jquery-hotkeys_0~20130707+git2d51e3a9+dfsg-2ubuntu1_all.deb ... Unpacking libjs-jquery-hotkeys (0~20130707+git2d51e3a9+dfsg-2ubuntu1) ... Selecting previously unselected package libbsd0:ppc64el. Preparing to unpack .../006-libbsd0_0.11.7-2_ppc64el.deb ... Unpacking libbsd0:ppc64el (0.11.7-2) ... Selecting previously unselected package libelf1:ppc64el. Preparing to unpack .../007-libelf1_0.188-2.1_ppc64el.deb ... Unpacking libelf1:ppc64el (0.188-2.1) ... Selecting previously unselected package libfribidi0:ppc64el. Preparing to unpack .../008-libfribidi0_1.0.8-2.1ubuntu1_ppc64el.deb ... Unpacking libfribidi0:ppc64el (1.0.8-2.1ubuntu1) ... Selecting previously unselected package libglib2.0-0:ppc64el. Preparing to unpack .../009-libglib2.0-0_2.74.5-1_ppc64el.deb ... Unpacking libglib2.0-0:ppc64el (2.74.5-1) ... Selecting previously unselected package libmpdec3:ppc64el. Preparing to unpack .../010-libmpdec3_2.5.1-2build2_ppc64el.deb ... Unpacking libmpdec3:ppc64el (2.5.1-2build2) ... Selecting previously unselected package libpython3.10-stdlib:ppc64el. Preparing to unpack .../011-libpython3.10-stdlib_3.10.9-1_ppc64el.deb ... Unpacking libpython3.10-stdlib:ppc64el (3.10.9-1) ... Selecting previously unselected package libicu72:ppc64el. Preparing to unpack .../012-libicu72_72.1-3ubuntu1_ppc64el.deb ... Unpacking libicu72:ppc64el (72.1-3ubuntu1) ... Selecting previously unselected package libxml2:ppc64el. Preparing to unpack .../013-libxml2_2.9.14+dfsg-1.1build1_ppc64el.deb ... Unpacking libxml2:ppc64el (2.9.14+dfsg-1.1build1) ... Selecting previously unselected package libyaml-0-2:ppc64el. Preparing to unpack .../014-libyaml-0-2_0.2.5-1_ppc64el.deb ... Unpacking libyaml-0-2:ppc64el (0.2.5-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../015-python3-pkg-resources_66.1.1-1_all.deb ... Unpacking python3-pkg-resources (66.1.1-1) ... Selecting previously unselected package python3.10. Preparing to unpack .../016-python3.10_3.10.9-1_ppc64el.deb ... Unpacking python3.10 (3.10.9-1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../017-bsdextrautils_2.38.1-4ubuntu1_ppc64el.deb ... Unpacking bsdextrautils (2.38.1-4ubuntu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../018-libmagic-mgc_1%3a5.44-3_ppc64el.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:ppc64el. Preparing to unpack .../019-libmagic1_1%3a5.44-3_ppc64el.deb ... Unpacking libmagic1:ppc64el (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../020-file_1%3a5.44-3_ppc64el.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../021-gettext-base_0.21-11_ppc64el.deb ... Unpacking gettext-base (0.21-11) ... Selecting previously unselected package libuchardet0:ppc64el. Preparing to unpack .../022-libuchardet0_0.0.7-1build2_ppc64el.deb ... Unpacking libuchardet0:ppc64el (0.0.7-1build2) ... Selecting previously unselected package groff-base. Preparing to unpack .../023-groff-base_1.22.4-9_ppc64el.deb ... Unpacking groff-base (1.22.4-9) ... Selecting previously unselected package libedit2:ppc64el. Preparing to unpack .../024-libedit2_3.1-20221030-2_ppc64el.deb ... Unpacking libedit2:ppc64el (3.1-20221030-2) ... Selecting previously unselected package libnghttp2-14:ppc64el. Preparing to unpack .../025-libnghttp2-14_1.52.0-1_ppc64el.deb ... Unpacking libnghttp2-14:ppc64el (1.52.0-1) ... Selecting previously unselected package libpipeline1:ppc64el. Preparing to unpack .../026-libpipeline1_1.5.7-1_ppc64el.deb ... Unpacking libpipeline1:ppc64el (1.5.7-1) ... Selecting previously unselected package libpsl5:ppc64el. Preparing to unpack .../027-libpsl5_0.21.2-1_ppc64el.deb ... Unpacking libpsl5:ppc64el (0.21.2-1) ... Selecting previously unselected package libxau6:ppc64el. Preparing to unpack .../028-libxau6_1%3a1.0.9-1build5_ppc64el.deb ... Unpacking libxau6:ppc64el (1:1.0.9-1build5) ... Selecting previously unselected package libxdmcp6:ppc64el. Preparing to unpack .../029-libxdmcp6_1%3a1.1.3-0ubuntu5_ppc64el.deb ... Unpacking libxdmcp6:ppc64el (1:1.1.3-0ubuntu5) ... Selecting previously unselected package libxcb1:ppc64el. Preparing to unpack .../030-libxcb1_1.15-1_ppc64el.deb ... Unpacking libxcb1:ppc64el (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../031-libx11-data_2%3a1.8.3-3_all.deb ... Unpacking libx11-data (2:1.8.3-3) ... Selecting previously unselected package libx11-6:ppc64el. Preparing to unpack .../032-libx11-6_2%3a1.8.3-3_ppc64el.deb ... Unpacking libx11-6:ppc64el (2:1.8.3-3) ... Selecting previously unselected package libxext6:ppc64el. Preparing to unpack .../033-libxext6_2%3a1.3.4-1build1_ppc64el.deb ... Unpacking libxext6:ppc64el (2:1.3.4-1build1) ... Selecting previously unselected package man-db. Preparing to unpack .../034-man-db_2.11.2-1_ppc64el.deb ... Unpacking man-db (2.11.2-1) ... Selecting previously unselected package m4. Preparing to unpack .../035-m4_1.4.19-3_ppc64el.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../036-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../037-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../038-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../039-autopoint_0.21-11_all.deb ... Unpacking autopoint (0.21-11) ... Selecting previously unselected package libtcl8.6:ppc64el. Preparing to unpack .../040-libtcl8.6_8.6.13+dfsg-2_ppc64el.deb ... Unpacking libtcl8.6:ppc64el (8.6.13+dfsg-2) ... Selecting previously unselected package libbrotli1:ppc64el. Preparing to unpack .../041-libbrotli1_1.0.9-2build7_ppc64el.deb ... Unpacking libbrotli1:ppc64el (1.0.9-2build7) ... Selecting previously unselected package libfreetype6:ppc64el. Preparing to unpack .../042-libfreetype6_2.12.1+dfsg-4_ppc64el.deb ... Unpacking libfreetype6:ppc64el (2.12.1+dfsg-4) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../043-fonts-dejavu-core_2.37-4_all.deb ... Unpacking fonts-dejavu-core (2.37-4) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../044-fontconfig-config_2.14.1-3ubuntu2_ppc64el.deb ... Unpacking fontconfig-config (2.14.1-3ubuntu2) ... Selecting previously unselected package libfontconfig1:ppc64el. Preparing to unpack .../045-libfontconfig1_2.14.1-3ubuntu2_ppc64el.deb ... Unpacking libfontconfig1:ppc64el (2.14.1-3ubuntu2) ... Selecting previously unselected package libxrender1:ppc64el. Preparing to unpack .../046-libxrender1_1%3a0.9.10-1.1_ppc64el.deb ... Unpacking libxrender1:ppc64el (1:0.9.10-1.1) ... Selecting previously unselected package libxft2:ppc64el. Preparing to unpack .../047-libxft2_2.3.6-1_ppc64el.deb ... Unpacking libxft2:ppc64el (2.3.6-1) ... Selecting previously unselected package x11-common. Preparing to unpack .../048-x11-common_1%3a7.7+23ubuntu2_all.deb ... Unpacking x11-common (1:7.7+23ubuntu2) ... Selecting previously unselected package libxss1:ppc64el. Preparing to unpack .../049-libxss1_1%3a1.2.3-1build2_ppc64el.deb ... Unpacking libxss1:ppc64el (1:1.2.3-1build2) ... Selecting previously unselected package libtk8.6:ppc64el. Preparing to unpack .../050-libtk8.6_8.6.13-2_ppc64el.deb ... Unpacking libtk8.6:ppc64el (8.6.13-2) ... Selecting previously unselected package tk8.6-blt2.5. Preparing to unpack .../051-tk8.6-blt2.5_2.5.3+dfsg-4.1build2_ppc64el.deb ... Unpacking tk8.6-blt2.5 (2.5.3+dfsg-4.1build2) ... Selecting previously unselected package blt. Preparing to unpack .../052-blt_2.5.3+dfsg-4.1build2_ppc64el.deb ... Unpacking blt (2.5.3+dfsg-4.1build2) ... Selecting previously unselected package cython3. Preparing to unpack .../053-cython3_0.29.32-2ubuntu1_ppc64el.deb ... Unpacking cython3 (0.29.32-2ubuntu1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../054-libdebhelper-perl_13.11.4ubuntu3_all.deb ... Unpacking libdebhelper-perl (13.11.4ubuntu3) ... Selecting previously unselected package libtool. Preparing to unpack .../055-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../056-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../057-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../058-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../059-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../060-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libdw1:ppc64el. Preparing to unpack .../061-libdw1_0.188-2.1_ppc64el.deb ... Unpacking libdw1:ppc64el (0.188-2.1) ... Selecting previously unselected package debugedit. Preparing to unpack .../062-debugedit_1%3a5.0-5_ppc64el.deb ... Unpacking debugedit (1:5.0-5) ... Selecting previously unselected package dwz. Preparing to unpack .../063-dwz_0.15-1_ppc64el.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package gettext. Preparing to unpack .../064-gettext_0.21-11_ppc64el.deb ... Unpacking gettext (0.21-11) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../065-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../066-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../067-debhelper_13.11.4ubuntu3_all.deb ... Unpacking debhelper (13.11.4ubuntu3) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../068-python3-lib2to3_3.11.2-2_all.deb ... Unpacking python3-lib2to3 (3.11.2-2) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../069-python3-distutils_3.11.2-2_all.deb ... Unpacking python3-distutils (3.11.2-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../070-dh-python_5.20230130_all.deb ... Unpacking dh-python (5.20230130) ... Selecting previously unselected package xml-core. Preparing to unpack .../071-xml-core_0.18+nmu1_all.deb ... Unpacking xml-core (0.18+nmu1) ... Selecting previously unselected package docutils-common. Preparing to unpack .../072-docutils-common_0.19+dfsg-6_all.deb ... Unpacking docutils-common (0.19+dfsg-6) ... Selecting previously unselected package python3-tomli. Preparing to unpack .../073-python3-tomli_2.0.1-2_all.deb ... Unpacking python3-tomli (2.0.1-2) ... Selecting previously unselected package python3-roman. Preparing to unpack .../074-python3-roman_3.3-3_all.deb ... Unpacking python3-roman (3.3-3) ... Selecting previously unselected package python3-docutils. Preparing to unpack .../075-python3-docutils_0.19+dfsg-6_all.deb ... Unpacking python3-docutils (0.19+dfsg-6) ... Selecting previously unselected package python3-certifi. Preparing to unpack .../076-python3-certifi_2022.9.24-1_all.deb ... Unpacking python3-certifi (2022.9.24-1) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../077-python3-chardet_5.1.0+dfsg-2_all.deb ... Unpacking python3-chardet (5.1.0+dfsg-2) ... Selecting previously unselected package python3-idna. Preparing to unpack .../078-python3-idna_3.3-1_all.deb ... Unpacking python3-idna (3.3-1) ... Selecting previously unselected package python3-six. Preparing to unpack .../079-python3-six_1.16.0-4_all.deb ... Unpacking python3-six (1.16.0-4) ... Selecting previously unselected package python3-urllib3. Preparing to unpack .../080-python3-urllib3_1.26.12-1_all.deb ... Unpacking python3-urllib3 (1.26.12-1) ... Selecting previously unselected package python3-requests. Preparing to unpack .../081-python3-requests_2.28.1+dfsg-1ubuntu1_all.deb ... Unpacking python3-requests (2.28.1+dfsg-1ubuntu1) ... Selecting previously unselected package python3-tomli-w. Preparing to unpack .../082-python3-tomli-w_1.0.0-2_all.deb ... Unpacking python3-tomli-w (1.0.0-2) ... Selecting previously unselected package flit. Preparing to unpack .../083-flit_3.8.0-3_all.deb ... Unpacking flit (3.8.0-3) ... Selecting previously unselected package fonts-glyphicons-halflings. Preparing to unpack .../084-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Selecting previously unselected package fonts-lyx. Preparing to unpack .../085-fonts-lyx_2.3.7-1_all.deb ... Unpacking fonts-lyx (2.3.7-1) ... Selecting previously unselected package libjs-bootstrap. Preparing to unpack .../086-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... Selecting previously unselected package libjs-bootswatch. Preparing to unpack .../087-libjs-bootswatch_3.3.7+dfsg2-1.1_all.deb ... Unpacking libjs-bootswatch (3.3.7+dfsg2-1.1) ... Selecting previously unselected package python3-sphinx-bootstrap-theme. Preparing to unpack .../088-python3-sphinx-bootstrap-theme_0.8.1-1_all.deb ... Unpacking python3-sphinx-bootstrap-theme (0.8.1-1) ... Selecting previously unselected package jupyter-sphinx-theme-common. Preparing to unpack .../089-jupyter-sphinx-theme-common_0.0.6+ds1-11_all.deb ... Unpacking jupyter-sphinx-theme-common (0.0.6+ds1-11) ... Selecting previously unselected package libblas3:ppc64el. Preparing to unpack .../090-libblas3_3.11.0-2_ppc64el.deb ... Unpacking libblas3:ppc64el (3.11.0-2) ... Selecting previously unselected package libboost1.74-dev:ppc64el. Preparing to unpack .../091-libboost1.74-dev_1.74.0-18.1ubuntu3_ppc64el.deb ... Unpacking libboost1.74-dev:ppc64el (1.74.0-18.1ubuntu3) ... Selecting previously unselected package libboost-dev:ppc64el. Preparing to unpack .../092-libboost-dev_1.74.0.3ubuntu7_ppc64el.deb ... Unpacking libboost-dev:ppc64el (1.74.0.3ubuntu7) ... Selecting previously unselected package libsasl2-modules-db:ppc64el. Preparing to unpack .../093-libsasl2-modules-db_2.1.28+dfsg-10_ppc64el.deb ... Unpacking libsasl2-modules-db:ppc64el (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:ppc64el. Preparing to unpack .../094-libsasl2-2_2.1.28+dfsg-10_ppc64el.deb ... Unpacking libsasl2-2:ppc64el (2.1.28+dfsg-10) ... Selecting previously unselected package libldap2:ppc64el. Preparing to unpack .../095-libldap2_2.6.3+dfsg-1~exp1ubuntu2_ppc64el.deb ... Unpacking libldap2:ppc64el (2.6.3+dfsg-1~exp1ubuntu2) ... Selecting previously unselected package librtmp1:ppc64el. Preparing to unpack .../096-librtmp1_2.4+20151223.gitfa8646d.1-2build4_ppc64el.deb ... Unpacking librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2build4) ... Selecting previously unselected package libssh-4:ppc64el. Preparing to unpack .../097-libssh-4_0.10.4-2_ppc64el.deb ... Unpacking libssh-4:ppc64el (0.10.4-2) ... Selecting previously unselected package libcurl4:ppc64el. Preparing to unpack .../098-libcurl4_7.87.0-2ubuntu2_ppc64el.deb ... Unpacking libcurl4:ppc64el (7.87.0-2ubuntu2) ... Selecting previously unselected package libdeflate0:ppc64el. Preparing to unpack .../099-libdeflate0_1.15-1_ppc64el.deb ... Unpacking libdeflate0:ppc64el (1.15-1) ... Selecting previously unselected package libexpat1-dev:ppc64el. Preparing to unpack .../100-libexpat1-dev_2.5.0-1_ppc64el.deb ... Unpacking libexpat1-dev:ppc64el (2.5.0-1) ... Selecting previously unselected package libgfortran5:ppc64el. Preparing to unpack .../101-libgfortran5_13-20230215-1ubuntu2_ppc64el.deb ... Unpacking libgfortran5:ppc64el (13-20230215-1ubuntu2) ... Selecting previously unselected package libgraphite2-3:ppc64el. Preparing to unpack .../102-libgraphite2-3_1.3.14-1build2_ppc64el.deb ... Unpacking libgraphite2-3:ppc64el (1.3.14-1build2) ... Selecting previously unselected package libharfbuzz0b:ppc64el. Preparing to unpack .../103-libharfbuzz0b_6.0.0+dfsg-3build1_ppc64el.deb ... Unpacking libharfbuzz0b:ppc64el (6.0.0+dfsg-3build1) ... Selecting previously unselected package libimagequant0:ppc64el. Preparing to unpack .../104-libimagequant0_2.17.0-1_ppc64el.deb ... Unpacking libimagequant0:ppc64el (2.17.0-1) ... Selecting previously unselected package libjpeg-turbo8:ppc64el. Preparing to unpack .../105-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... Selecting previously unselected package libjpeg8:ppc64el. Preparing to unpack .../106-libjpeg8_8c-2ubuntu11_ppc64el.deb ... Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... Selecting previously unselected package libjs-jquery-metadata. Preparing to unpack .../107-libjs-jquery-metadata_12-4_all.deb ... Unpacking libjs-jquery-metadata (12-4) ... Selecting previously unselected package libjs-jquery-tablesorter. Preparing to unpack .../108-libjs-jquery-tablesorter_1%3a2.31.3+dfsg1-3_all.deb ... Unpacking libjs-jquery-tablesorter (1:2.31.3+dfsg1-3) ... Selecting previously unselected package libjs-jquery-throttle-debounce. Preparing to unpack .../109-libjs-jquery-throttle-debounce_1.1+dfsg.1-2_all.deb ... Unpacking libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../110-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../111-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../112-libjs-sphinxdoc_5.3.0-3_all.deb ... Unpacking libjs-sphinxdoc (5.3.0-3) ... Selecting previously unselected package libjson-perl. Preparing to unpack .../113-libjson-perl_4.10000-1_all.deb ... Unpacking libjson-perl (4.10000-1) ... Selecting previously unselected package libopenblas0-pthread:ppc64el. Preparing to unpack .../114-libopenblas0-pthread_0.3.21+ds-4_ppc64el.deb ... Unpacking libopenblas0-pthread:ppc64el (0.3.21+ds-4) ... Selecting previously unselected package liblapack3:ppc64el. Preparing to unpack .../115-liblapack3_3.11.0-2_ppc64el.deb ... Unpacking liblapack3:ppc64el (3.11.0-2) ... Selecting previously unselected package liblbfgsb0:ppc64el. Preparing to unpack .../116-liblbfgsb0_3.0+dfsg.3-11_ppc64el.deb ... Unpacking liblbfgsb0:ppc64el (3.0+dfsg.3-11) ... Selecting previously unselected package liblcms2-2:ppc64el. Preparing to unpack .../117-liblcms2-2_2.14-2_ppc64el.deb ... Unpacking liblcms2-2:ppc64el (2.14-2) ... Selecting previously unselected package liblerc4:ppc64el. Preparing to unpack .../118-liblerc4_4.0.0+ds-2ubuntu2_ppc64el.deb ... Unpacking liblerc4:ppc64el (4.0.0+ds-2ubuntu2) ... Selecting previously unselected package libllvm14:ppc64el. Preparing to unpack .../119-libllvm14_1%3a14.0.6-12_ppc64el.deb ... Unpacking libllvm14:ppc64el (1:14.0.6-12) ... Selecting previously unselected package liblua5.3-0:ppc64el. Preparing to unpack .../120-liblua5.3-0_5.3.6-2_ppc64el.deb ... Unpacking liblua5.3-0:ppc64el (5.3.6-2) ... Selecting previously unselected package libnorm1:ppc64el. Preparing to unpack .../121-libnorm1_1.5.9+dfsg-2_ppc64el.deb ... Unpacking libnorm1:ppc64el (1.5.9+dfsg-2) ... Selecting previously unselected package libopenblas0:ppc64el. Preparing to unpack .../122-libopenblas0_0.3.21+ds-4_ppc64el.deb ... Unpacking libopenblas0:ppc64el (0.3.21+ds-4) ... Selecting previously unselected package libopenblas-pthread-dev:ppc64el. Preparing to unpack .../123-libopenblas-pthread-dev_0.3.21+ds-4_ppc64el.deb ... Unpacking libopenblas-pthread-dev:ppc64el (0.3.21+ds-4) ... Selecting previously unselected package libopenblas-dev:ppc64el. Preparing to unpack .../124-libopenblas-dev_0.3.21+ds-4_ppc64el.deb ... Unpacking libopenblas-dev:ppc64el (0.3.21+ds-4) ... Selecting previously unselected package libpgm-5.3-0:ppc64el. Preparing to unpack .../125-libpgm-5.3-0_5.3.128~dfsg-2_ppc64el.deb ... Unpacking libpgm-5.3-0:ppc64el (5.3.128~dfsg-2) ... Selecting previously unselected package libpython3.11:ppc64el. Preparing to unpack .../126-libpython3.11_3.11.2-4_ppc64el.deb ... Unpacking libpython3.11:ppc64el (3.11.2-4) ... Selecting previously unselected package zlib1g-dev:ppc64el. Preparing to unpack .../127-zlib1g-dev_1%3a1.2.13.dfsg-1ubuntu4_ppc64el.deb ... Unpacking zlib1g-dev:ppc64el (1:1.2.13.dfsg-1ubuntu4) ... Selecting previously unselected package libpython3.11-dev:ppc64el. Preparing to unpack .../128-libpython3.11-dev_3.11.2-4_ppc64el.deb ... Unpacking libpython3.11-dev:ppc64el (3.11.2-4) ... Selecting previously unselected package libpython3-dev:ppc64el. Preparing to unpack .../129-libpython3-dev_3.11.2-1_ppc64el.deb ... Unpacking libpython3-dev:ppc64el (3.11.2-1) ... Selecting previously unselected package libpython3-all-dev:ppc64el. Preparing to unpack .../130-libpython3-all-dev_3.11.2-1_ppc64el.deb ... Unpacking libpython3-all-dev:ppc64el (3.11.2-1) ... Selecting previously unselected package libqhull-r8.0:ppc64el. Preparing to unpack .../131-libqhull-r8.0_2020.2-5_ppc64el.deb ... Unpacking libqhull-r8.0:ppc64el (2020.2-5) ... Selecting previously unselected package libraqm0:ppc64el. Preparing to unpack .../132-libraqm0_0.7.0-4.1_ppc64el.deb ... Unpacking libraqm0:ppc64el (0.7.0-4.1) ... Selecting previously unselected package libsodium23:ppc64el. Preparing to unpack .../133-libsodium23_1.0.18-1build2_ppc64el.deb ... Unpacking libsodium23:ppc64el (1.0.18-1build2) ... Selecting previously unselected package libjbig0:ppc64el. Preparing to unpack .../134-libjbig0_2.1-6ubuntu1_ppc64el.deb ... Unpacking libjbig0:ppc64el (2.1-6ubuntu1) ... Selecting previously unselected package libwebp7:ppc64el. Preparing to unpack .../135-libwebp7_1.2.4-0.1build1_ppc64el.deb ... Unpacking libwebp7:ppc64el (1.2.4-0.1build1) ... Selecting previously unselected package libtiff6:ppc64el. Preparing to unpack .../136-libtiff6_4.5.0-4ubuntu1_ppc64el.deb ... Unpacking libtiff6:ppc64el (4.5.0-4ubuntu1) ... Selecting previously unselected package libwebpdemux2:ppc64el. Preparing to unpack .../137-libwebpdemux2_1.2.4-0.1build1_ppc64el.deb ... Unpacking libwebpdemux2:ppc64el (1.2.4-0.1build1) ... Selecting previously unselected package libwebpmux3:ppc64el. Preparing to unpack .../138-libwebpmux3_1.2.4-0.1build1_ppc64el.deb ... Unpacking libwebpmux3:ppc64el (1.2.4-0.1build1) ... Selecting previously unselected package libxsimd-dev:ppc64el. Preparing to unpack .../139-libxsimd-dev_8.1.0-7_ppc64el.deb ... Unpacking libxsimd-dev:ppc64el (8.1.0-7) ... Selecting previously unselected package libxslt1.1:ppc64el. Preparing to unpack .../140-libxslt1.1_1.1.35-1_ppc64el.deb ... Unpacking libxslt1.1:ppc64el (1.1.35-1) ... Selecting previously unselected package libzmq5:ppc64el. Preparing to unpack .../141-libzmq5_4.3.4-6_ppc64el.deb ... Unpacking libzmq5:ppc64el (4.3.4-6) ... Selecting previously unselected package llvm-14-runtime. Preparing to unpack .../142-llvm-14-runtime_1%3a14.0.6-12_ppc64el.deb ... Unpacking llvm-14-runtime (1:14.0.6-12) ... Selecting previously unselected package llvm-14-linker-tools. Preparing to unpack .../143-llvm-14-linker-tools_1%3a14.0.6-12_ppc64el.deb ... Unpacking llvm-14-linker-tools (1:14.0.6-12) ... Selecting previously unselected package libpfm4:ppc64el. Preparing to unpack .../144-libpfm4_4.12.1+git12-g678bca9-1_ppc64el.deb ... Unpacking libpfm4:ppc64el (4.12.1+git12-g678bca9-1) ... Selecting previously unselected package llvm-14. Preparing to unpack .../145-llvm-14_1%3a14.0.6-12_ppc64el.deb ... Unpacking llvm-14 (1:14.0.6-12) ... Selecting previously unselected package pandoc-data. Preparing to unpack .../146-pandoc-data_2.17.1.1-1.1ubuntu1_all.deb ... Unpacking pandoc-data (2.17.1.1-1.1ubuntu1) ... Selecting previously unselected package pandoc. Preparing to unpack .../147-pandoc_2.17.1.1-1.1ubuntu1_ppc64el.deb ... Unpacking pandoc (2.17.1.1-1.1ubuntu1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../148-python3-typing-extensions_4.4.0-1_all.deb ... Unpacking python3-typing-extensions (4.4.0-1) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../149-python3-more-itertools_8.10.0-2_all.deb ... Unpacking python3-more-itertools (8.10.0-2) ... Selecting previously unselected package python3-zipp. Preparing to unpack .../150-python3-zipp_1.0.0-6_all.deb ... Unpacking python3-zipp (1.0.0-6) ... Selecting previously unselected package python3-importlib-metadata. Preparing to unpack .../151-python3-importlib-metadata_4.12.0-1_all.deb ... Unpacking python3-importlib-metadata (4.12.0-1) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../152-python3-packaging_23.0-1_all.deb ... Unpacking python3-packaging (23.0-1) ... Selecting previously unselected package python3-pep517. Preparing to unpack .../153-python3-pep517_0.13.0-2_all.deb ... Unpacking python3-pep517 (0.13.0-2) ... Selecting previously unselected package python3-toml. Preparing to unpack .../154-python3-toml_0.10.2-1_all.deb ... Unpacking python3-toml (0.10.2-1) ... Selecting previously unselected package python3-wheel. Preparing to unpack .../155-python3-wheel_0.38.4-1_all.deb ... Unpacking python3-wheel (0.38.4-1) ... Selecting previously unselected package python3-build. Preparing to unpack .../156-python3-build_0.9.0-1_all.deb ... Unpacking python3-build (0.9.0-1) ... Selecting previously unselected package python3-installer. Preparing to unpack .../157-python3-installer_0.6.0+dfsg1-1_all.deb ... Unpacking python3-installer (0.6.0+dfsg1-1) ... Selecting previously unselected package pybuild-plugin-pyproject. Preparing to unpack .../158-pybuild-plugin-pyproject_5.20230130_all.deb ... Unpacking pybuild-plugin-pyproject (5.20230130) ... Selecting previously unselected package python-babel-localedata. Preparing to unpack .../159-python-babel-localedata_2.10.3-1_all.deb ... Unpacking python-babel-localedata (2.10.3-1) ... Selecting previously unselected package python-matplotlib-data. Preparing to unpack .../160-python-matplotlib-data_3.5.2-4_all.deb ... Unpacking python-matplotlib-data (3.5.2-4) ... Selecting previously unselected package python-tinycss2-common. Preparing to unpack .../161-python-tinycss2-common_1.2.1-2_all.deb ... Unpacking python-tinycss2-common (1.2.1-2) ... Selecting previously unselected package python3-all. Preparing to unpack .../162-python3-all_3.11.2-1_ppc64el.deb ... Unpacking python3-all (3.11.2-1) ... Selecting previously unselected package python3.11-dev. Preparing to unpack .../163-python3.11-dev_3.11.2-4_ppc64el.deb ... Unpacking python3.11-dev (3.11.2-4) ... Selecting previously unselected package python3-dev. Preparing to unpack .../164-python3-dev_3.11.2-1_ppc64el.deb ... Unpacking python3-dev (3.11.2-1) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../165-python3-all-dev_3.11.2-1_ppc64el.deb ... Unpacking python3-all-dev (3.11.2-1) ... Selecting previously unselected package python3-sniffio. Preparing to unpack .../166-python3-sniffio_1.2.0-1_all.deb ... Unpacking python3-sniffio (1.2.0-1) ... Selecting previously unselected package python3-anyio. Preparing to unpack .../167-python3-anyio_3.6.2-1_all.deb ... Unpacking python3-anyio (3.6.2-1) ... Selecting previously unselected package python3-appdirs. Preparing to unpack .../168-python3-appdirs_1.4.4-3_all.deb ... Unpacking python3-appdirs (1.4.4-3) ... Selecting previously unselected package python3-cffi-backend:ppc64el. Preparing to unpack .../169-python3-cffi-backend_1.15.1-5_ppc64el.deb ... Unpacking python3-cffi-backend:ppc64el (1.15.1-5) ... Selecting previously unselected package python3-argon2. Preparing to unpack .../170-python3-argon2_21.1.0-2_ppc64el.deb ... Unpacking python3-argon2 (21.1.0-2) ... Selecting previously unselected package python3-attr. Preparing to unpack .../171-python3-attr_22.2.0-1_all.deb ... Unpacking python3-attr (22.2.0-1) ... Selecting previously unselected package python3-tz. Preparing to unpack .../172-python3-tz_2022.7.1-1_all.deb ... Unpacking python3-tz (2022.7.1-1) ... Selecting previously unselected package python3-babel. Preparing to unpack .../173-python3-babel_2.10.3-1_all.deb ... Unpacking python3-babel (2.10.3-1) ... Selecting previously unselected package python3-gast. Preparing to unpack .../174-python3-gast_0.5.2-2_all.deb ... Unpacking python3-gast (0.5.2-2) ... Selecting previously unselected package python3-beniget. Preparing to unpack .../175-python3-beniget_0.4.1-3_all.deb ... Unpacking python3-beniget (0.4.1-3) ... Selecting previously unselected package python3-webencodings. Preparing to unpack .../176-python3-webencodings_0.5.1-5_all.deb ... Unpacking python3-webencodings (0.5.1-5) ... Selecting previously unselected package python3-html5lib. Preparing to unpack .../177-python3-html5lib_1.1-3_all.deb ... Unpacking python3-html5lib (1.1-3) ... Selecting previously unselected package python3-bleach. Preparing to unpack .../178-python3-bleach_5.0.1-2_all.deb ... Unpacking python3-bleach (5.0.1-2) ... Selecting previously unselected package python3-brotli. Preparing to unpack .../179-python3-brotli_1.0.9-2build7_ppc64el.deb ... Unpacking python3-brotli (1.0.9-2build7) ... Selecting previously unselected package python3-soupsieve. Preparing to unpack .../180-python3-soupsieve_2.4-1_all.deb ... Unpacking python3-soupsieve (2.4-1) ... Selecting previously unselected package python3-bs4. Preparing to unpack .../181-python3-bs4_4.11.2-2_all.deb ... Unpacking python3-bs4 (4.11.2-2) ... Selecting previously unselected package python3-commonmark. Preparing to unpack .../182-python3-commonmark_0.9.1-4_all.deb ... Unpacking python3-commonmark (0.9.1-4) ... Selecting previously unselected package python3-coverage. Preparing to unpack .../183-python3-coverage_6.5.0+dfsg1-2_ppc64el.deb ... Unpacking python3-coverage (6.5.0+dfsg1-2) ... Selecting previously unselected package python3-cycler. Preparing to unpack .../184-python3-cycler_0.11.0-1_all.deb ... Unpacking python3-cycler (0.11.0-1) ... Selecting previously unselected package python3-dateutil. Preparing to unpack .../185-python3-dateutil_2.8.2-1_all.deb ... Unpacking python3-dateutil (2.8.2-1) ... Selecting previously unselected package python3-decorator. Preparing to unpack .../186-python3-decorator_5.1.1-3_all.deb ... Unpacking python3-decorator (5.1.1-3) ... Selecting previously unselected package python3-defusedxml. Preparing to unpack .../187-python3-defusedxml_0.7.1-2_all.deb ... Unpacking python3-defusedxml (0.7.1-2) ... Selecting previously unselected package python3-entrypoints. Preparing to unpack .../188-python3-entrypoints_0.4-2_all.deb ... Unpacking python3-entrypoints (0.4-2) ... Selecting previously unselected package python3-execnet. Preparing to unpack .../189-python3-execnet_1.9.0-1_all.deb ... Unpacking python3-execnet (1.9.0-1) ... Selecting previously unselected package python3-fastjsonschema. Preparing to unpack .../190-python3-fastjsonschema_2.16.2-1_all.deb ... Unpacking python3-fastjsonschema (2.16.2-1) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../191-python3-numpy_1%3a1.24.2-1_ppc64el.deb ... Unpacking python3-numpy (1:1.24.2-1) ... Selecting previously unselected package python3-ply. Preparing to unpack .../192-python3-ply_3.11-5_all.deb ... Unpacking python3-ply (3.11-5) ... Selecting previously unselected package python3-pythran. Preparing to unpack .../193-python3-pythran_0.11.0+ds-7_ppc64el.deb ... Unpacking python3-pythran (0.11.0+ds-7) ... Selecting previously unselected package python3-scipy. Preparing to unpack .../194-python3-scipy_1.10.0-12_ppc64el.deb ... Unpacking python3-scipy (1.10.0-12) ... Selecting previously unselected package python3-ufolib2. Preparing to unpack .../195-python3-ufolib2_0.14.0+dfsg1-1_all.deb ... Unpacking python3-ufolib2 (0.14.0+dfsg1-1) ... Selecting previously unselected package python3-mpmath. Preparing to unpack .../196-python3-mpmath_1.2.1-2_all.deb ... Unpacking python3-mpmath (1.2.1-2) ... Selecting previously unselected package python3-sympy. Preparing to unpack .../197-python3-sympy_1.11.1-1_all.deb ... Unpacking python3-sympy (1.11.1-1) ... Selecting previously unselected package python3-fs. Preparing to unpack .../198-python3-fs_2.4.16-2_all.deb ... Unpacking python3-fs (2.4.16-2) ... Selecting previously unselected package python3-lxml:ppc64el. Preparing to unpack .../199-python3-lxml_4.9.2-1_ppc64el.deb ... Unpacking python3-lxml:ppc64el (4.9.2-1) ... Selecting previously unselected package python3-lz4. Preparing to unpack .../200-python3-lz4_4.0.2+dfsg-1_ppc64el.deb ... Unpacking python3-lz4 (4.0.2+dfsg-1) ... Selecting previously unselected package unicode-data. Preparing to unpack .../201-unicode-data_15.0.0-1_all.deb ... Unpacking unicode-data (15.0.0-1) ... Selecting previously unselected package python3-fonttools. Preparing to unpack .../202-python3-fonttools_4.38.0-1_ppc64el.deb ... Unpacking python3-fonttools (4.38.0-1) ... Selecting previously unselected package python3-imagesize. Preparing to unpack .../203-python3-imagesize_1.4.1-1_all.deb ... Unpacking python3-imagesize (1.4.1-1) ... Selecting previously unselected package python3-iniconfig. Preparing to unpack .../204-python3-iniconfig_1.1.1-2_all.deb ... Unpacking python3-iniconfig (1.1.1-2) ... Selecting previously unselected package python3-isort. Preparing to unpack .../205-python3-isort_5.6.4-1_all.deb ... Unpacking python3-isort (5.6.4-1) ... Selecting previously unselected package python3-markupsafe. Preparing to unpack .../206-python3-markupsafe_2.1.2-1_ppc64el.deb ... Unpacking python3-markupsafe (2.1.2-1) ... Selecting previously unselected package python3-jinja2. Preparing to unpack .../207-python3-jinja2_3.0.3-2_all.deb ... Unpacking python3-jinja2 (3.0.3-2) ... Selecting previously unselected package python3-json5. Preparing to unpack .../208-python3-json5_0.9.10-1_all.deb ... Unpacking python3-json5 (0.9.10-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../209-python3-setuptools_66.1.1-1_all.deb ... Unpacking python3-setuptools (66.1.1-1) ... Selecting previously unselected package python3-pyrsistent:ppc64el. Preparing to unpack .../210-python3-pyrsistent_0.18.1-1build2_ppc64el.deb ... Unpacking python3-pyrsistent:ppc64el (0.18.1-1build2) ... Selecting previously unselected package python3-jsonschema. Preparing to unpack .../211-python3-jsonschema_4.6.0-3ubuntu1_all.deb ... Unpacking python3-jsonschema (4.6.0-3ubuntu1) ... Selecting previously unselected package python3-traitlets. Preparing to unpack .../212-python3-traitlets_5.5.0-1_all.deb ... Unpacking python3-traitlets (5.5.0-1) ... Selecting previously unselected package python3-jupyter-core. Preparing to unpack .../213-python3-jupyter-core_4.12.0-1_all.deb ... Unpacking python3-jupyter-core (4.12.0-1) ... Selecting previously unselected package python3-nest-asyncio. Preparing to unpack .../214-python3-nest-asyncio_1.5.4-1_all.deb ... Unpacking python3-nest-asyncio (1.5.4-1) ... Selecting previously unselected package python3-tornado. Preparing to unpack .../215-python3-tornado_6.2.0-3_ppc64el.deb ... Unpacking python3-tornado (6.2.0-3) ... Selecting previously unselected package python3-py. Preparing to unpack .../216-python3-py_1.11.0-1_all.deb ... Unpacking python3-py (1.11.0-1) ... Selecting previously unselected package python3-zmq. Preparing to unpack .../217-python3-zmq_24.0.1-4_ppc64el.deb ... Unpacking python3-zmq (24.0.1-4) ... Selecting previously unselected package python3-jupyter-client. Preparing to unpack .../218-python3-jupyter-client_7.4.9-2_all.deb ... Unpacking python3-jupyter-client (7.4.9-2) ... Selecting previously unselected package python3-pygments. Preparing to unpack .../219-python3-pygments_2.14.0+dfsg-1_all.deb ... Unpacking python3-pygments (2.14.0+dfsg-1) ... Selecting previously unselected package python3-jupyterlab-pygments. Preparing to unpack .../220-python3-jupyterlab-pygments_0.2.2-3_all.deb ... Unpacking python3-jupyterlab-pygments (0.2.2-3) ... Selecting previously unselected package python3-nbformat. Preparing to unpack .../221-python3-nbformat_5.5.0-1_all.deb ... Unpacking python3-nbformat (5.5.0-1) ... Selecting previously unselected package python3-nbclient. Preparing to unpack .../222-python3-nbclient_0.7.2-1_all.deb ... Unpacking python3-nbclient (0.7.2-1) ... Selecting previously unselected package python3-pandocfilters. Preparing to unpack .../223-python3-pandocfilters_1.5.0-1_all.deb ... Unpacking python3-pandocfilters (1.5.0-1) ... Selecting previously unselected package python3-tinycss2. Preparing to unpack .../224-python3-tinycss2_1.2.1-2_all.deb ... Unpacking python3-tinycss2 (1.2.1-2) ... Selecting previously unselected package python3-nbconvert. Preparing to unpack .../225-python3-nbconvert_6.5.3-3_all.deb ... Unpacking python3-nbconvert (6.5.3-3) ... Selecting previously unselected package python3-prometheus-client. Preparing to unpack .../226-python3-prometheus-client_0.16.0-0.1_all.deb ... Unpacking python3-prometheus-client (0.16.0-0.1) ... Selecting previously unselected package python3-send2trash. Preparing to unpack .../227-python3-send2trash_1.8.1~b0-2_all.deb ... Unpacking python3-send2trash (1.8.1~b0-2) ... Selecting previously unselected package python3-ptyprocess. Preparing to unpack .../228-python3-ptyprocess_0.7.0-5_all.deb ... Unpacking python3-ptyprocess (0.7.0-5) ... Selecting previously unselected package python3-terminado. Preparing to unpack .../229-python3-terminado_0.17.0-1_all.deb ... Unpacking python3-terminado (0.17.0-1) ... Selecting previously unselected package python3-websocket. Preparing to unpack .../230-python3-websocket_1.2.3-1_all.deb ... Unpacking python3-websocket (1.2.3-1) ... Selecting previously unselected package python3-jupyter-server. Preparing to unpack .../231-python3-jupyter-server_1.23.3-1_all.deb ... Unpacking python3-jupyter-server (1.23.3-1) ... Selecting previously unselected package sphinx-common. Preparing to unpack .../232-sphinx-common_5.3.0-3_all.deb ... Unpacking sphinx-common (5.3.0-3) ... Selecting previously unselected package python3-alabaster. Preparing to unpack .../233-python3-alabaster_0.7.12-1_all.deb ... Unpacking python3-alabaster (0.7.12-1) ... Selecting previously unselected package python3-snowballstemmer. Preparing to unpack .../234-python3-snowballstemmer_2.2.0-2_all.deb ... Unpacking python3-snowballstemmer (2.2.0-2) ... Selecting previously unselected package python3-sphinx. Preparing to unpack .../235-python3-sphinx_5.3.0-3_all.deb ... Unpacking python3-sphinx (5.3.0-3) ... Selecting previously unselected package python3-nbsphinx. Preparing to unpack .../236-python3-nbsphinx_0.8.11+ds-1_all.deb ... Unpacking python3-nbsphinx (0.8.11+ds-1) ... Selecting previously unselected package python3-recommonmark. Preparing to unpack .../237-python3-recommonmark_0.7.1+ds-5_all.deb ... Unpacking python3-recommonmark (0.7.1+ds-5) ... Selecting previously unselected package python3-jupyter-sphinx-theme. Preparing to unpack .../238-python3-jupyter-sphinx-theme_0.0.6+ds1-11_all.deb ... Unpacking python3-jupyter-sphinx-theme (0.0.6+ds1-11) ... Selecting previously unselected package python3-jupyterlab-server. Preparing to unpack .../239-python3-jupyterlab-server_2.16.5-1_all.deb ... Unpacking python3-jupyterlab-server (2.16.5-1) ... Selecting previously unselected package python3-kiwisolver. Preparing to unpack .../240-python3-kiwisolver_1.4.4-1_ppc64el.deb ... Unpacking python3-kiwisolver (1.4.4-1) ... Selecting previously unselected package python3-llvmlite. Preparing to unpack .../241-python3-llvmlite_0.39.1-2_ppc64el.deb ... Unpacking python3-llvmlite (0.39.1-2) ... Selecting previously unselected package libopenjp2-7:ppc64el. Preparing to unpack .../242-libopenjp2-7_2.5.0-1build1_ppc64el.deb ... Unpacking libopenjp2-7:ppc64el (2.5.0-1build1) ... Selecting previously unselected package python3-pil:ppc64el. Preparing to unpack .../243-python3-pil_9.4.0-1.1build1_ppc64el.deb ... Unpacking python3-pil:ppc64el (9.4.0-1.1build1) ... Selecting previously unselected package python3-tk:ppc64el. Preparing to unpack .../244-python3-tk_3.11.2-2_ppc64el.deb ... Unpacking python3-tk:ppc64el (3.11.2-2) ... Selecting previously unselected package python3-pil.imagetk:ppc64el. Preparing to unpack .../245-python3-pil.imagetk_9.4.0-1.1build1_ppc64el.deb ... Unpacking python3-pil.imagetk:ppc64el (9.4.0-1.1build1) ... Selecting previously unselected package python3-pyparsing. Preparing to unpack .../246-python3-pyparsing_3.0.9-1_all.deb ... Unpacking python3-pyparsing (3.0.9-1) ... Selecting previously unselected package python3-matplotlib. Preparing to unpack .../247-python3-matplotlib_3.5.2-4_ppc64el.deb ... Unpacking python3-matplotlib (3.5.2-4) ... Selecting previously unselected package python3-numba. Preparing to unpack .../248-python3-numba_0.56.4+dfsg-2_ppc64el.deb ... Unpacking python3-numba (0.56.4+dfsg-2) ... Selecting previously unselected package python3-numpydoc. Preparing to unpack .../249-python3-numpydoc_1.5.0-1_all.deb ... Unpacking python3-numpydoc (1.5.0-1) ... Selecting previously unselected package python3-pandas-lib:ppc64el. Preparing to unpack .../250-python3-pandas-lib_1.5.3+dfsg-2_ppc64el.deb ... Unpacking python3-pandas-lib:ppc64el (1.5.3+dfsg-2) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../251-python3-pandas_1.5.3+dfsg-2_all.deb ... Unpacking python3-pandas (1.5.3+dfsg-2) ... Selecting previously unselected package python3-pbr. Preparing to unpack .../252-python3-pbr_5.11.0-0ubuntu1_all.deb ... Unpacking python3-pbr (5.11.0-0ubuntu1) ... Selecting previously unselected package python3-tenacity. Preparing to unpack .../253-python3-tenacity_8.2.1-1_all.deb ... Unpacking python3-tenacity (8.2.1-1) ... Selecting previously unselected package python3-plotly. Preparing to unpack .../254-python3-plotly_5.4.1+dfsg-1_all.deb ... Unpacking python3-plotly (5.4.1+dfsg-1) ... Selecting previously unselected package python3-pluggy. Preparing to unpack .../255-python3-pluggy_1.0.0+repack-1_all.deb ... Unpacking python3-pluggy (1.0.0+repack-1) ... Selecting previously unselected package python3-pytest. Preparing to unpack .../256-python3-pytest_7.2.1-2_all.deb ... Unpacking python3-pytest (7.2.1-2) ... Selecting previously unselected package libjs-jquery-isonscreen. Preparing to unpack .../257-libjs-jquery-isonscreen_1.2.0-1.1_all.deb ... Unpacking libjs-jquery-isonscreen (1.2.0-1.1) ... Selecting previously unselected package python3-pytest-cov. Preparing to unpack .../258-python3-pytest-cov_4.0.0-1_all.deb ... Unpacking python3-pytest-cov (4.0.0-1) ... Selecting previously unselected package python3-pytest-xdist. Preparing to unpack .../259-python3-pytest-xdist_3.1.0-1_all.deb ... Unpacking python3-pytest-xdist (3.1.0-1) ... Selecting previously unselected package python3-scitrack. Preparing to unpack .../260-python3-scitrack_2021.5.3-3_all.deb ... Unpacking python3-scitrack (2021.5.3-3) ... Selecting previously unselected package python3-sphinx-gallery. Preparing to unpack .../261-python3-sphinx-gallery_0.10.1-3_all.deb ... Unpacking python3-sphinx-gallery (0.10.1-3) ... Selecting previously unselected package python3-tinydb. Preparing to unpack .../262-python3-tinydb_3.15.2-4_all.deb ... Unpacking python3-tinydb (3.15.2-4) ... Selecting previously unselected package python3-tqdm. Preparing to unpack .../263-python3-tqdm_4.64.1-1_all.deb ... Unpacking python3-tqdm (4.64.1-1) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../264-sbuild-build-depends-main-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:ppc64el (1.5.7-1) ... Setting up libgraphite2-3:ppc64el (1.3.14-1build2) ... Setting up liblcms2-2:ppc64el (2.14-2) ... Setting up libxau6:ppc64el (1:1.0.9-1build5) ... Setting up libpsl5:ppc64el (0.21.2-1) ... Setting up libboost1.74-dev:ppc64el (1.74.0-18.1ubuntu3) ... Setting up libsodium23:ppc64el (1.0.18-1build2) ... Setting up libicu72:ppc64el (72.1-3ubuntu1) ... Setting up liblerc4:ppc64el (4.0.0+ds-2ubuntu2) ... Setting up bsdextrautils (2.38.1-4ubuntu1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:ppc64el (0.2.5-1) ... Setting up libglib2.0-0:ppc64el (2.74.5-1) ... No schema files found: doing nothing. Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Setting up libpgm-5.3-0:ppc64el (5.3.128~dfsg-2) ... Setting up fonts-lyx (2.3.7-1) ... Setting up libpython3.11-stdlib:ppc64el (3.11.2-4) ... Setting up libdebhelper-perl (13.11.4ubuntu3) ... Setting up libbrotli1:ppc64el (1.0.9-2build7) ... Setting up libnorm1:ppc64el (1.5.9+dfsg-2) ... Setting up x11-common (1:7.7+23ubuntu2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:ppc64el (1.52.0-1) ... Setting up libmagic1:ppc64el (1:5.44-3) ... Setting up libdeflate0:ppc64el (1.15-1) ... Setting up gettext-base (0.21-11) ... Setting up m4 (1.4.19-3) ... Setting up libqhull-r8.0:ppc64el (2020.2-5) ... Setting up file (1:5.44-3) ... Setting up libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... Setting up libjbig0:ppc64el (2.1-6ubuntu1) ... Setting up python-babel-localedata (2.10.3-1) ... Setting up libsasl2-modules-db:ppc64el (2.1.28+dfsg-10) ... Setting up unicode-data (15.0.0-1) ... Setting up libxsimd-dev:ppc64el (8.1.0-7) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:ppc64el (3.11.0-2) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode Setting up libpfm4:ppc64el (4.12.1+git12-g678bca9-1) ... Setting up libexpat1-dev:ppc64el (2.5.0-1) ... Setting up libfreetype6:ppc64el (2.12.1+dfsg-4) ... Setting up libx11-data (2:1.8.3-3) ... Setting up librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libjs-bootswatch (3.3.7+dfsg2-1.1) ... Setting up libfribidi0:ppc64el (1.0.8-2.1ubuntu1) ... Setting up libimagequant0:ppc64el (2.17.0-1) ... Setting up libtcl8.6:ppc64el (8.6.13+dfsg-2) ... Setting up libpython3.10-minimal:ppc64el (3.10.9-1) ... Setting up autopoint (0.21-11) ... Setting up fonts-dejavu-core (2.37-4) ... Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... Setting up libsasl2-2:ppc64el (2.1.28+dfsg-10) ... Setting up libssh-4:ppc64el (0.10.4-2) ... Setting up libgfortran5:ppc64el (13-20230215-1ubuntu2) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:ppc64el (1.2.4-0.1build1) ... Setting up zlib1g-dev:ppc64el (1:1.2.13.dfsg-1ubuntu4) ... Setting up libuchardet0:ppc64el (0.0.7-1build2) ... Setting up liblua5.3-0:ppc64el (5.3.6-2) ... Setting up python-tinycss2-common (1.2.1-2) ... Setting up libjson-perl (4.10000-1) ... Setting up libmpdec3:ppc64el (2.5.1-2build2) ... Setting up libopenjp2-7:ppc64el (2.5.0-1build1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libharfbuzz0b:ppc64el (6.0.0+dfsg-3build1) ... Setting up sgml-base (1.31) ... Setting up libboost-dev:ppc64el (1.74.0.3ubuntu7) ... Setting up pandoc-data (2.17.1.1-1.1ubuntu1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libjs-jquery-hotkeys (0~20130707+git2d51e3a9+dfsg-2ubuntu1) ... Setting up python-matplotlib-data (3.5.2-4) ... Setting up libwebpmux3:ppc64el (1.2.4-0.1build1) ... Setting up libbsd0:ppc64el (0.11.7-2) ... Setting up libelf1:ppc64el (0.188-2.1) ... Setting up libxml2:ppc64el (2.9.14+dfsg-1.1build1) ... Setting up libldap2:ppc64el (2.6.3+dfsg-1~exp1ubuntu2) ... Setting up libjs-bootstrap (3.4.1+dfsg-3) ... Setting up libpython3-stdlib:ppc64el (3.11.2-1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.11 (3.11.2-4) ... Setting up libdw1:ppc64el (0.188-2.1) ... Setting up libxdmcp6:ppc64el (1:1.1.3-0ubuntu5) ... Setting up liblapack3:ppc64el (3.11.0-2) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode Setting up libxcb1:ppc64el (1.15-1) ... Setting up gettext (0.21-11) ... Setting up libopenblas0-pthread:ppc64el (0.3.21+ds-4) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode update-alternatives: using /usr/lib/powerpc64le-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode update-alternatives: using /usr/lib/powerpc64le-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/powerpc64le-linux-gnu/libopenblas.so.0 (libopenblas.so.0-powerpc64le-linux-gnu) in auto mode Setting up libzmq5:ppc64el (4.3.4-6) ... Setting up libpython3.11:ppc64el (3.11.2-4) ... Setting up libtool (2.4.7-5) ... Setting up fontconfig-config (2.14.1-3ubuntu2) ... Setting up libwebpdemux2:ppc64el (1.2.4-0.1build1) ... Setting up libedit2:ppc64el (3.1-20221030-2) ... Setting up python3 (3.11.2-1) ... Setting up python3-pandocfilters (1.5.0-1) ... Setting up python3.10-minimal (3.10.9-1) ... Setting up python3-markupsafe (2.1.2-1) ... Setting up python3-webencodings (0.5.1-5) ... Setting up python3-tz (2022.7.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up python3-six (1.16.0-4) ... Setting up libpython3.10-stdlib:ppc64el (3.10.9-1) ... Setting up dh-autoreconf (20) ... Setting up python3-roman (3.3-3) ... Setting up python3-decorator (5.1.1-3) ... Setting up python3-jinja2 (3.0.3-2) ... Setting up python3-packaging (23.0-1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up pandoc (2.17.1.1-1.1ubuntu1) ... Setting up python3-pyparsing (3.0.9-1) ... Setting up python3-certifi (2022.9.24-1) ... Setting up python3-sphinx-bootstrap-theme (0.8.1-1) ... Setting up python3-snowballstemmer (2.2.0-2) ... Setting up libpython3.11-dev:ppc64el (3.11.2-4) ... Setting up python3-nest-asyncio (1.5.4-1) ... Setting up python3-brotli (1.0.9-2build7) ... Setting up libjs-jquery-metadata (12-4) ... Setting up libraqm0:ppc64el (0.7.0-4.1) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-kiwisolver (1.4.4-1) ... Setting up libjs-jquery-isonscreen (1.2.0-1.1) ... Setting up python3-idna (3.3-1) ... Setting up cython3 (0.29.32-2ubuntu1) ... Setting up jupyter-sphinx-theme-common (0.0.6+ds1-11) ... Setting up python3-typing-extensions (4.4.0-1) ... Setting up python3-html5lib (1.1-3) ... Setting up libjs-sphinxdoc (5.3.0-3) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-installer (0.6.0+dfsg1-1) ... Setting up python3-isort (5.6.4-1) ... Setting up python3-urllib3 (1.26.12-1) ... Setting up python3-pluggy (1.0.0+repack-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up python3-fastjsonschema (2.16.2-1) ... Setting up libllvm14:ppc64el (1:14.0.6-12) ... Setting up python3-pyrsistent:ppc64el (0.18.1-1build2) ... Setting up dwz (0.15-1) ... Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-3) ... Setting up libopenblas0:ppc64el (0.3.21+ds-4) ... Setting up groff-base (1.22.4-9) ... Setting up libtiff6:ppc64el (4.5.0-4ubuntu1) ... Setting up xml-core (0.18+nmu1) ... Setting up python3-traitlets (5.5.0-1) ... Setting up python3-scitrack (2021.5.3-3) ... Setting up libxslt1.1:ppc64el (1.1.35-1) ... Setting up debugedit (1:5.0-5) ... Setting up libcurl4:ppc64el (7.87.0-2ubuntu2) ... Setting up libx11-6:ppc64el (2:1.8.3-3) ... Setting up python3-dateutil (2.8.2-1) ... Setting up libfontconfig1:ppc64el (2.14.1-3ubuntu2) ... Setting up python3-mpmath (1.2.1-2) ... Setting up llvm-14-linker-tools (1:14.0.6-12) ... Setting up python3-execnet (1.9.0-1) ... Setting up python3-lib2to3 (3.11.2-2) ... Setting up python3-tomli-w (1.0.0-2) ... Setting up python3-appdirs (1.4.4-3) ... Setting up python3-soupsieve (2.4-1) ... Setting up python3-websocket (1.2.3-1) ... Setting up python3-cffi-backend:ppc64el (1.15.1-5) ... Setting up liblbfgsb0:ppc64el (3.0+dfsg.3-11) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-ptyprocess (0.7.0-5) ... Setting up python3-commonmark (0.9.1-4) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-entrypoints (0.4-2) ... Setting up python3-distutils (3.11.2-2) ... Setting up libopenblas-pthread-dev:ppc64el (0.3.21+ds-4) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/powerpc64le-linux-gnu/libblas.so (libblas.so-powerpc64le-linux-gnu) in auto mode update-alternatives: using /usr/lib/powerpc64le-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so (liblapack.so-powerpc64le-linux-gnu) in auto mode update-alternatives: using /usr/lib/powerpc64le-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/powerpc64le-linux-gnu/libopenblas.so (libopenblas.so-powerpc64le-linux-gnu) in auto mode Setting up dh-python (5.20230130) ... Setting up python3-more-itertools (8.10.0-2) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sniffio (1.2.0-1) ... Setting up python3-sympy (1.11.1-1) ... Setting up python3-attr (22.2.0-1) ... Setting up python3-tornado (6.2.0-3) ... Setting up python3-send2trash (1.8.1~b0-2) ... Setting up python3-tinycss2 (1.2.1-2) ... Setting up libpython3-dev:ppc64el (3.11.2-1) ... Setting up python3.10 (3.10.9-1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-tomli (2.0.1-2) ... Setting up libxrender1:ppc64el (1:0.9.10-1.1) ... Setting up python3-py (1.11.0-1) ... Setting up python3-anyio (3.6.2-1) ... Setting up python3-babel (2.10.3-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-lz4 (4.0.2+dfsg-1) ... Setting up python3-defusedxml (0.7.1-2) ... Setting up python3-json5 (0.9.10-1) ... Setting up python3-pbr (5.11.0-0ubuntu1) ... Setting up python3.11-dev (3.11.2-4) ... Setting up python3-pytest (7.2.1-2) ... Setting up python3-alabaster (0.7.12-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3-tenacity (8.2.1-1) ... Setting up python3-ply (3.11-5) ... Setting up python3-tqdm (4.64.1-1) ... Setting up python3-tinydb (3.15.2-4) ... Setting up python3-gast (0.5.2-2) ... Setting up libxext6:ppc64el (2:1.3.4-1build1) ... Setting up python3-all (3.11.2-1) ... Setting up python3-coverage (6.5.0+dfsg1-2) ... Setting up python3-pytest-cov (4.0.0-1) ... Setting up python3-zipp (1.0.0-6) ... Setting up man-db (2.11.2-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up python3-wheel (0.38.4-1) ... Setting up python3-bs4 (4.11.2-2) ... Setting up python3-bleach (5.0.1-2) ... Setting up python3-fs (2.4.16-2) ... Setting up python3-beniget (0.4.1-3) ... Setting up python3-prometheus-client (0.16.0-0.1) ... Setting up libopenblas-dev:ppc64el (0.3.21+ds-4) ... Setting up python3-pygments (2.14.0+dfsg-1) ... Setting up python3-chardet (5.1.0+dfsg-2) ... Setting up llvm-14-runtime (1:14.0.6-12) ... Setting up python3-jsonschema (4.6.0-3ubuntu1) ... Setting up libpython3-all-dev:ppc64el (3.11.2-1) ... Setting up python3-zmq (24.0.1-4) ... Setting up sphinx-common (5.3.0-3) ... Setting up python3-dev (3.11.2-1) ... Setting up python3-requests (2.28.1+dfsg-1ubuntu1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-terminado (0.17.0-1) ... Setting up python3-lxml:ppc64el (4.9.2-1) ... Setting up python3-argon2 (21.1.0-2) ... Setting up libxss1:ppc64el (1:1.2.3-1build2) ... Setting up python3-jupyter-core (4.12.0-1) ... Setting up llvm-14 (1:14.0.6-12) ... Setting up python3-all-dev (3.11.2-1) ... Setting up libxft2:ppc64el (2.3.6-1) ... Setting up python3-importlib-metadata (4.12.0-1) ... Setting up python3-pytest-xdist (3.1.0-1) ... Setting up libtk8.6:ppc64el (8.6.13-2) ... Setting up python3-pandas-lib:ppc64el (1.5.3+dfsg-2) ... Setting up debhelper (13.11.4ubuntu3) ... Setting up python3-nbformat (5.5.0-1) ... Setting up python3-jupyterlab-pygments (0.2.2-3) ... Setting up python3-llvmlite (0.39.1-2) ... Setting up python3-pandas (1.5.3+dfsg-2) ... Setting up python3-pep517 (0.13.0-2) ... Setting up python3-plotly (5.4.1+dfsg-1) ... Setting up python3-pythran (0.11.0+ds-7) ... Setting up python3-jupyter-client (7.4.9-2) ... Setting up python3-build (0.9.0-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1build2) ... Setting up python3-scipy (1.10.0-12) ... Setting up pybuild-plugin-pyproject (5.20230130) ... Setting up blt (2.5.3+dfsg-4.1build2) ... Setting up python3-tk:ppc64el (3.11.2-2) ... Setting up python3-numba (0.56.4+dfsg-2) ... update-alternatives: using /usr/share/python3-numba/numba to provide /usr/bin/numba (numba) in auto mode Setting up python3-nbclient (0.7.2-1) ... Setting up python3-nbconvert (6.5.3-3) ... Setting up python3-jupyter-server (1.23.3-1) ... Setting up python3-jupyterlab-server (2.16.5-1) ... Setting up python3-fonttools (4.38.0-1) ... Setting up python3-pil:ppc64el (9.4.0-1.1build1) ... Setting up python3-pil.imagetk:ppc64el (9.4.0-1.1build1) ... Setting up python3-ufolib2 (0.14.0+dfsg1-1) ... Setting up python3-matplotlib (3.5.2-4) ... Processing triggers for libc-bin (2.37-0ubuntu1) ... Processing triggers for systemd (252.5-2ubuntu1) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.19+dfsg-6) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.19+dfsg-6) ... Setting up flit (3.8.0-3) ... Setting up python3-sphinx (5.3.0-3) ... Setting up python3-sphinx-gallery (0.10.1-3) ... Setting up python3-nbsphinx (0.8.11+ds-1) ... Setting up python3-recommonmark (0.7.1+ds-5) ... Setting up python3-numpydoc (1.5.0-1) ... Setting up python3-jupyter-sphinx-theme (0.0.6+ds1-11) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (ppc64el included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-139-generic #156-Ubuntu SMP Fri Jan 20 17:27:42 UTC 2023 ppc64el (ppc64le) Toolchain package versions: binutils_2.40-2ubuntu2 dpkg-dev_1.21.20ubuntu2 g++-12_12.2.0-14ubuntu2 gcc-12_12.2.0-14ubuntu2 libc6-dev_2.37-0ubuntu1 libstdc++-12-dev_12.2.0-14ubuntu2 libstdc++6_13-20230215-1ubuntu2 linux-libc-dev_6.1.0-14.14 Package versions: adduser_3.129ubuntu1 advancecomp_2.5-1 apt_2.5.6 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-11 autotools-dev_20220109.1 base-files_12.3ubuntu1 base-passwd_3.6.1 bash_5.2.15-2ubuntu1 binutils_2.40-2ubuntu2 binutils-common_2.40-2ubuntu2 binutils-powerpc64le-linux-gnu_2.40-2ubuntu2 blt_2.5.3+dfsg-4.1build2 bsdextrautils_2.38.1-4ubuntu1 bsdutils_1:2.38.1-4ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016ubuntu1 coreutils_9.1-1ubuntu2 cpp_4:12.2.0-3ubuntu1 cpp-12_12.2.0-14ubuntu2 cython3_0.29.32-2ubuntu1 dash_0.5.12-2ubuntu1 debconf_1.5.82 debhelper_13.11.4ubuntu3 debianutils_5.7-0.4 debugedit_1:5.0-5 dh-autoreconf_20 dh-python_5.20230130 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 docutils-common_0.19+dfsg-6 dpkg_1.21.20ubuntu2 dpkg-dev_1.21.20ubuntu2 dwz_0.15-1 e2fsprogs_1.47.0-1ubuntu1 fakeroot_1.31-1ubuntu1 file_1:5.44-3 findutils_4.9.0-3ubuntu1 flit_3.8.0-3 fontconfig-config_2.14.1-3ubuntu2 fonts-dejavu-core_2.37-4 fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3 fonts-lyx_2.3.7-1 g++_4:12.2.0-3ubuntu1 g++-12_12.2.0-14ubuntu2 gcc_4:12.2.0-3ubuntu1 gcc-12_12.2.0-14ubuntu2 gcc-12-base_12.2.0-14ubuntu2 gcc-13-base_13-20230215-1ubuntu2 gettext_0.21-11 gettext-base_0.21-11 gpg_2.2.40-1ubuntu2 gpg-agent_2.2.40-1ubuntu2 gpgconf_2.2.40-1ubuntu2 gpgv_2.2.40-1ubuntu2 grep_3.8-5 groff-base_1.22.4-9 gzip_1.12-1ubuntu1 hostname_3.23+nmu1ubuntu1 init_1.65.2 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 jupyter-sphinx-theme-common_0.0.6+ds1-11 libacl1_2.3.1-3 libapparmor1_3.0.8-1ubuntu1 libapt-pkg6.0_2.5.6 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.3 libasan8_13-20230215-1ubuntu2 libassuan0_2.5.5-5 libatomic1_13-20230215-1ubuntu2 libattr1_1:2.5.1-4 libaudit-common_1:3.0.9-1 libaudit1_1:3.0.9-1 libbinutils_2.40-2ubuntu2 libblas3_3.11.0-2 libblkid1_2.38.1-4ubuntu1 libboost-dev_1.74.0.3ubuntu7 libboost1.74-dev_1.74.0-18.1ubuntu3 libbrotli1_1.0.9-2build7 libbsd0_0.11.7-2 libbz2-1.0_1.0.8-5build1 libc-bin_2.37-0ubuntu1 libc-dev-bin_2.37-0ubuntu1 libc6_2.37-0ubuntu1 libc6-dev_2.37-0ubuntu1 libcap-ng0_0.8.3-1build1 libcap2_1:2.66-3ubuntu2 libcc1-0_13-20230215-1ubuntu2 libcom-err2_1.47.0-1ubuntu1 libcrypt-dev_1:4.4.33-2 libcrypt1_1:4.4.33-2 libcryptsetup12_2:2.6.1-1ubuntu1 libctf-nobfd0_2.40-2ubuntu2 libctf0_2.40-2ubuntu2 libcurl4_7.87.0-2ubuntu2 libdb5.3_5.3.28+dfsg2-1 libdebconfclient0_0.267ubuntu1 libdebhelper-perl_13.11.4ubuntu3 libdeflate0_1.15-1 libdevmapper1.02.1_2:1.02.185-1ubuntu1 libdpkg-perl_1.21.20ubuntu2 libdw1_0.188-2.1 libedit2_3.1-20221030-2 libelf1_0.188-2.1 libexpat1_2.5.0-1 libexpat1-dev_2.5.0-1 libext2fs2_1.47.0-1ubuntu1 libfakeroot_1.31-1ubuntu1 libfdisk1_2.38.1-4ubuntu1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.1-1 libfontconfig1_2.14.1-3ubuntu2 libfreetype6_2.12.1+dfsg-4 libfribidi0_1.0.8-2.1ubuntu1 libgcc-12-dev_12.2.0-14ubuntu2 libgcc-s1_13-20230215-1ubuntu2 libgcrypt20_1.10.1-3ubuntu1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_13-20230215-1ubuntu2 libglib2.0-0_2.74.5-1 libgmp10_2:6.2.1+dfsg1-1.1ubuntu1 libgnutls30_3.7.8-5ubuntu1 libgomp1_13-20230215-1ubuntu2 libgpg-error0_1.46-1 libgraphite2-3_1.3.14-1build2 libgssapi-krb5-2_1.20.1-1build1 libharfbuzz0b_6.0.0+dfsg-3build1 libhogweed6_3.8.1-2 libicu72_72.1-3ubuntu1 libidn2-0_2.3.3-1build1 libimagequant0_2.17.0-1 libip4tc2_1.8.7-1ubuntu7 libisl23_0.25-1 libitm1_13-20230215-1ubuntu2 libjansson4_2.14-2 libjbig0_2.1-6ubuntu1 libjpeg-turbo8_2.1.5-2ubuntu1 libjpeg8_8c-2ubuntu11 libjs-bootstrap_3.4.1+dfsg-3 libjs-bootswatch_3.3.7+dfsg2-1.1 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-hotkeys_0~20130707+git2d51e3a9+dfsg-2ubuntu1 libjs-jquery-isonscreen_1.2.0-1.1 libjs-jquery-metadata_12-4 libjs-jquery-tablesorter_1:2.31.3+dfsg1-3 libjs-jquery-throttle-debounce_1.1+dfsg.1-2 libjs-jquery-ui_1.13.2+dfsg-1 libjs-sphinxdoc_5.3.0-3 libjs-underscore_1.13.4~dfsg+~1.11.4-3 libjson-c5_0.16-2 libjson-perl_4.10000-1 libk5crypto3_1.20.1-1build1 libkeyutils1_1.6.3-2 libkmod2_30+20221128-1ubuntu1 libkrb5-3_1.20.1-1build1 libkrb5support0_1.20.1-1build1 liblapack3_3.11.0-2 liblbfgsb0_3.0+dfsg.3-11 liblcms2-2_2.14-2 libldap2_2.6.3+dfsg-1~exp1ubuntu2 liblerc4_4.0.0+ds-2ubuntu2 libllvm14_1:14.0.6-12 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblsan0_13-20230215-1ubuntu2 liblua5.3-0_5.3.6-2 liblz4-1_1.9.4-1 liblzma5_5.4.1-0.2 libmagic-mgc_1:5.44-3 libmagic1_1:5.44-3 libmd0_1.0.4-2 libmount1_2.38.1-4ubuntu1 libmpc3_1.3.1-1 libmpdec3_2.5.1-2build2 libmpfr6_4.2.0-1 libncurses6_6.4-2 libncursesw6_6.4-2 libnettle8_3.8.1-2 libnghttp2-14_1.52.0-1 libnorm1_1.5.9+dfsg-2 libnpth0_1.6-3build2 libnsl-dev_1.3.0-2build2 libnsl2_1.3.0-2build2 libopenblas-dev_0.3.21+ds-4 libopenblas-pthread-dev_0.3.21+ds-4 libopenblas0_0.3.21+ds-4 libopenblas0-pthread_0.3.21+ds-4 libopenjp2-7_2.5.0-1build1 libp11-kit0_0.24.1-2ubuntu1 libpam-modules_1.5.2-5ubuntu1 libpam-modules-bin_1.5.2-5ubuntu1 libpam-runtime_1.5.2-5ubuntu1 libpam0g_1.5.2-5ubuntu1 libpcre2-8-0_10.42-1 libperl5.36_5.36.0-7 libpfm4_4.12.1+git12-g678bca9-1 libpgm-5.3-0_5.3.128~dfsg-2 libpipeline1_1.5.7-1 libpng16-16_1.6.39-2 libproc2-0_2:4.0.3-1ubuntu1 libprocps8_2:3.3.17-7ubuntu1 libpsl5_0.21.2-1 libpython3-all-dev_3.11.2-1 libpython3-dev_3.11.2-1 libpython3-stdlib_3.11.2-1 libpython3.10-minimal_3.10.9-1 libpython3.10-stdlib_3.10.9-1 libpython3.11_3.11.2-4 libpython3.11-dev_3.11.2-4 libpython3.11-minimal_3.11.2-4 libpython3.11-stdlib_3.11.2-4 libqhull-r8.0_2020.2-5 libquadmath0_13-20230215-1ubuntu2 libraqm0_0.7.0-4.1 libreadline8_8.2-1.3 librtmp1_2.4+20151223.gitfa8646d.1-2build4 libsasl2-2_2.1.28+dfsg-10 libsasl2-modules-db_2.1.28+dfsg-10 libseccomp2_2.5.4-1ubuntu2 libselinux1_3.4-1build3 libsemanage-common_3.4-1build3 libsemanage2_3.4-1build3 libsepol2_3.4-2 libsmartcols1_2.38.1-4ubuntu1 libsodium23_1.0.18-1build2 libsqlite3-0_3.40.1-1 libss2_1.47.0-1ubuntu1 libssh-4_0.10.4-2 libssl3_3.0.8-1ubuntu1 libstdc++-12-dev_12.2.0-14ubuntu2 libstdc++6_13-20230215-1ubuntu2 libsub-override-perl_0.09-4 libsystemd-shared_252.5-2ubuntu1 libsystemd0_252.5-2ubuntu1 libtasn1-6_4.19.0-2 libtcl8.6_8.6.13+dfsg-2 libtiff6_4.5.0-4ubuntu1 libtinfo6_6.4-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtk8.6_8.6.13-2 libtool_2.4.7-5 libtsan2_13-20230215-1ubuntu2 libubsan1_13-20230215-1ubuntu2 libuchardet0_0.0.7-1build2 libudev1_252.5-2ubuntu1 libunistring2_1.0-2 libuuid1_2.38.1-4ubuntu1 libwebp7_1.2.4-0.1build1 libwebpdemux2_1.2.4-0.1build1 libwebpmux3_1.2.4-0.1build1 libx11-6_2:1.8.3-3 libx11-data_2:1.8.3-3 libxau6_1:1.0.9-1build5 libxcb1_1.15-1 libxdmcp6_1:1.1.3-0ubuntu5 libxext6_2:1.3.4-1build1 libxft2_2.3.6-1 libxml2_2.9.14+dfsg-1.1build1 libxrender1_1:0.9.10-1.1 libxsimd-dev_8.1.0-7 libxslt1.1_1.1.35-1 libxss1_1:1.2.3-1build2 libxxhash0_0.8.1-1 libyaml-0-2_0.2.5-1 libzmq5_4.3.4-6 libzstd1_1.5.4+dfsg2-3 linux-libc-dev_6.1.0-14.14 llvm-14_1:14.0.6-12 llvm-14-linker-tools_1:14.0.6-12 llvm-14-runtime_1:14.0.6-12 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-1ubuntu1 logsave_1.47.0-1ubuntu1 lsb-base_11.6 lto-disabled-list_38 m4_1.4.19-3 make_4.3-4.1build1 man-db_2.11.2-1 mawk_1.3.4.20200120-3.1 media-types_10.0.0 mount_2.38.1-4ubuntu1 ncurses-base_6.4-2 ncurses-bin_6.4-2 openssl_3.0.8-1ubuntu1 optipng_0.7.7-2build1 pandoc_2.17.1.1-1.1ubuntu1 pandoc-data_2.17.1.1-1.1ubuntu1 passwd_1:4.13+dfsg1-1ubuntu1 patch_2.7.6-7build2 perl_5.36.0-7 perl-base_5.36.0-7 perl-modules-5.36_5.36.0-7 pinentry-curses_1.2.1-1ubuntu1 pkgbinarymangler_152 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.3-1ubuntu1 pybuild-plugin-pyproject_5.20230130 python-babel-localedata_2.10.3-1 python-matplotlib-data_3.5.2-4 python-tinycss2-common_1.2.1-2 python3_3.11.2-1 python3-alabaster_0.7.12-1 python3-all_3.11.2-1 python3-all-dev_3.11.2-1 python3-anyio_3.6.2-1 python3-appdirs_1.4.4-3 python3-argon2_21.1.0-2 python3-attr_22.2.0-1 python3-babel_2.10.3-1 python3-beniget_0.4.1-3 python3-bleach_5.0.1-2 python3-brotli_1.0.9-2build7 python3-bs4_4.11.2-2 python3-build_0.9.0-1 python3-certifi_2022.9.24-1 python3-cffi-backend_1.15.1-5 python3-chardet_5.1.0+dfsg-2 python3-commonmark_0.9.1-4 python3-coverage_6.5.0+dfsg1-2 python3-cycler_0.11.0-1 python3-dateutil_2.8.2-1 python3-decorator_5.1.1-3 python3-defusedxml_0.7.1-2 python3-dev_3.11.2-1 python3-distutils_3.11.2-2 python3-docutils_0.19+dfsg-6 python3-entrypoints_0.4-2 python3-execnet_1.9.0-1 python3-fastjsonschema_2.16.2-1 python3-fonttools_4.38.0-1 python3-fs_2.4.16-2 python3-gast_0.5.2-2 python3-html5lib_1.1-3 python3-idna_3.3-1 python3-imagesize_1.4.1-1 python3-importlib-metadata_4.12.0-1 python3-iniconfig_1.1.1-2 python3-installer_0.6.0+dfsg1-1 python3-isort_5.6.4-1 python3-jinja2_3.0.3-2 python3-json5_0.9.10-1 python3-jsonschema_4.6.0-3ubuntu1 python3-jupyter-client_7.4.9-2 python3-jupyter-core_4.12.0-1 python3-jupyter-server_1.23.3-1 python3-jupyter-sphinx-theme_0.0.6+ds1-11 python3-jupyterlab-pygments_0.2.2-3 python3-jupyterlab-server_2.16.5-1 python3-kiwisolver_1.4.4-1 python3-lib2to3_3.11.2-2 python3-llvmlite_0.39.1-2 python3-lxml_4.9.2-1 python3-lz4_4.0.2+dfsg-1 python3-markupsafe_2.1.2-1 python3-matplotlib_3.5.2-4 python3-minimal_3.11.2-1 python3-more-itertools_8.10.0-2 python3-mpmath_1.2.1-2 python3-nbclient_0.7.2-1 python3-nbconvert_6.5.3-3 python3-nbformat_5.5.0-1 python3-nbsphinx_0.8.11+ds-1 python3-nest-asyncio_1.5.4-1 python3-numba_0.56.4+dfsg-2 python3-numpy_1:1.24.2-1 python3-numpydoc_1.5.0-1 python3-packaging_23.0-1 python3-pandas_1.5.3+dfsg-2 python3-pandas-lib_1.5.3+dfsg-2 python3-pandocfilters_1.5.0-1 python3-pbr_5.11.0-0ubuntu1 python3-pep517_0.13.0-2 python3-pil_9.4.0-1.1build1 python3-pil.imagetk_9.4.0-1.1build1 python3-pkg-resources_66.1.1-1 python3-plotly_5.4.1+dfsg-1 python3-pluggy_1.0.0+repack-1 python3-ply_3.11-5 python3-prometheus-client_0.16.0-0.1 python3-ptyprocess_0.7.0-5 python3-py_1.11.0-1 python3-pygments_2.14.0+dfsg-1 python3-pyparsing_3.0.9-1 python3-pyrsistent_0.18.1-1build2 python3-pytest_7.2.1-2 python3-pytest-cov_4.0.0-1 python3-pytest-xdist_3.1.0-1 python3-pythran_0.11.0+ds-7 python3-recommonmark_0.7.1+ds-5 python3-requests_2.28.1+dfsg-1ubuntu1 python3-roman_3.3-3 python3-scipy_1.10.0-12 python3-scitrack_2021.5.3-3 python3-send2trash_1.8.1~b0-2 python3-setuptools_66.1.1-1 python3-six_1.16.0-4 python3-sniffio_1.2.0-1 python3-snowballstemmer_2.2.0-2 python3-soupsieve_2.4-1 python3-sphinx_5.3.0-3 python3-sphinx-bootstrap-theme_0.8.1-1 python3-sphinx-gallery_0.10.1-3 python3-sympy_1.11.1-1 python3-tenacity_8.2.1-1 python3-terminado_0.17.0-1 python3-tinycss2_1.2.1-2 python3-tinydb_3.15.2-4 python3-tk_3.11.2-2 python3-toml_0.10.2-1 python3-tomli_2.0.1-2 python3-tomli-w_1.0.0-2 python3-tornado_6.2.0-3 python3-tqdm_4.64.1-1 python3-traitlets_5.5.0-1 python3-typing-extensions_4.4.0-1 python3-tz_2022.7.1-1 python3-ufolib2_0.14.0+dfsg1-1 python3-urllib3_1.26.12-1 python3-webencodings_0.5.1-5 python3-websocket_1.2.3-1 python3-wheel_0.38.4-1 python3-zipp_1.0.0-6 python3-zmq_24.0.1-4 python3.10_3.10.9-1 python3.10-minimal_3.10.9-1 python3.11_3.11.2-4 python3.11-dev_3.11.2-4 python3.11-minimal_3.11.2-4 readline-common_8.2-1.3 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.17+nmu1 sgml-base_1.31 sphinx-common_5.3.0-3 systemd_252.5-2ubuntu1 systemd-sysv_252.5-2ubuntu1 sysvinit-utils_3.05-7ubuntu2 tar_1.34+dfsg-1.1 tk8.6-blt2.5_2.5.3+dfsg-4.1build2 tzdata_2022g-2ubuntu1 ubuntu-keyring_2021.03.26 unicode-data_15.0.0-1 usrmerge_33ubuntu1 util-linux_2.38.1-4ubuntu1 util-linux-extra_2.38.1-4ubuntu1 x11-common_1:7.7+23ubuntu2 xml-core_0.18+nmu1 xz-utils_5.4.1-0.2 zlib1g_1:1.2.13.dfsg-1ubuntu4 zlib1g-dev_1:1.2.13.dfsg-1ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: python-cogent Binary: python3-cogent3, python-cogent-doc Architecture: any all Version: 2023.2.12a1+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Homepage: https://github.com/cogent3/cogent3 Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/python-cogent Vcs-Git: https://salsa.debian.org/med-team/python-cogent.git Testsuite: autopkgtest, autopkgtest-pkg-python Testsuite-Triggers: python3-pytest Build-Depends: debhelper-compat (= 13), dh-python, flit, cython3, pandoc, pybuild-plugin-pyproject, python3-all-dev, python3-matplotlib, python3-numba, python3-numpy, python3-pandas, python3-scitrack, python3-tqdm, python3-tinydb, python3-sphinx, python3-numpydoc, python3-nbsphinx, python3-sphinx-bootstrap-theme, python3-sphinx-gallery, python3-pytest , python3-pytest-cov , python3-pytest-xdist , python3-plotly , python3-typing-extensions , python3-isort, python3-scipy, python3-chardet, python3-jupyterlab-server, python3-jupyter-sphinx-theme Package-List: python-cogent-doc deb doc optional arch=all python3-cogent3 deb python optional arch=any Checksums-Sha1: 75cfbd5007acea7e4ff14308379ed4ee57053877 3084176 python-cogent_2023.2.12a1+dfsg.orig.tar.xz 9f5bc5dc0e9bb6f0b87b047a0595ec66cc60025e 11300 python-cogent_2023.2.12a1+dfsg-1.debian.tar.xz Checksums-Sha256: 9c4221e7e0ed880786b624a79347f2a0b12e818e8894c9fd93c56bb6b7b5a2c0 3084176 python-cogent_2023.2.12a1+dfsg.orig.tar.xz 8906452c84fc0f095f913c328974701ce303fef1d2c2d62f0d897840825a58fa 11300 python-cogent_2023.2.12a1+dfsg-1.debian.tar.xz Files: d044303a26f1057e2b97f9c9132009e4 3084176 python-cogent_2023.2.12a1+dfsg.orig.tar.xz 2121094677c82f4be9ac979a06f02e3e 11300 python-cogent_2023.2.12a1+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmP1zCkRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFlWA//bG+Ct2K1V5pL9o4fp1KD11vn4dxgXhJp uWi4iH42NsPhOtlFGMzBaCaKyLjADGSllXpoupeqaMXslnbLRBmAnSzcpVatYPmv 0IMJLbvRvm+k+LvYCdZ1ozabtq4CRy2T5Vx1KtjbI8lcGJZAilQ2AW6eC/SzrVUk Su6b4d7YQ+BHwc9GCc2TH/sKn+LM+7DmqWD9oBPZDYymWx26tCNwYhKjlYH2fD5F t37AWXYveRY0KQX0Va0cG4nc8as2hsCE8DT5MDRggIufZNi186t1su35s+Vah/ak FNWRBQinY866e3hmMlYLxaFpLbbIk6M5iGe3LNpbsO2adf1T0tXQlEH9srPbfa3f UQZEyezIccKP07fXeTFupd+IYkOsSDaN8ZGTtwd0Q76lObSOQtRl8IeOOaN5PcE8 8ymnm23ytBDd4wPzEKTz7hzXtrgRwMYQJOInWEVrRsFYJEwCaqE2dg6GhSxS39en TY5P00lfA0kFx1oF4VGoO/v3mmrOOSE4XzmiXXqGwWxncwgmT0wkf+5mGtXJYYSS ogrto78ldR3K5z/5KCPrNZ9pJ5/zbuoQNRdgmQupk6ThYs/RDv75SSQu/DmcGYVb Go6x0+9njZDYWO8hP+s5WahUh50+ShH8jbEZtpS9Y0FbhwBGkjsBV5GHe4P8YYSk GI2aGxYdGrg= =b7kN -----END PGP SIGNATURE----- gpgv: Signature made Wed Feb 22 08:02:49 2023 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-cogent_2023.2.12a1+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting python-cogent in /<> dpkg-source: info: unpacking python-cogent_2023.2.12a1+dfsg.orig.tar.xz dpkg-source: info: unpacking python-cogent_2023.2.12a1+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying sphinx.patch dpkg-source: info: applying fix_interpreter.patch dpkg-source: info: applying remove-jupyter-sphinx.patch dpkg-source: info: applying ignore_tests_accessing_network.patch dpkg-source: info: applying fix-build-on-single-cpu-systems.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-25612566 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-25612566 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-25612566 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package python-cogent dpkg-buildpackage: info: source version 2023.2.12a1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture ppc64el debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild dh_autoreconf_clean -O--buildsystem=pybuild debian/rules override_dh_clean make[1]: Entering directory '/<>' #These files are rebuilt on-the-fly for f in `find -name '*.c'` ; do \ head -n 1 "$f" | grep -q '^/\* Generated by Cython' && rm "$f" ; \ done rm -rf build build-stamp rm -rf doc/_build dh_clean make[1]: Leaving directory '/<>' debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build I: pybuild plugin_pyproject:107: Building wheel for python3.11 with "build" module I: pybuild base:240: python3.11 -m build --skip-dependency-check --no-isolation --wheel --outdir /<>/.pybuild/cpython3_3.11_cogent3 * Building wheel... Successfully built cogent3-2023.2.12a1-py3-none-any.whl I: pybuild plugin_pyproject:119: Unpacking wheel built for python3.11 with "installer" module set -x; cd doc; PYTHONPATH=/<> http_proxy='127.0.0.1:9' /usr/bin/make html + cd doc + PYTHONPATH=/<> http_proxy=127.0.0.1:9 /usr/bin/make html make[2]: Entering directory '/<>/doc' sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v5.3.0 making output directory... done WARNING: html_static_path entry '_static' does not exist WARNING: The config value `today' has type `date', defaults to `str'. [autosummary] generating autosummary for: api/__init__/cogent3.__init__.available_apps.rst, api/__init__/cogent3.__init__.available_codes.rst, api/__init__/cogent3.__init__.available_models.rst, api/__init__/cogent3.__init__.available_moltypes.rst, api/__init__/cogent3.__init__.get_code.rst, api/__init__/cogent3.__init__.get_model.rst, api/__init__/cogent3.__init__.get_moltype.rst, api/__init__/cogent3.__init__.load_aligned_seqs.rst, api/__init__/cogent3.__init__.load_delimited.rst, api/__init__/cogent3.__init__.load_seq.rst, ..., examples/scope_model_params_on_trees.rst, examples/seq_features.rst, examples/simple.rst, examples/simulate_alignment.rst, examples/testing_multi_loci.rst, general.rst, index.rst, install.rst, licenses.rst, pycogent.rst building [mo]: targets for 0 po files that are out of date building [html]: targets for 125 source files that are out of date updating environment: [new config] 125 added, 0 changed, 0 removed reading sources... [ 0%] api/__init__/cogent3.__init__.available_apps reading sources... [ 1%] api/__init__/cogent3.__init__.available_codes reading sources... [ 2%] api/__init__/cogent3.__init__.available_models reading sources... [ 3%] api/__init__/cogent3.__init__.available_moltypes reading sources... [ 4%] api/__init__/cogent3.__init__.get_code reading sources... [ 4%] api/__init__/cogent3.__init__.get_model reading sources... [ 5%] api/__init__/cogent3.__init__.get_moltype reading sources... [ 6%] api/__init__/cogent3.__init__.load_aligned_seqs reading sources... [ 7%] api/__init__/cogent3.__init__.load_delimited reading sources... [ 8%] api/__init__/cogent3.__init__.load_seq reading sources... [ 8%] api/__init__/cogent3.__init__.load_table reading sources... [ 9%] api/__init__/cogent3.__init__.load_tree reading sources... [ 10%] api/__init__/cogent3.__init__.load_unaligned_seqs reading sources... [ 11%] api/__init__/cogent3.__init__.make_aligned_seqs reading sources... [ 12%] api/__init__/cogent3.__init__.make_seq reading sources... [ 12%] api/__init__/cogent3.__init__.make_table reading sources... [ 13%] api/__init__/cogent3.__init__.make_tree reading sources... [ 14%] api/__init__/cogent3.__init__.make_unaligned_seqs reading sources... [ 15%] api/alignment/alignment reading sources... [ 16%] api/alignment/classes/cogent3.core.alignment.Alignment reading sources... [ 16%] api/alignment/classes/cogent3.core.alignment.ArrayAlignment reading sources... [ 17%] api/alignment/classes/cogent3.core.alignment.SequenceCollection reading sources... [ 18%] api/alphabet/alphabet reading sources... [ 19%] api/alphabet/classes/cogent3.core.alphabet.Alphabet reading sources... [ 20%] api/apps/composable.define_app reading sources... [ 20%] api/genetic_code/classes/cogent3.core.genetic_code.GeneticCode reading sources... [ 21%] api/genetic_code/genetic_code reading sources... [ 22%] api/index reading sources... [ 23%] api/moltype/classes/cogent3.core.moltype.MolType reading sources... [ 24%] api/moltype/moltype reading sources... [ 24%] api/sequence/classes/cogent3.core.sequence.DnaSequence reading sources... [ 25%] api/sequence/classes/cogent3.core.sequence.ProteinSequence reading sources... [ 26%] api/sequence/classes/cogent3.core.sequence.RnaSequence reading sources... [ 27%] api/sequence/sequence reading sources... [ 28%] api/table/classes/cogent3.parse.table.FilteringParser reading sources... [ 28%] api/table/classes/cogent3.util.table.Columns reading sources... [ 29%] api/table/classes/cogent3.util.table.Table reading sources... [ 30%] api/table/table reading sources... [ 31%] api/tree/classes/cogent3.core.tree.PhyloNode reading sources... [ 32%] api/tree/tree reading sources... [ 32%] app/align-codon reading sources... [ 33%] app/align-nucleotide reading sources... [ 34%] app/align-protein reading sources... [ 35%] app/app-get reading sources... [ 36%] app/app-help reading sources... [ 36%] app/app-overview reading sources... [ 37%] app/available-apps reading sources... [ 38%] app/dstore reading sources... [ 39%] app/evo-ancestral-states reading sources... [ 40%] app/evo-dt-nuc-model reading sources... [ 40%] app/evo-extract-model-stats reading sources... [ 41%] app/evo-hypothesis reading sources... [ 42%] app/evo-model reading sources... [ 43%] app/evo-model-timehet reading sources... [ 44%] app/evo-model-with-tree reading sources... [ 44%] app/evo-natsel_neutral reading sources... [ 45%] app/evo-natsel_sitehet reading sources... [ 46%] app/evo-natsel_timehet reading sources... [ 47%] app/evo-natsel_zhang reading sources... [ 48%] app/evo-nstat-codon-model reading sources... [ 48%] app/evo-tr-codon-model reading sources... [ 49%] app/evo-tr-nuc-model reading sources... [ 50%] app/index reading sources... [ 51%] app/not-completed reading sources... [ 52%] app/user_function reading sources... [ 52%] cookbook/DNA_and_RNA_sequences reading sources... [ 53%] cookbook/alignments reading sources... [ 54%] cookbook/alphabet reading sources... [ 55%] cookbook/annotations reading sources... [ 56%] cookbook/building_alignments reading sources... [ 56%] cookbook/building_phylogenies reading sources... [ 57%] cookbook/calc_genetic_distance reading sources... [ 58%] cookbook/evo_modelling reading sources... [ 59%] cookbook/genetic_code reading sources... [ 60%] cookbook/index reading sources... [ 60%] cookbook/loading_sequences reading sources... [ 61%] cookbook/loading_tabular reading sources... [ 62%] cookbook/manipulating_biological_data reading sources... [ 63%] cookbook/moltypes reading sources... [ 64%] cookbook/protein_sequences reading sources... [ 64%] cookbook/simple_trees reading sources... [ 65%] cookbook/tables reading sources... [ 66%] cookbook/useful_utilities reading sources... [ 67%] cookbook/what_codes reading sources... [ 68%] data_file_links reading sources... [ 68%] draw/aln/plot_aln-coevolution reading sources... [ 69%] draw/aln/plot_aln-dotplot-1 reading sources... [ 70%] draw/aln/plot_aln-dotplot-2 reading sources... [ 71%] draw/aln/plot_aln-gaps-per-seq reading sources... [ 72%] draw/aln/plot_aln-info-plot reading sources... [ 72%] draw/aln/plot_aln-seqlogo reading sources... [ 73%] draw/index reading sources... [ 74%] draw/tree/plot_tree-angular reading sources... [ 75%] draw/tree/plot_tree-circular reading sources... [ 76%] draw/tree/plot_tree-radial reading sources... [ 76%] draw/tree/plot_tree-square reading sources... [ 77%] draw/tree/plot_tree-support reading sources... [ 78%] examples/align_codons_to_protein reading sources... [ 79%] examples/calculate_UPGMA_cluster reading sources... [ 80%] examples/calculate_neigbourjoining_tree reading sources... [ 80%] examples/calculate_pairwise_distances reading sources... [ 81%] examples/codon_models reading sources... [ 82%] examples/coevolution reading sources... [ 83%] examples/complete_seq_features reading sources... [ 84%] examples/empirical_protein_models reading sources... [ 84%] examples/hmm_par_heterogeneity reading sources... [ 85%] examples/index reading sources... [ 86%] examples/manipulating_tree_nodes reading sources... [ 87%] examples/neutral_test reading sources... [ 88%] examples/parallel reading sources... [ 88%] examples/parametric_bootstrap reading sources... [ 89%] examples/period_estimation reading sources... [ 90%] examples/phylo_by_ls reading sources... [ 91%] examples/rate_heterogeneity reading sources... [ 92%] examples/relative_rate reading sources... [ 92%] examples/scope_model_params_on_trees reading sources... [ 93%] examples/seq_features reading sources... [ 94%] examples/simple reading sources... [ 95%] examples/simulate_alignment reading sources... [ 96%] examples/testing_multi_loci reading sources... [ 96%] general reading sources... [ 97%] index reading sources... [ 98%] install reading sources... [ 99%] licenses reading sources... [100%] pycogent /<>/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.entropy_per_seq:11: CRITICAL: Unexpected section title. Notes ----- /<>/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.annotation._Annotatable.add_feature:1: WARNING: Field list ends without a blank line; unexpected unindent. /<>/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.entropy_per_seq:11: CRITICAL: Unexpected section title. Notes ----- /<>/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.ArrayAlignment:7: WARNING: Field list ends without a blank line; unexpected unindent. /<>/doc/app/align-codon.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/align-codon.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_unaligned", format="fasta") seqs = loader("data/SCA1-cds.fasta") /<>/doc/app/align-codon.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app codon_aligner = get_app("progressive_align", "codon") aligned = codon_aligner(seqs) aligned /<>/doc/app/align-codon.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nt_aligner = get_app("progressive_align", "codon", distance="paralinear") aligned = nt_aligner(seqs) aligned /<>/doc/app/align-codon.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)" codon_aligner = get_app("progressive_align", "codon", guide_tree=tree) aligned = codon_aligner(seqs) aligned /<>/doc/app/align-codon.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: codon_aligner = get_app("progressive_align", "codon", guide_tree=tree, indel_rate=0.001, indel_length=0.01 ) aligned = codon_aligner(seqs) aligned /<>/doc/app/align-codon.rst:76: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: codon_aligner = get_app("progressive_align", "CNFHKY", guide_tree=tree, param_vals=dict(omega=0.1, kappa=3) ) aligned = codon_aligner(seqs) aligned /<>/doc/app/align-codon.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned.info /<>/doc/app/align-nucleotide.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/align-nucleotide.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_unaligned", format="fasta") seqs = loader("data/SCA1-cds.fasta") /<>/doc/app/align-nucleotide.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app nt_aligner = get_app("progressive_align", "nucleotide") aligned = nt_aligner(seqs) aligned /<>/doc/app/align-nucleotide.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nt_aligner = get_app("progressive_align", "nucleotide", distance="TN93") aligned = nt_aligner(seqs) aligned /<>/doc/app/align-nucleotide.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)" nt_aligner = get_app("progressive_align", "nucleotide", guide_tree=tree) aligned = nt_aligner(seqs) aligned /<>/doc/app/align-nucleotide.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)" nt_aligner = get_app("progressive_align", "F81", guide_tree=tree) aligned = nt_aligner(seqs) aligned /<>/doc/app/align-nucleotide.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned.info /<>/doc/app/align-protein.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/align-protein.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_unaligned", format="fasta") to_aa = get_app("translate_seqs") process = loader + to_aa seqs = process("data/SCA1-cds.fasta") /<>/doc/app/align-protein.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app aa_aligner = get_app("progressive_align", "protein") aligned = aa_aligner(seqs) aligned /<>/doc/app/align-protein.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aa_aligner = get_app("progressive_align", "protein", distance="paralinear") aligned = aa_aligner(seqs) aligned /<>/doc/app/align-protein.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned.info /<>/doc/app/app-get.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app just_nucs = get_app("omit_degenerates", moltype="dna") just_nucs /<>/doc/app/app-help.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import app_help app_help("omit_degenerates") /<>/doc/app/app-overview.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/app-overview.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from pathlib import Path from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /<>/doc/app/app-overview.rst:89: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, suffix="fa", mode="w") loader = get_app("load_aligned", format="fasta", moltype="dna") cpos3 = get_app("take_codon_positions", 3) writer = get_app("write_seqs", out_dstore, format="fasta") /<>/doc/app/app-overview.rst:102: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data = loader("data/primate_brca1.fasta") just3rd = cpos3(data) m = writer(just3rd) /<>/doc/app/app-overview.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: process = loader + cpos3 + writer m = process("data/primate_brca1.fasta") /<>/doc/app/app-overview.rst:127: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore = open_data_store("data", suffix="fasta", mode="r") result = process.apply_to(dstore) /<>/doc/app/app-overview.rst:142: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.summary_logs /<>/doc/app/app-overview.rst:151: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.describe /<>/doc/app/app-overview.rst:157: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.summary_not_completed /<>/doc/app/app-overview.rst:164: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result = process.apply_to(dstore, show_progress=True) /<>/doc/app/available-apps.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_apps available_apps() /<>/doc/app/dstore.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/dstore.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import open_data_store dstore = open_data_store("data/raw.zip", suffix="fa*", limit=5, mode="r") /<>/doc/app/dstore.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: m = dstore[0] m /<>/doc/app/dstore.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: m.read()[:20] # truncating /<>/doc/app/dstore.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for m in dstore: print(m) /<>/doc/app/dstore.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore = open_data_store("data/demo-locked.sqlitedb") dstore.describe /<>/doc/app/dstore.rst:76: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.unlock(force=True) /<>/doc/app/dstore.rst:85: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.summary_logs /<>/doc/app/dstore.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.logs /<>/doc/app/dstore.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(dstore.logs[0].read()[:225]) # truncated for clarity /<>/doc/app/evo-ancestral-states.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-ancestral-states.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta") aln = loader("data/primate_brca1.fasta") gn = get_app("model", "GN", tree="data/primate_brca1.tree") result = gn(aln) /<>/doc/app/evo-ancestral-states.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: reconstuctor = get_app("ancestral_states") states_result = reconstuctor(result) states_result /<>/doc/app/evo-ancestral-states.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: states_result["edge.0"] /<>/doc/app/evo-ancestral-states.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.tree.get_figure(contemporaneous=True).show(width=500, height=500) /<>/doc/app/evo-dt-nuc-model.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-dt-nuc-model.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") model = get_app("model", "BH", tree="data/primate_brca1.tree") result = model(aln) result /<>/doc/app/evo-dt-nuc-model.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /<>/doc/app/evo-dt-nuc-model.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = result.tree fig = tree.get_figure() fig.scale_bar = "top right" fig.show(width=500, height=500) /<>/doc/app/evo-dt-nuc-model.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulator = get_app("tabulate_stats") stats = tabulator(result) stats /<>/doc/app/evo-dt-nuc-model.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: stats["edge motif motif2 params"] /<>/doc/app/evo-extract-model-stats.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-extract-model-stats.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") model = get_app("model", "GN", tree="data/primate_brca1.tree") result = model(aln) /<>/doc/app/evo-extract-model-stats.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulator = get_app("tabulate_stats") tabulated = tabulator(result) tabulated /<>/doc/app/evo-extract-model-stats.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["edge params"] /<>/doc/app/evo-extract-model-stats.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["global params"] /<>/doc/app/evo-extract-model-stats.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["motif params"] /<>/doc/app/evo-hypothesis.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-hypothesis.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") tree = "data/primate_brca1.tree" null = get_app("model", "GTR", tree=tree, optimise_motif_probs=True) alt = get_app("model", "GN", tree=tree, optimise_motif_probs=True) hyp = get_app("hypothesis", null, alt) result = hyp(aln) type(result) /<>/doc/app/evo-hypothesis.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result /<>/doc/app/evo-hypothesis.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.LR, result.df, result.pvalue /<>/doc/app/evo-hypothesis.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.null /<>/doc/app/evo-hypothesis.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.null.lf /<>/doc/app/evo-hypothesis.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /<>/doc/app/evo-model.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-model.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") select_seqs = get_app("take_named_seqs", "Human", "Rhesus", "Galago") process = loader + select_seqs aln = process("data/primate_brca1.fasta") aln.names /<>/doc/app/evo-model.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = get_app("model", "GN") gn /<>/doc/app/evo-model.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted = gn(aln) type(fitted) /<>/doc/app/evo-model.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted /<>/doc/app/evo-model.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lf /<>/doc/app/evo-model.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lnL, fitted.nfp /<>/doc/app/evo-model.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.source /<>/doc/app/evo-model.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.tree, fitted.alignment /<>/doc/app/evo-model.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.total_length(length_as="paralinear") /<>/doc/app/evo-model.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = get_app("model", "GN", split_codons=True) fitted = gn(aln) fitted /<>/doc/app/evo-model.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted[3] /<>/doc/app/evo-model-timehet.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-model-timehet.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3 import get_app tree = load_tree("data/primate_brca1.tree") fig = tree.get_figure(contemporaneous=True) fig.style_edges( "Human", tip2="Orangutan", outgroup="Galago", line=dict(color="red") ) fig.show(width=500, height=500) /<>/doc/app/evo-model-timehet.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: time_het = get_app("model", "GN", tree=tree, time_het=[dict(tip_names=["Human", "Orangutan"], outgroup_name="Galago")], ) /<>/doc/app/evo-model-timehet.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: loader = get_app("load_aligned", format="fasta") aln = loader("data/primate_brca1.fasta") result = time_het(aln) /<>/doc/app/evo-model-timehet.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /<>/doc/app/evo-model-with-tree.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-model-with-tree.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") aln.names /<>/doc/app/evo-model-with-tree.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3 import get_app tree = load_tree("data/primate_brca1.tree") gn = get_app("model", "GN", tree=tree) gn /<>/doc/app/evo-model-with-tree.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = get_app("model", "GN", tree="data/primate_brca1.tree") gn /<>/doc/app/evo-model-with-tree.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted = gn(aln) fitted /<>/doc/app/evo-model-with-tree.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lf /<>/doc/app/evo-natsel_neutral.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-natsel_neutral.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") omega_eq_1 = get_app("natsel_neutral", "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False ) result = omega_eq_1(aln) type(result) /<>/doc/app/evo-natsel_neutral.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result /<>/doc/app/evo-natsel_neutral.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /<>/doc/app/evo-natsel_sitehet.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-natsel_sitehet.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") sites_differ = get_app("natsel_sitehet", "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False ) result = sites_differ(aln) result /<>/doc/app/evo-natsel_sitehet.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /<>/doc/app/evo-natsel_sitehet.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = result.alt.lf.get_bin_probs() bprobs[:, :20] /<>/doc/app/evo-natsel_timehet.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-natsel_timehet.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") hc_differ = get_app("natsel_timehet", "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False, tip1="Human", tip2="Chimpanzee", ) result = hc_differ(aln) result /<>/doc/app/evo-natsel_timehet.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /<>/doc/app/evo-natsel_zhang.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-natsel_zhang.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from IPython.core.display import HTML from numpy import array from cogent3 import make_table header = ['Site Class', 'Proportion', 'Background Edges', 'Foreground Edges'] data = {'Site Class': array(['0', '1', '2a', '2b'], dtype=' 1', '0 < omega0 < 1'], dtype='>/doc/app/evo-natsel_zhang.rst:31: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") zhang_test = get_app("natsel_zhang", "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False, tip1="Human", tip2="Chimpanzee", ) result = zhang_test(aln) result /<>/doc/app/evo-natsel_zhang.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /<>/doc/app/evo-natsel_zhang.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = result.alt.lf.get_bin_probs() bprobs[:, :20] /<>/doc/app/evo-natsel_zhang.rst:64: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tab = get_app("tabulate_stats") stats = tab(result.alt) stats /<>/doc/app/evo-natsel_zhang.rst:70: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: stats["edge bin params"][:10] # truncating the table /<>/doc/app/evo-nstat-codon-model.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-nstat-codon-model.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") /<>/doc/app/evo-nstat-codon-model.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = get_app("model", "GNC", tree="data/primate_brca1.tree") result = model(aln) result /<>/doc/app/evo-nstat-codon-model.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /<>/doc/app/evo-nstat-codon-model.rst:37: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = result.tree fig = tree.get_figure() fig.scale_bar = "top right" fig.show(width=500, height=500) /<>/doc/app/evo-tr-codon-model.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-tr-codon-model.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_models available_models("codon") /<>/doc/app/evo-tr-codon-model.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") model = get_app("model", "CNFGTR", tree="data/primate_brca1.tree", optimise_motif_probs=True, ) result = model(aln) result /<>/doc/app/evo-tr-codon-model.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /<>/doc/app/evo-tr-nuc-model.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-tr-nuc-model.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_models available_models("nucleotide") /<>/doc/app/evo-tr-nuc-model.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") model = get_app("model", "GTR", tree="data/primate_brca1.tree", optimise_motif_probs=True ) result = model(aln) result /<>/doc/app/evo-tr-nuc-model.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /<>/doc/app/not-completed.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/not-completed.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app reader = get_app("load_aligned", format="fasta") select_seqs = get_app("take_named_seqs", "Mouse", "Human") aln = reader("data/primate_brca1.fasta") result = select_seqs(aln) result /<>/doc/app/not-completed.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result == False result.type result.message /<>/doc/app/not-completed.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = reader("primate_brca1.fasta") result /<>/doc/app/not-completed.rst:54: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: process = reader + select_seqs result = process("data/primate_brca1.fasta") result /<>/doc/app/not-completed.rst:62: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = process("primate_brca1.fasta") result /<>/doc/app/user_function.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app.composable import define_app from cogent3.app.typing import AlignedSeqsType @define_app def up_to(val: AlignedSeqsType, index=2) -> AlignedSeqsType: return val[:index] /<>/doc/app/user_function.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: first4 = up_to(index=4) first4 /<>/doc/app/user_function.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=dict(a="GCAAGCGTTTAT", b="GCTTTTGTCAAT"), array_align=False, moltype="dna" ) result = first4(aln) result /<>/doc/app/user_function.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from typing import Union from cogent3.app.composable import define_app from cogent3.app.typing import SeqsCollectionType, SerialisableType T = Union[SeqsCollectionType, SerialisableType] @define_app def rename_seqs(seqs: SeqsCollectionType) -> T: """upper case names""" return seqs.rename_seqs(lambda x: x.upper()) renamer = rename_seqs() result = renamer(aln) result /<>/doc/app/user_function.rst:76: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app.composable import define_app from cogent3.app.typing import AlignedSeqsType, PairwiseDistanceType @define_app def get_dists(aln: AlignedSeqsType, calc="hamming") -> PairwiseDistanceType: return aln.distance_matrix(calc=calc, show_progress=False) percent_dist = get_dists(calc="percent") result = percent_dist(aln) result /<>/doc/cookbook/DNA_and_RNA_sequences.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA my_seq = DNA.make_seq("AGTACACTGGT") my_seq print(my_seq) str(my_seq) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import RNA rnaseq = RNA.make_seq("ACGUACGUACGUACGU") /<>/doc/cookbook/DNA_and_RNA_sequences.rst:41: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA my_seq = DNA.make_seq("AGTACACTGGT") print(my_seq.to_fasta()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import RNA rnaseq = RNA.make_seq("ACGUACGUACGUACGU") rnaseq.to_fasta() /<>/doc/cookbook/DNA_and_RNA_sequences.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", "my_gene", moltype="dna") my_seq type(my_seq) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:74: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") my_seq.name = "my_gene" print(my_seq.to_fasta()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:85: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA my_seq = DNA.make_seq("AGTACACTGGT") print(my_seq.complement()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:95: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(my_seq.rc()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:101: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(my_seq.rc()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA my_seq = DNA.make_seq("GCTTGGGAAAGTCAAATGGAA", "protein-X") pep = my_seq.get_translation() type(pep) print(pep.to_fasta()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:122: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA my_seq = DNA.make_seq("ACGTACGTACGTACGT") print(my_seq.to_rna()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:132: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import RNA rnaseq = RNA.make_seq("ACGUACGUACGUACGU") print(rnaseq.to_dna()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:142: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA a = DNA.make_seq("AGTACACTGGT") a.can_pair(a.complement()) a.can_pair(a.rc()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:153: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA my_seq = DNA.make_seq("AGTACACTGGT") extra_seq = DNA.make_seq("CTGAC") long_seq = my_seq + extra_seq long_seq str(long_seq) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:166: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq[1:6] /<>/doc/cookbook/DNA_and_RNA_sequences.rst:177: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA seq = DNA.make_array_seq("ATGATGATGATG") pos3 = seq[2::3] assert str(pos3) == "GGGG" /<>/doc/cookbook/DNA_and_RNA_sequences.rst:190: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA seq = DNA.make_seq("ATGATGATGATG") indices = [(i, i + 2) for i in range(len(seq))[::3]] pos12 = seq.add_feature("pos12", "pos12", indices) pos12 = pos12.get_slice() assert str(pos12) == "ATATATAT" /<>/doc/cookbook/DNA_and_RNA_sequences.rst:211: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import RNA s = RNA.make_seq("--AUUAUGCUAU-UAu--") print(s.degap()) /<>/doc/cookbook/alignments.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/alignments.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs, make_unaligned_seqs dna = {"seq1": "ATGACC", "seq2": "ATCGCC"} seqs = make_aligned_seqs(data=dna, moltype="dna") print(type(seqs)) seqs = make_unaligned_seqs(dna, moltype="dna") print(type(seqs)) /<>/doc/cookbook/alignments.rst:41: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs dna = {"seq1": "ATGACC", "seq2": "ATCGCC"} seqs = make_aligned_seqs(data=dna, moltype="dna", array_align=True) print(type(seqs)) print(seqs) /<>/doc/cookbook/alignments.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs seqs = load_unaligned_seqs("data/test.paml") print(seqs) /<>/doc/cookbook/alignments.rst:70: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", ) print(aln) new_seqs = make_aligned_seqs( [("seq0", "ATG-AGT-AGG"), ("seq4", "ATGCC------")], moltype="dna" ) new_aln = aln.add_seqs(new_seqs) print(new_aln) /<>/doc/cookbook/alignments.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new_aln = aln.add_seqs(new_seqs, before_name="seq2") print(new_aln) new_aln = aln.add_seqs(new_seqs, after_name="seq2") print(new_aln) /<>/doc/cookbook/alignments.rst:104: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", ) ref_aln = make_aligned_seqs( [("seq3", "ATAGGATG"), ("seq0", "ATG-AGCG"), ("seq4", "ATGCTGGG")], moltype="dna", ) new_aln = aln.add_from_ref_aln(ref_aln) print(new_aln) /<>/doc/cookbook/alignments.rst:126: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", ) new_aln = aln.get_degapped_relative_to("seq1") print(new_aln) /<>/doc/cookbook/alignments.rst:145: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", array_align=False, ) seq = aln.get_seq("seq1") seq.name type(seq) seq.is_gapped() /<>/doc/cookbook/alignments.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = aln.get_gapped_seq("seq1") seq.is_gapped() print(seq) /<>/doc/cookbook/alignments.rst:169: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.names aln.names /<>/doc/cookbook/alignments.rst:179: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_unaligned_seqs fn = "data/long_testseqs.fasta" seqs = load_unaligned_seqs(fn, moltype="dna") my_seq = seqs.seqs[0] my_seq[:24] str(my_seq[:24]) type(my_seq) aln = load_aligned_seqs(fn, moltype="dna") aln.seqs[0][:24] print(aln.seqs[0][:24]) /<>/doc/cookbook/alignments.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/test.paml", moltype="dna") aln.names new = aln.take_seqs(["Human", "HowlerMon"]) new.names /<>/doc/cookbook/alignments.rst:207: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/test.paml", array_align=False, moltype="dna") seq = aln.get_seq("Human") new = aln.take_seqs(["Human", "HowlerMon"]) id(new.get_seq("Human")) == id(aln.get_seq("Human")) /<>/doc/cookbook/alignments.rst:222: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs from cogent3.core.alignment import Alignment seq = load_unaligned_seqs("data/test.paml") aln = Alignment(seq) fasta_1 = seq fasta_2 = aln assert fasta_1 == fasta_2 /<>/doc/cookbook/alignments.rst:238: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = [("a", "ACG---"), ("b", "CCTGGG")] aln = make_aligned_seqs(data=data) dna = aln.to_dna() dna /<>/doc/cookbook/alignments.rst:249: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = [("a", "ACG---"), ("b", "CCUGGG")] aln = make_aligned_seqs(data=data) rna = aln.to_rna() rna /<>/doc/cookbook/alignments.rst:260: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = [("x", "TYV"), ("y", "TE-")] aln = make_aligned_seqs(data=data) prot = aln.to_protein() prot /<>/doc/cookbook/alignments.rst:277: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") degapped = aln.degap() print(type(degapped)) /<>/doc/cookbook/alignments.rst:292: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs dna = {"seq1": "ATGACC", "seq2": "ATCGCC"} aln = make_aligned_seqs(data=dna, moltype="dna") aln.write("sample.fasta") /<>/doc/cookbook/alignments.rst:302: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.write("sample", format="fasta") /<>/doc/cookbook/alignments.rst:308: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.io import remove_files remove_files(["sample", "sample.fasta"], error_on_missing=False) /<>/doc/cookbook/alignments.rst:317: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.core.alignment import Alignment seq = load_aligned_seqs("data/long_testseqs.fasta") aln = Alignment(seq) fasta_align = aln /<>/doc/cookbook/alignments.rst:329: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.core.alignment import Alignment seq = load_aligned_seqs("data/test.paml") aln = Alignment(seq) got = aln.to_phylip() print(got) /<>/doc/cookbook/alignments.rst:342: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.core.alignment import Alignment seq = load_aligned_seqs("data/test.paml") aln = Alignment(seq) string_list = aln.to_dict().values() /<>/doc/cookbook/alignments.rst:359: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs fn = "data/long_testseqs.fasta" aln = load_aligned_seqs(fn, moltype="dna") print(aln[:24]) /<>/doc/cookbook/alignments.rst:369: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: TypeError from cogent3 import load_unaligned_seqs fn = "data/long_testseqs.fasta" seqs = load_unaligned_seqs(fn) print(seqs[:24]) /<>/doc/cookbook/alignments.rst:381: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seq = load_aligned_seqs("data/test.paml") column_four = aln[3] /<>/doc/cookbook/alignments.rst:391: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") region = aln[50:70] /<>/doc/cookbook/alignments.rst:401: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") col = aln[113:115].iter_positions() type(col) list(col) /<>/doc/cookbook/alignments.rst:415: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ATGATGATG---", "seq2": "ATGATGATGATG"}, array_align=False ) list(range(len(aln))[2::3]) indices = [(i, i + 1) for i in range(len(aln))[2::3]] indices pos3 = aln.add_feature("pos3", "pos3", indices) pos3 = pos3.get_slice() print(pos3) /<>/doc/cookbook/alignments.rst:434: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ATGATGATG---", "seq2": "ATGATGATGATG"}, array_align=True ) pos3 = aln[2::3] print(pos3) /<>/doc/cookbook/alignments.rst:454: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ACGTAA---", "seq2": "ACGACA---", "seq3": "ACGCAATGA"}, moltype="dna", ) new = aln.trim_stop_codons() print(new) /<>/doc/cookbook/alignments.rst:467: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data={ "seq1": "ACGTAA---", "seq2": "ACGAC----", # terminal codon incomplete "seq3": "ACGCAATGA", }, moltype="dna", ) new = aln.trim_stop_codons(allow_partial=True) print(new) /<>/doc/cookbook/alignments.rst:485: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGGTG---"), ("seq2", "ATGAAGGTGATG"), ("seq3", "ATGAAGGNGATG"), ], moltype="dna", ) /<>/doc/cookbook/alignments.rst:500: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nucs = aln.no_degenerates() print(nucs) /<>/doc/cookbook/alignments.rst:507: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: trinucs = aln.no_degenerates(motif_length=3) print(trinucs) /<>/doc/cookbook/alignments.rst:515: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") pos = aln.variable_positions() just_variable_aln = aln.take_positions(pos) print(just_variable_aln[:10]) /<>/doc/cookbook/alignments.rst:527: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") pos = aln.variable_positions() just_constant_aln = aln.take_positions(pos, negate=True) print(just_constant_aln[:10]) /<>/doc/cookbook/alignments.rst:541: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") variable_codons = aln.filtered( lambda x: len(set(map(tuple, x))) > 1, motif_length=3 ) print(just_variable_aln[:9]) /<>/doc/cookbook/alignments.rst:553: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = aln.to_type(array_align=False) variable_codons = aln.filtered(lambda x: len(set("".join(x))) > 1, motif_length=3) print(just_variable_aln[:9]) /<>/doc/cookbook/alignments.rst:567: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") aln.take_seqs(["Human", "Mouse"]) /<>/doc/cookbook/alignments.rst:576: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.take_seqs(["Human", "Mouse"], negate=True) /<>/doc/cookbook/alignments.rst:585: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGGTG---"), ("seq2", "ATGAAGGTGATG"), ("seq3", "ATGAAGGNGATG"), ], moltype="dna", ) def no_N_chars(s): return "N" not in s aln.take_seqs_if(no_N_chars) /<>/doc/cookbook/alignments.rst:605: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.take_seqs_if(no_N_chars, negate=True) /<>/doc/cookbook/alignments.rst:617: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGGTG---"), ("seq2", "ATGAAGGTGATG"), ("seq3", "ATGAAGGNGATG"), ], moltype="dna", ) counts = aln.counts() print(counts) counts = aln.counts(motif_length=3) print(counts) counts = aln.counts(include_ambiguity=True) print(counts) /<>/doc/cookbook/alignments.rst:645: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta", moltype="dna") motif_probs = aln.get_motif_probs() print(motif_probs) /<>/doc/cookbook/alignments.rst:655: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA, load_aligned_seqs trinuc_alphabet = DNA.alphabet.get_word_alphabet(3) aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta", moltype="dna") motif_probs = aln.get_motif_probs(alphabet=trinuc_alphabet) for m in sorted(motif_probs, key=lambda x: motif_probs[x], reverse=True): print("%s %.3f" % (m, motif_probs[m])) /<>/doc/cookbook/alignments.rst:669: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs(data=[("a", "AACAAC"), ("b", "AAGAAG")], moltype="dna") motif_probs = aln.get_motif_probs() assert motif_probs["T"] == 0.0 motif_probs = aln.get_motif_probs(pseudocount=1e-6) assert 0 < motif_probs["T"] <= 1e-6 /<>/doc/cookbook/alignments.rst:681: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = [("a", "AACGTAAG"), ("b", "AACGTAAG")] aln = make_aligned_seqs(data=seqs, moltype="dna") dinuc_alphabet = DNA.alphabet.get_word_alphabet(2) motif_probs = aln.get_motif_probs(alphabet=dinuc_alphabet) assert motif_probs["AA"] == 0.25 /<>/doc/cookbook/alignments.rst:691: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = [("my_seq", "AAAGTAAG")] aln = make_aligned_seqs(data=seqs, moltype="dna") my_seq = aln.get_seq("my_seq") my_seq.count("AA") "AAA".count("AA") "AAAA".count("AA") /<>/doc/cookbook/alignments.rst:702: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq seq = make_seq(moltype="dna", seq="AAAGTAAG") seq di_nucs = [seq[i : i + 2] for i in range(len(seq) - 1)] sum([nn == "AA" for nn in di_nucs]) /<>/doc/cookbook/alignments.rst:717: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") col = aln[113:115].iter_positions() c1, c2 = list(col) c1, c2 list(filter(lambda x: x == "-", c1)) list(filter(lambda x: x == "-", c2)) /<>/doc/cookbook/alignments.rst:731: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") for column in aln[113:150].iter_positions(): ungapped = list(filter(lambda x: x == "-", column)) gap_fraction = len(ungapped) * 1.0 / len(column) print(gap_fraction) /<>/doc/cookbook/alignments.rst:746: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGG-TG--"), ("seq2", "ATG-AGGTGATG"), ("seq3", "ATGAAG--GATG"), ], moltype="dna", ) seq_to_aln_map = aln.get_gapped_seq("seq1").gap_maps()[0] /<>/doc/cookbook/alignments.rst:762: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq_to_aln_map[3] seq_to_aln_map[8] /<>/doc/cookbook/alignments.rst:771: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln_to_seq_map = aln.get_gapped_seq("seq1").gap_maps()[1] aln_to_seq_map[3] aln_to_seq_map[8] /<>/doc/cookbook/alignments.rst:779: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: KeyError seq_pos = aln_to_seq_map[7] /<>/doc/cookbook/alignments.rst:793: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data=[ ("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG"), ], moltype="dna", ) print(aln.omit_gap_runs(2)) /<>/doc/cookbook/alignments.rst:807: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data=[ ("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG"), ], moltype="dna", ) print(aln.omit_gap_pos(0.40)) /<>/doc/cookbook/alignments.rst:821: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data=[ ("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG"), ], moltype="dna", ) filtered_aln = aln.omit_gap_seqs(0.50) print(filtered_aln) /<>/doc/cookbook/alignments.rst:836: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(filtered_aln.omit_gap_pos()) /<>/doc/cookbook/alphabet.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA, PROTEIN print(DNA.alphabet) print(PROTEIN.alphabet) /<>/doc/cookbook/alphabet.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: PROTEIN.alphabet.moltype == PROTEIN /<>/doc/cookbook/alphabet.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dinuc_alphabet = DNA.alphabet.get_word_alphabet(2) print(dinuc_alphabet) trinuc_alphabet = DNA.alphabet.get_word_alphabet(3) print(trinuc_alphabet) /<>/doc/cookbook/alphabet.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = "TAGT" indices = DNA.alphabet.to_indices(seq) indices /<>/doc/cookbook/alphabet.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = DNA.alphabet.from_indices([0, 2, 3, 0]) seq /<>/doc/cookbook/alphabet.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = DNA.alphabet.from_ordinals_to_seq([0, 2, 3, 0]) seq /<>/doc/cookbook/annotations.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/annotations.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.genbank import RichGenbankParser parser = RichGenbankParser(open("data/ST_genome_part.gb")) for accession, seq in parser: print(accession) /<>/doc/cookbook/annotations.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: cds = seq.get_annotations_matching("CDS") print(cds) /<>/doc/cookbook/annotations.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core.annotation import Feature def add_annotation(seq, feature, spans): type_ = feature["type"] if type_ != "CDS": return name = feature.get("locus_tag", None) if name and not isinstance(name, str): name = " ".join(name) seq.add_annotation(Feature, type_, name, spans) parser = RichGenbankParser( open("data/ST_genome_part.gb"), add_annotation=add_annotation ) for accession, seq in parser: # just reading one accession,sequence break genes = seq.get_annotations_matching("CDS") print(genes) /<>/doc/cookbook/annotations.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA from cogent3.core.annotation import Feature s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) print(s1[10:15]) # this will be exon 1 print(s1[30:40]) # this will be exon 2 print(s1[45:48]) # this will be exon 3 s2 = DNA.make_seq("CGAAACGTTT", name="seq2") s3 = DNA.make_seq("CGAAACGTTT", name="seq3") /<>/doc/cookbook/annotations.rst:83: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA from cogent3.core.annotation import Feature s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) exon1 = s1.add_annotation(Feature, "exon", "A", [(10, 15)]) exon2 = s1.add_annotation(Feature, "exon", "B", [(30, 40)]) /<>/doc/cookbook/annotations.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) exon3 = s1.add_feature("exon", "C", [(45, 48)]) /<>/doc/cookbook/annotations.rst:111: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s2 = DNA.make_seq("CGAAACGTTT", name="seq2") cpgs_series = s2.add_feature("cpgsite", "cpg", [(0, 2), (5, 7)]) s3 = DNA.make_seq("CGAAACGTTT", name="seq3") cpg1 = s3.add_feature("cpgsite", "cpg", [(0, 2)]) cpg2 = s3.add_feature("cpgsite", "cpg", [(5, 7)]) /<>/doc/cookbook/annotations.rst:126: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) exon1 = s1.add_feature("exon", "A", [(10, 15)]) exon2 = s1.add_feature("exon", "B", [(30, 40)]) exon3 = s1.add_feature("exon", "C", [(45, 48)]) cds = s1.get_region_covering_all([exon1, exon2, exon3]) /<>/doc/cookbook/annotations.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: cds.get_coordinates() /<>/doc/cookbook/annotations.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_cds = cds.get_shadow() not_cds /<>/doc/cookbook/annotations.rst:159: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: cds /<>/doc/cookbook/annotations.rst:168: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln1 = make_aligned_seqs( data=[["x", "-AAACCCCCA"], ["y", "TTTT--TTTT"]], array_align=False ) seq_exon = aln1.get_seq("x").add_feature("exon", "A", [(3, 8)]) /<>/doc/cookbook/annotations.rst:182: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core.annotation import Variable red_data = aln1.add_annotation( Variable, "redline", "align", [((0, 15), 1), ((15, 30), 2), ((30, 45), 3)] ) /<>/doc/cookbook/annotations.rst:195: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) exon1 = s1.add_feature("exon", "A", [(10, 15)]) exon2 = s1.add_feature("exon", "B", [(30, 40)]) s1[exon1] s1[10:15] /<>/doc/cookbook/annotations.rst:209: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: s1[exon2] exon2.get_slice() /<>/doc/cookbook/annotations.rst:217: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) exon1 = s1.add_feature("exon", "A", [(10, 15)]) exon2 = s1.add_feature("exon", "B", [(30, 40)]) exon3 = s1.add_feature("exon", "C", [(45, 48)]) cds = s1.get_region_covering_all([exon1, exon2, exon3]) print(s1[cds]) print(s1[exon1, exon2, exon3]) /<>/doc/cookbook/annotations.rst:233: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s1) print(s1[exon1, exon2, exon3]) print(s1[exon2]) print(s1[exon3]) print(s1[exon1, exon3, exon2]) /<>/doc/cookbook/annotations.rst:244: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError s1[1:10, 9:15] s1[exon1, exon1] /<>/doc/cookbook/annotations.rst:252: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s1.get_region_covering_all([exon3, exon3]).get_slice()) /<>/doc/cookbook/annotations.rst:259: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s1[exon2]) ex2_start = exon2[0:3] print(s1[ex2_start]) ex2_end = exon2[-3:] print(s1[ex2_end]) /<>/doc/cookbook/annotations.rst:272: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError aln1[seq_exon] /<>/doc/cookbook/annotations.rst:282: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln2 = make_aligned_seqs( data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x") match_exon = seq.add_feature("exon", "A", [(3, 8)]) aln2.get_seq("x").copy_annotations(seq) copied = list(aln2.get_annotations_from_seq("x", "exon")) copied /<>/doc/cookbook/annotations.rst:295: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln2 = make_aligned_seqs(data=[["x", "-AAAA"], ["y", "TTTTT"]], array_align=False) seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x") match_exon = seq.add_feature("exon", "A", [(5, 8)]) aln2.get_seq("x").copy_annotations(seq) copied = list(aln2.get_annotations_from_seq("x", "exon")) copied copied[0].get_slice() /<>/doc/cookbook/annotations.rst:307: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: # new test aln2 = make_aligned_seqs( data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x") match_exon = seq.add_feature("exon", "A", [(5, 8)]) aln2.get_seq("y").copy_annotations(seq) copied = list(aln2.get_annotations_from_seq("y", "exon")) copied /<>/doc/cookbook/annotations.rst:321: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln2 = make_aligned_seqs( data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) diff_len_seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCCCCCCCCCC", "x") nonmatch = diff_len_seq.add_feature("repeat", "A", [(12, 14)]) aln2.get_seq("y").copy_annotations(diff_len_seq) copied = list(aln2.get_annotations_from_seq("y", "repeat")) copied /<>/doc/cookbook/annotations.rst:337: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln_exon = aln1.get_annotations_from_any_seq("exon") print(aln1[aln_exon]) /<>/doc/cookbook/annotations.rst:345: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError cpgsite2 = s2.get_annotations_matching("cpgsite") print(s2[cpgsite2]) cpgsite3 = s3.get_annotations_matching("cpgsite") s2[cpgsite3] /<>/doc/cookbook/annotations.rst:358: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: # this test is new dont_exist = s2.get_annotations_matching("dont_exist") dont_exist s2[dont_exist] /<>/doc/cookbook/annotations.rst:370: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln3 = make_aligned_seqs( data=[["x", "C-CCCAAAAA"], ["y", "-T----TTTT"]], array_align=False ) exon = aln3.get_seq("x").add_feature("exon", "ex1", [(0, 4)]) print(exon.get_slice()) aln_exons = list(aln3.get_annotations_from_seq("x", "exon")) print(aln_exons) print(aln3[aln_exons]) /<>/doc/cookbook/annotations.rst:388: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unified = aln_exons[0].as_one_span() print(aln3[unified]) /<>/doc/cookbook/annotations.rst:398: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: plus = DNA.make_seq("CCCCCAAAAAAAAAATTTTTTTTTTAAAGG") plus_rpt = plus.add_feature("blah", "a", [(5, 15), (25, 28)]) print(plus[plus_rpt]) minus = plus.rc() print(minus) minus_rpt = minus.get_annotations_matching("blah") print(minus[minus_rpt]) /<>/doc/cookbook/annotations.rst:413: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.genbank import RichGenbankParser parser = RichGenbankParser(open("data/ST_genome_part.gb")) seq = [seq for accession, seq in parser][0] no_cds = seq.with_masked_annotations("CDS") print(no_cds[150:400]) /<>/doc/cookbook/annotations.rst:429: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[["x", "C-CCCAAAAAGGGAA"], ["y", "-T----TTTTG-GTT"]], moltype="dna", array_align=False, ) exon = aln.get_seq("x").add_feature("exon", "norwegian", [(0, 4)]) print(aln.with_masked_annotations("exon", mask_char="?")) /<>/doc/cookbook/annotations.rst:443: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rc = aln.rc() print(rc) print(rc.with_masked_annotations("exon", mask_char="?")) /<>/doc/cookbook/annotations.rst:452: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s = DNA.make_seq("CCCCAAAAAGGGAA", "x") exon = s.add_feature("exon", "norwegian", [(0, 4)]) rpt = s.add_feature("repeat", "norwegian", [(9, 12)]) rc = s.rc() print(s.with_masked_annotations("exon", shadow=True)) print(rc.with_masked_annotations("exon", shadow=True)) print(s.with_masked_annotations(["exon", "repeat"], shadow=True)) print(rc.with_masked_annotations(["exon", "repeat"], shadow=True)) /<>/doc/cookbook/annotations.rst:468: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s = DNA.make_seq("ATGACCCTGTAAAAAATGTGTTAACCC", name="a") cds1 = s.add_feature("cds", "cds1", [(0, 12)]) cds2 = s.add_feature("cds", "cds2", [(15, 24)]) all_cds = s.get_annotations_matching("cds") all_cds /<>/doc/cookbook/annotations.rst:483: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.genbank import RichGenbankParser parser = RichGenbankParser(open("data/ST_genome_part.gb")) seq = [seq for accession, seq in parser][0] all_cds = seq.get_annotations_matching("CDS") coding_seqs = seq.get_region_covering_all(all_cds) coding_seqs coding_seqs.get_slice() noncoding_seqs = coding_seqs.get_shadow() noncoding_seqs noncoding_seqs.get_slice() /<>/doc/cookbook/annotations.rst:502: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) print(aln) exon = aln.get_seq("x").add_feature("exon", "1", [(3, 8)]) aln_exons = aln.get_annotations_from_seq("x", "exon") aln_exons = aln.get_annotations_from_any_seq("exon") aln_exons /<>/doc/cookbook/annotations.rst:522: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA seq = DNA.make_seq("aaaccggttt" * 10) v = seq.add_feature("exon", "exon", [(20, 35)]) v = seq.add_feature("repeat_unit", "repeat_unit", [(39, 49)]) v = seq.add_feature("repeat_unit", "rep2", [(49, 60)]) /<>/doc/cookbook/annotations.rst:536: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.util.io import remove_files remove_files(["annotated_%d.png" % i for i in range(1, 4)], error_on_missing=False) /<>/doc/cookbook/building_alignments.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/building_alignments.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs, make_tree from cogent3.align.progressive import TreeAlign /<>/doc/cookbook/building_alignments.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = load_unaligned_seqs("data/test2.fasta", moltype="dna") aln, tree = TreeAlign("HKY85", seqs, show_progress=False) aln /<>/doc/cookbook/building_alignments.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = make_tree( "(((NineBande:0.013,Mouse:0.185):0.023,DogFaced:0.046):0.027,Human:0.034,HowlerMon:0.019)" ) params = {"kappa": 4.0} aln, tree = TreeAlign( "HKY85", seqs, tree=tree, param_vals=params, show_progress=False ) aln /<>/doc/cookbook/building_alignments.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs, make_tree from cogent3.align.progressive import TreeAlign seqs = load_unaligned_seqs("data/test2.fasta", moltype="dna") tree = make_tree( "((NineBande:0.058,Mouse:0.595):0.079,DogFaced:0.142,(HowlerMon:0.062,Human:0.103):0.079)" ) params = {"kappa": 4.0, "omega": 1.3} aln, tree = TreeAlign( "MG94HKY", seqs, tree=tree, param_vals=params, show_progress=False ) aln /<>/doc/cookbook/building_alignments.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_unaligned_seqs from cogent3.align.progressive import TreeAlign from cogent3.evolve.models import get_model seqs = [ ( "hum", "AAGCAGATCCAGGAAAGCAGCGAGAATGGCAGCCTGGCCGCGCGCCAGGAGAGGCAGGCCCAGGTCAACCTCACT", ), ( "mus", "AAGCAGATCCAGGAGAGCGGCGAGAGCGGCAGCCTGGCCGCGCGGCAGGAGAGGCAGGCCCAAGTCAACCTCACG", ), ("rat", "CTGAACAAGCAGCCACTTTCAAACAAGAAA"), ] unaligned_DNA = make_unaligned_seqs(seqs, moltype="dna") print(unaligned_DNA) /<>/doc/cookbook/building_alignments.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(unaligned_DNA.get_translation()) /<>/doc/cookbook/building_alignments.rst:94: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aligned_aa_seqs = [ ("hum", "KQIQESSENGSLAARQERQAQVNLT"), ("mus", "KQIQESGESGSLAARQERQAQVNLT"), ("rat", "LNKQ------PLS---------NKK"), ] aligned_aa = make_aligned_seqs(aligned_aa_seqs, moltype="protein") /<>/doc/cookbook/building_alignments.rst:107: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned_DNA = aligned_aa.replace_seqs(unaligned_DNA, aa_to_codon=True) aligned_DNA /<>/doc/cookbook/building_phylogenies.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/building_phylogenies.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") tree = aln.quick_tree(calc="TN93", show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) /<>/doc/cookbook/building_phylogenies.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = aln.quick_tree(calc="TN93", bootstrap=100, show_progress=False) /<>/doc/cookbook/building_phylogenies.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="TN93") tree = dists.quick_tree(show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) /<>/doc/cookbook/building_phylogenies.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.phylo import nj aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="TN93") tree = nj.nj(dists, show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) /<>/doc/cookbook/building_phylogenies.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.phylo import nj dists = {("a", "b"): 2.7, ("c", "b"): 2.33, ("c", "a"): 0.73} tree = nj.nj(dists, show_progress=False) print(tree.ascii_art()) /<>/doc/cookbook/building_phylogenies.rst:76: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.phylo.least_squares import WLS from cogent3.util.deserialise import deserialise_object dists = deserialise_object("data/dists_for_phylo.json") ls = WLS(dists) stat, tree = ls.trex(a=5, k=5, show_progress=False) /<>/doc/cookbook/building_phylogenies.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve.models import F81 from cogent3.phylo.maximum_likelihood import ML aln = load_aligned_seqs("data/primate_brca1.fasta") ml = ML(F81(), aln) /<>/doc/cookbook/calc_genetic_distance.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/calc_genetic_distance.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_distances available_distances() /<>/doc/cookbook/calc_genetic_distance.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="tn93", show_progress=False) dists /<>/doc/cookbook/calc_genetic_distance.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_distance_calculator, load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta") dist_calc = get_distance_calculator("tn93", alignment=aln) dist_calc /<>/doc/cookbook/calc_genetic_distance.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dist_calc.run(show_progress=False) dists = dist_calc.get_pairwise_distances() dists /<>/doc/cookbook/calc_genetic_distance.rst:54: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dist_calc.stderr /<>/doc/cookbook/calc_genetic_distance.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_model, load_aligned_seqs from cogent3.evolve import distance aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") d = distance.EstimateDistances(aln, submodel=get_model("F81")) d.run(show_progress=False) dists = d.get_pairwise_distances() dists /<>/doc/cookbook/evo_modelling.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/evo_modelling.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_models available_models() /<>/doc/cookbook/evo_modelling.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model hky = get_model("HKY85") print(hky) /<>/doc/cookbook/evo_modelling.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("GTR", with_rate=True, distribution="gamma") print(sub_mod) /<>/doc/cookbook/evo_modelling.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("CNFGTR", with_rate=True, distribution="gamma") print(sub_mod) /<>/doc/cookbook/evo_modelling.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("JTT92", with_rate=True, distribution="gamma") print(sub_mod) /<>/doc/cookbook/evo_modelling.rst:80: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree from cogent3.evolve.models import get_model sub_mod = get_model("F81") tree = make_tree("(a,b,(c,d))") lf = sub_mod.make_likelihood_function(tree) /<>/doc/cookbook/evo_modelling.rst:94: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs, make_tree from cogent3.evolve.models import get_model sub_mod = get_model("F81") tree = make_tree("(a,b,(c,d))") lf = sub_mod.make_likelihood_function(tree) aln = make_aligned_seqs( [("a", "ACGT"), ("b", "AC-T"), ("c", "ACGT"), ("d", "AC-T")] ) lf.set_alignment(aln) /<>/doc/cookbook/evo_modelling.rst:112: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") print(tree.ascii_art()) /<>/doc/cookbook/evo_modelling.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule( "omega", tip_names=["Human", "Orangutan"], outgroup_name="Galago", clade=True, init=0.5, ) /<>/doc/cookbook/evo_modelling.rst:134: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /<>/doc/cookbook/evo_modelling.rst:145: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", is_constant=True) /<>/doc/cookbook/evo_modelling.rst:160: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", init=0.1) /<>/doc/cookbook/evo_modelling.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", init=0.1, lower=1e-9, upper=20.0) /<>/doc/cookbook/evo_modelling.rst:190: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("F81") lf = sm.make_likelihood_function(tree) lf.set_param_rule("length", upper=1.0) /<>/doc/cookbook/evo_modelling.rst:207: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model sm = get_model("GTR", with_rate=True, distribution="gamma") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree, bins=4, digits=2) lf.set_param_rule("bprobs", is_constant=True) /<>/doc/cookbook/evo_modelling.rst:222: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model sm = get_model("GTR", with_rate=True, distribution="gamma") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree, bins=4, sites_independent=False, digits=2) lf.set_param_rule("bprobs", is_constant=True) /<>/doc/cookbook/evo_modelling.rst:239: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.optimise(show_progress=False) /<>/doc/cookbook/evo_modelling.rst:253: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=True, max_restarts=5, show_progress=False) /<>/doc/cookbook/evo_modelling.rst:259: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=False, global_tolerance=1.0, show_progress=False) /<>/doc/cookbook/evo_modelling.rst:265: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False, max_restarts=5, tolerance=1e-8) /<>/doc/cookbook/evo_modelling.rst:276: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) try: lf.optimise( show_progress=False, limit_action="raise", max_evaluations=10, return_calculator=True, ) except ArithmeticError as err: print(err) /<>/doc/cookbook/evo_modelling.rst:303: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model sm = get_model("GTR") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree) aln = load_aligned_seqs("data/primate_brca1.fasta") lf.set_alignment(aln) lf.optimise(local=True, show_progress=False) lf /<>/doc/cookbook/evo_modelling.rst:321: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lnL = lf.lnL lnL /<>/doc/cookbook/evo_modelling.rst:326: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nfp = lf.nfp nfp /<>/doc/cookbook/evo_modelling.rst:338: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_aic() /<>/doc/cookbook/evo_modelling.rst:344: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_aic(second_order=True) /<>/doc/cookbook/evo_modelling.rst:353: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_bic() /<>/doc/cookbook/evo_modelling.rst:367: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: a_g = lf.get_param_value("A/G") a_g /<>/doc/cookbook/evo_modelling.rst:372: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: human = lf.get_param_value("length", "Human") human /<>/doc/cookbook/evo_modelling.rst:380: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mprobs = lf.get_motif_probs() mprobs /<>/doc/cookbook/evo_modelling.rst:388: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tables = lf.get_statistics(with_motif_probs=True, with_titles=True) tables[0] # just displaying the first /<>/doc/cookbook/evo_modelling.rst:398: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.set_param_rule( "length", tip_names=["Human", "Chimpanzee"], outgroup_name="Galago", clade=True, is_independent=False, ) lf.set_name("Null Hypothesis") lf.optimise(local=True, show_progress=False) null_lnL = lf.lnL null_nfp = lf.nfp lf /<>/doc/cookbook/evo_modelling.rst:423: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("length", is_independent=True) lf.set_name("Alt Hypothesis") lf.optimise(local=True, show_progress=False) alt_lnL = lf.lnL alt_nfp = lf.nfp lf /<>/doc/cookbook/evo_modelling.rst:434: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from scipy.stats.distributions import chi2 LR = 2 * (alt_lnL - null_lnL) # the likelihood ratio statistic df = alt_nfp - null_nfp # the test degrees of freedom p = chi2.sf(LR, df) print(f"LR={LR:.4f} ; df={df}; p={df:.4f}") /<>/doc/cookbook/evo_modelling.rst:450: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.set_param_rule( "length", tip_names=["Human", "Chimpanzee"], outgroup_name="Galago", clade=True, is_independent=False, ) lf.set_name("Null Hypothesis") lf.optimise(local=True, show_progress=False) sim_aln = lf.simulate_alignment() sim_aln[:60] /<>/doc/cookbook/evo_modelling.rst:478: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("HKY85") lf = sm.make_likelihood_function(tree) lf.set_alignment(aln) lf.optimise(local=True, show_progress=False) kappa_lo, kappa_mle, kappa_hi = lf.get_param_interval("kappa") print(f"lo={kappa_lo:.2f} ; mle={kappa_mle:.2f} ; hi={kappa_hi:.2f}") human_lo, human_mle, human_hi = lf.get_param_interval("length", "Human") print(f"lo={human_lo:.2f} ; mle={human_mle:.2f} ; hi={human_hi:.2f}") /<>/doc/cookbook/evo_modelling.rst:501: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model aln = make_aligned_seqs(data=dict(a="ACGG", b="ATAG", c="ATGG")) tree = make_tree(tip_names=aln.names) sm = get_model("F81") lf = sm.make_likelihood_function(tree) lf.set_alignment(aln) json = lf.to_json() json[:60] # just truncating the displayed string /<>/doc/cookbook/evo_modelling.rst:516: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.deserialise import deserialise_object newlf = deserialise_object(json) newlf /<>/doc/cookbook/evo_modelling.rst:528: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.optimise(show_progress=False) /<>/doc/cookbook/evo_modelling.rst:542: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ancestors = lf.likely_ancestral_seqs() ancestors[:60] /<>/doc/cookbook/evo_modelling.rst:549: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ancestral_probs = lf.reconstruct_ancestral_seqs() ancestral_probs["root"][:5] /<>/doc/cookbook/genetic_code.rst:4: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code.translate("TTTGCAAAC") /<>/doc/cookbook/genetic_code.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code, make_seq standard_code = get_code(1) seq = make_seq("ATGCTAACATAAA", moltype="dna") translations = standard_code.sixframes(seq) print(translations) /<>/doc/cookbook/genetic_code.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code, make_seq standard_code = get_code(1) seq = make_seq("ATGCTAACATAAA", moltype="dna") stops_frame1 = standard_code.get_stop_indices(seq, start=0) stops_frame1 stop_index = stops_frame1[0] seq[stop_index : stop_index + 3] /<>/doc/cookbook/genetic_code.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code, make_seq standard_code = get_code(1) standard_code["TTT"] /<>/doc/cookbook/genetic_code.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: standard_code["A"] /<>/doc/cookbook/genetic_code.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code["TTT"] /<>/doc/cookbook/genetic_code.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code["A"] /<>/doc/cookbook/genetic_code.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: targets = ["A", "C"] codons = [standard_code[aa] for aa in targets] codons flat_list = sum(codons, []) flat_list /<>/doc/cookbook/genetic_code.rst:89: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGTT", moltype="dna") sorted(my_seq.codon_alphabet()) len(my_seq.codon_alphabet()) /<>/doc/cookbook/genetic_code.rst:102: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("ATGCACTGGTAA", name="my_gene", moltype="dna") codons = my_seq.get_in_motif_size(3) print(codons) /<>/doc/cookbook/genetic_code.rst:115: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.core.alphabet import AlphabetError /<>/doc/cookbook/genetic_code.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AlphabetError pep = my_seq.get_translation() /<>/doc/cookbook/genetic_code.rst:128: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("ATGCACTGGTAA", name="my_gene", moltype="dna") seq = my_seq.trim_stop_codon() pep = seq.get_translation() print(pep.to_fasta()) print(type(pep)) /<>/doc/cookbook/genetic_code.rst:141: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("CAAATGTATTAA", name="my_gene", moltype="dna") pep = my_seq[:-3].get_translation() print(pep.to_fasta()) /<>/doc/cookbook/loading_sequences.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/loading_sequences.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta", moltype="dna") type(aln) /<>/doc/cookbook/loading_sequences.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.info.source /<>/doc/cookbook/loading_sequences.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs seqs = load_unaligned_seqs("data/long_testseqs.fasta", moltype="dna") type(seqs) /<>/doc/cookbook/loading_sequences.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("https://raw.githubusercontent.com/cogent3/cogent3/develop/doc/data/long_testseqs.fasta", moltype="dna") /<>/doc/cookbook/loading_sequences.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta", moltype="dna", format="fasta") aln /<>/doc/cookbook/loading_sequences.rst:75: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs protein_seqs = [">seq1", "DEKQL-RG", ">seq2", "DDK--SRG"] proteins_loaded = make_aligned_seqs(protein_seqs) proteins_loaded.moltype print(proteins_loaded) proteins_loaded = make_aligned_seqs(protein_seqs, moltype="protein") print(proteins_loaded) /<>/doc/cookbook/loading_sequences.rst:94: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs seqs = {"seq1": "AATCG-A", "seq2": "AATCGGA"} seqs_loaded = make_aligned_seqs(seqs) /<>/doc/cookbook/loading_sequences.rst:104: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs seqs = [">seq1", "AATCG-A", ">seq2", "AATCGGA"] seqs_loaded = make_aligned_seqs(seqs) print(seqs_loaded) /<>/doc/cookbook/loading_sequences.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs DNA_seqs = [ ">sample1 Mus musculus", "AACCTGC--C", ">sample2 Gallus gallus", "AAC-TGCAAC", ] loaded_seqs = make_aligned_seqs( DNA_seqs, moltype="dna", label_to_name=lambda x: x.split()[0] ) loaded_seqs /<>/doc/cookbook/loading_sequences.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_unaligned_seqs seqs = {"seq1": "AATCA", "seq2": "AATCGGA"} seqs = make_unaligned_seqs(data=seqs, moltype="dna") seqs /<>/doc/cookbook/loading_sequences.rst:157: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.fasta import MinimalFastaParser f = open("data/long_testseqs.fasta") seqs = [(name, seq) for name, seq in MinimalFastaParser(f)] seqs /<>/doc/cookbook/loading_sequences.rst:170: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.fasta import LabelParser def latin_to_common(latin): return {"Homo sapiens": "human", "Pan troglodtyes": "chimp"}[latin] label_parser = LabelParser( "%(species)s", [[1, "species", latin_to_common]], split_with=":" ) for label in ">abcd:Homo sapiens:misc", ">abcd:Pan troglodtyes:misc": label = label_parser(label) print(label, type(label)) /<>/doc/cookbook/loading_sequences.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.fasta import LabelParser, MinimalFastaParser fasta_data = [ ">gi|10047090|ref|NP_055147.1| small muscle protein, X-linked [Homo sapiens]", "MNMSKQPVSNVRAIQANINIPMGAFRPGAGQPPRRKECTPEVEEGVPPTSDEEKKPIPGAKKLPGPAVNL", "SEIQNIKSELKYVPKAEQ", ">gi|10047092|ref|NP_037391.1| neuronal protein [Homo sapiens]", "MANRGPSYGLSREVQEKIEQKYDADLENKLVDWIILQCAEDIEHPPPGRAHFQKWLMDGTVLCKLINSLY", "PPGQEPIPKISESKMAFKQMEQISQFLKAAETYGVRTTDIFQTVDLWEGKDMAAVQRTLMALGSVAVTKD", ] label_to_name = LabelParser( "%(ref)s", [[1, "gi", str], [3, "ref", str], [4, "description", str]], split_with="|", ) for name, seq in MinimalFastaParser(fasta_data, label_to_name=label_to_name): print(name) print(name.info.gi) print(name.info.description) /<>/doc/cookbook/loading_tabular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/loading_tabular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table /<>/doc/cookbook/loading_tabular.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("https://raw.githubusercontent.com/cogent3/cogent3/develop/doc/data/stats.tsv") /<>/doc/cookbook/loading_tabular.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", sep="\t") table /<>/doc/cookbook/loading_tabular.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import load_delimited header, rows, title, legend = load_delimited("data/CerebellumDukeDNaseSeq.pk", header=False, sep="\t") rows[:4] /<>/doc/cookbook/loading_tabular.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=False, sep="\t") rows = list(reader("data/CerebellumDukeDNaseSeq.pk")) rows[:4] /<>/doc/cookbook/loading_tabular.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", limit=2) table /<>/doc/cookbook/loading_tabular.rst:93: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t" ) table = load_table("data/stats.tsv", reader=reader, digits=1) table /<>/doc/cookbook/loading_tabular.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t", negate=True ) table = load_table("data/stats.tsv", reader=reader, digits=1) table /<>/doc/cookbook/loading_tabular.rst:118: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=["Locus", "Ratio"], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table /<>/doc/cookbook/loading_tabular.rst:128: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=[0, -1], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table /<>/doc/cookbook/loading_tabular.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=True, sep="\t") data = list(reader("data/stats.tsv")) /<>/doc/cookbook/loading_tabular.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data[:2] /<>/doc/cookbook/loading_tabular.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["A", "B", "C"] rows = [range(3), range(3, 6), range(6, 9), range(9, 12)] table = make_table(header=["A", "B", "C"], data=rows) table /<>/doc/cookbook/loading_tabular.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(A=[0, 3, 6], B=[1, 4, 7], C=[2, 5, 8]) table = make_table(data=data) table /<>/doc/cookbook/loading_tabular.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(header=["C", "A", "B"], data=data) table /<>/doc/cookbook/loading_tabular.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", index_name="Locus") table["NP_055852"] /<>/doc/cookbook/loading_tabular.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table["NP_055852", "Region"] /<>/doc/cookbook/loading_tabular.rst:210: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from pandas import DataFrame from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) df = DataFrame(data=data) table = make_table(data_frame=df) table /<>/doc/cookbook/loading_tabular.rst:224: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table(header=["a", "b"], data=[[0, "a"], [3, "c"]]) table /<>/doc/cookbook/loading_tabular.rst:236: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table /<>/doc/cookbook/loading_tabular.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table d2D = { "edge.parent": { "NineBande": "root", "edge.1": "root", "DogFaced": "root", "Human": "edge.0", }, "x": { "NineBande": 1.0, "edge.1": 1.0, "DogFaced": 1.0, "Human": 1.0, }, "length": { "NineBande": 4.0, "edge.1": 4.0, "DogFaced": 4.0, "Human": 4.0, }, } table = make_table( data=d2D, ) table /<>/doc/cookbook/loading_tabular.rst:279: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( header=["abcd", "data"], data=[[range(1, 6), "0"], ["x", 5.0], ["y", None]], missing_data="*", digits=1, ) table /<>/doc/cookbook/loading_tabular.rst:294: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table /<>/doc/cookbook/moltypes.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/moltypes.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_moltypes available_moltypes() /<>/doc/cookbook/moltypes.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seqs = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna") /<>/doc/cookbook/moltypes.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_moltype dna = get_moltype("dna") dna /<>/doc/cookbook/moltypes.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.ambiguities /<>/doc/cookbook/moltypes.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.degenerates /<>/doc/cookbook/moltypes.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.complement("AGG") /<>/doc/cookbook/moltypes.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = dna.make_seq("AGGCTT", name="seq1") seq /<>/doc/cookbook/moltypes.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rna = get_moltype("rna") rna.is_valid("ACGUACGUACGUACGU") /<>/doc/cookbook/moltypes.rst:87: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core import moltype as mt DNAgapped = mt.MolType( seq_constructor=mt.DnaSequence, motifset=mt.IUPAC_DNA_chars, ambiguities=mt.IUPAC_DNA_ambiguities, complements=mt.IUPAC_DNA_ambiguities_complements, pairs=mt.DnaStandardPairs, gaps=".", ) seq = DNAgapped.make_seq("ACG.") seq /<>/doc/cookbook/moltypes.rst:104: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA from cogent3.core.sequence import DnaSequence DnaSequence.moltype = DNA /<>/doc/cookbook/protein_sequences.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/protein_sequences.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import PROTEIN p = PROTEIN.make_seq("THISISAPRQTEIN", "myProtein") type(p) str(p) /<>/doc/cookbook/protein_sequences.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core.genetic_code import DEFAULT as standard_code standard_code.translate("TTTGCAAAC") /<>/doc/cookbook/protein_sequences.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seq = load_aligned_seqs("data/abglobin_aa.phylip", moltype="protein") /<>/doc/cookbook/simple_trees.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/simple_trees.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /<>/doc/cookbook/simple_trees.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.write("data/temp.tree") /<>/doc/cookbook/simple_trees.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") names = tr.get_node_names() names[:4] /<>/doc/cookbook/simple_trees.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: names[4:] names_nodes = tr.get_nodes_dict() names_nodes["Human"] /<>/doc/cookbook/simple_trees.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.get_node_matching_name("Mouse") /<>/doc/cookbook/simple_trees.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") tr.name /<>/doc/cookbook/simple_trees.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: hu.name /<>/doc/cookbook/simple_trees.rst:70: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] type(hu) /<>/doc/cookbook/simple_trees.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(tr) /<>/doc/cookbook/simple_trees.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() for n in nodes.items(): print(n) /<>/doc/cookbook/simple_trees.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for n in tr.iter_tips(): print(n) /<>/doc/cookbook/simple_trees.rst:106: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for n in tr.iter_nontips(): print(n.get_newick()) /<>/doc/cookbook/simple_trees.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") edges = tr.get_connecting_edges("edge.1", "Human") for edge in edges: print(edge.name) /<>/doc/cookbook/simple_trees.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] mu = nodes["Mouse"] hu.distance(mu) hu.is_tip() /<>/doc/cookbook/simple_trees.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] mu = nodes["Mouse"] lca = hu.last_common_ancestor(mu) lca /<>/doc/cookbook/simple_trees.rst:154: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(lca) /<>/doc/cookbook/simple_trees.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") for a in hu.ancestors(): print(a.name) /<>/doc/cookbook/simple_trees.rst:173: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") node = tr.get_node_matching_name("edge.1") children = list(node.iter_tips()) + list(node.iter_nontips()) for child in children: print(child.name) /<>/doc/cookbook/simple_trees.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") dists = tr.get_distances() /<>/doc/cookbook/simple_trees.rst:195: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: human_dists = [names for names in dists if "Human" in names] for dist in human_dists: print(dist, dists[dist]) /<>/doc/cookbook/simple_trees.rst:204: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.max_tip_tip_distance() /<>/doc/cookbook/simple_trees.rst:214: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") tips = hu.tips_within_distance(0.2) for t in tips: print(t) /<>/doc/cookbook/simple_trees.rst:230: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.rooted_at("edge.0").ascii_art()) /<>/doc/cookbook/simple_trees.rst:240: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.root_at_midpoint().ascii_art()) /<>/doc/cookbook/simple_trees.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.ascii_art()) /<>/doc/cookbook/simple_trees.rst:254: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /<>/doc/cookbook/simple_trees.rst:261: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.rooted_with_tip("Mouse").ascii_art()) /<>/doc/cookbook/simple_trees.rst:271: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.get_newick() /<>/doc/cookbook/simple_trees.rst:278: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.get_newick(with_distances=True) /<>/doc/cookbook/simple_trees.rst:285: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") xml = tr.get_xml() for line in xml.splitlines(): print(line) /<>/doc/cookbook/simple_trees.rst:299: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /<>/doc/cookbook/simple_trees.rst:309: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for t in tr.preorder(): print(t.get_newick()) /<>/doc/cookbook/simple_trees.rst:320: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for t in tr.postorder(): print(t.get_newick()) /<>/doc/cookbook/simple_trees.rst:334: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for tip in tr.iter_nontips(): tip_names = tip.get_tip_names() print(tip_names) sub_tree = tr.get_sub_tree(tip_names) print(sub_tree.ascii_art()) /<>/doc/cookbook/simple_trees.rst:348: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.util.io import remove_files remove_files(["data/temp.tree", "data/temp.pdf"], error_on_missing=False) /<>/doc/cookbook/simple_trees.rst:364: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree simple_tree_string = "(B:0.2,(D:0.4)E:0.5)F;" simple_tree = make_tree(simple_tree_string) print(simple_tree.ascii_art()) /<>/doc/cookbook/simple_trees.rst:372: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree.prune() print(simple_tree.ascii_art()) /<>/doc/cookbook/simple_trees.rst:377: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(simple_tree) /<>/doc/cookbook/simple_trees.rst:384: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr1 = load_tree("data/test.tree") print(tr1.get_newick()) /<>/doc/cookbook/simple_trees.rst:391: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr2 = tr1.unrooted_deepcopy() print(tr2.get_newick()) /<>/doc/cookbook/simple_trees.rst:401: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tree_string = "(B:0.2,H:0.2,(C:0.3,D:0.4,E:0.1)F:0.5)G;" tr = make_tree(tree_string) print(tr.ascii_art()) /<>/doc/cookbook/simple_trees.rst:409: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.bifurcating().ascii_art()) /<>/doc/cookbook/simple_trees.rst:422: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /<>/doc/cookbook/simple_trees.rst:429: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.balanced().ascii_art()) /<>/doc/cookbook/simple_trees.rst:438: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr1 = make_tree("(B:0.2,(C:0.2,D:0.2)F:0.2)G;") tr2 = make_tree("((C:0.1,D:0.1)F:0.1,B:0.1)G;") tr1.same_topology(tr2) /<>/doc/cookbook/simple_trees.rst:452: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = make_tree("(B:0.2,(C:0.3,D:0.4)F:0.5)G;") print(tr.ascii_art()) /<>/doc/cookbook/simple_trees.rst:459: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.set_tip_distances() for t in tr.preorder(): print(t.name, t.TipDistance) /<>/doc/cookbook/simple_trees.rst:468: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = make_tree("(B:0.2,(C:0.3,D:0.4)F:0.5)G;") print(tr) /<>/doc/cookbook/simple_trees.rst:475: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.scale_branch_lengths() print(tr) /<>/doc/cookbook/simple_trees.rst:485: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = make_tree("(B:3,(C:2,D:4)F:5)G;") d, tips = tr.tip_to_tip_distances() for i, t in enumerate(tips): print(t.name, d[i]) /<>/doc/cookbook/simple_trees.rst:505: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr1 = make_tree("(B:2,(C:3,D:4)F:5)G;") tr2 = make_tree("(C:2,(B:3,D:4)F:5)G;") tr1.compare_by_tip_distances(tr2) /<>/doc/cookbook/tables.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory cookbook/loading_tabular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory cookbook/loading_tabular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table cookbook/loading_tabular.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("https://raw.githubusercontent.com/cogent3/cogent3/develop/doc/data/stats.tsv") cookbook/loading_tabular.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", sep="\t") table cookbook/loading_tabular.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import load_delimited header, rows, title, legend = load_delimited("data/CerebellumDukeDNaseSeq.pk", header=False, sep="\t") rows[:4] cookbook/loading_tabular.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=False, sep="\t") rows = list(reader("data/CerebellumDukeDNaseSeq.pk")) rows[:4] cookbook/loading_tabular.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", limit=2) table cookbook/loading_tabular.rst:93: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t" ) table = load_table("data/stats.tsv", reader=reader, digits=1) table cookbook/loading_tabular.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t", negate=True ) table = load_table("data/stats.tsv", reader=reader, digits=1) table cookbook/loading_tabular.rst:118: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=["Locus", "Ratio"], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table cookbook/loading_tabular.rst:128: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=[0, -1], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table cookbook/loading_tabular.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=True, sep="\t") data = list(reader("data/stats.tsv")) cookbook/loading_tabular.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data[:2] cookbook/loading_tabular.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["A", "B", "C"] rows = [range(3), range(3, 6), range(6, 9), range(9, 12)] table = make_table(header=["A", "B", "C"], data=rows) table cookbook/loading_tabular.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(A=[0, 3, 6], B=[1, 4, 7], C=[2, 5, 8]) table = make_table(data=data) table cookbook/loading_tabular.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(header=["C", "A", "B"], data=data) table cookbook/loading_tabular.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", index_name="Locus") table["NP_055852"] cookbook/loading_tabular.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table["NP_055852", "Region"] cookbook/loading_tabular.rst:210: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from pandas import DataFrame from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) df = DataFrame(data=data) table = make_table(data_frame=df) table cookbook/loading_tabular.rst:224: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table(header=["a", "b"], data=[[0, "a"], [3, "c"]]) table cookbook/loading_tabular.rst:236: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table cookbook/loading_tabular.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table d2D = { "edge.parent": { "NineBande": "root", "edge.1": "root", "DogFaced": "root", "Human": "edge.0", }, "x": { "NineBande": 1.0, "edge.1": 1.0, "DogFaced": 1.0, "Human": 1.0, }, "length": { "NineBande": 4.0, "edge.1": 4.0, "DogFaced": 4.0, "Human": 4.0, }, } table = make_table( data=d2D, ) table cookbook/loading_tabular.rst:279: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( header=["abcd", "data"], data=[[range(1, 6), "0"], ["x", 5.0], ["y", None]], missing_data="*", digits=1, ) table cookbook/loading_tabular.rst:294: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table /<>/doc/cookbook/tables.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table.columns["a"] = [1, 3, 5] table.columns["b"] = [2, 4, 6] table /<>/doc/cookbook/tables.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data, title="Sample title", legend="a legend") table /<>/doc/cookbook/tables.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table.title = "My title" table /<>/doc/cookbook/tables.rst:57: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") for row in table: print(row) break /<>/doc/cookbook/tables.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for row in table: print(row["Locus"]) /<>/doc/cookbook/tables.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3, 5], b=["a", "c", "d"]) table = make_table(data=data) table.shape[0] == 3 /<>/doc/cookbook/tables.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.shape[1] == 2 /<>/doc/cookbook/tables.rst:100: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table.columns /<>/doc/cookbook/tables.rst:107: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Region"] /<>/doc/cookbook/tables.rst:113: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for name in table.columns: print(name) /<>/doc/cookbook/tables.rst:121: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table /<>/doc/cookbook/tables.rst:128: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table[:2, "Region":] /<>/doc/cookbook/tables.rst:135: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table[:2, :1] /<>/doc/cookbook/tables.rst:145: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table.format_column("Ratio", "%.1e") table /<>/doc/cookbook/tables.rst:158: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", digits=1, space=2) table /<>/doc/cookbook/tables.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.space = " " table /<>/doc/cookbook/tables.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table h = ["name", "A/C", "A/G", "A/T", "C/A"] rows = [["tardigrade", 0.0425, 0.1424, 0.0226, 0.0391]] wrap_table = make_table(header=h, data=rows, max_width=30) wrap_table /<>/doc/cookbook/tables.rst:184: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: wrap_table = make_table(header=h, data=rows, max_width=30, index_name="name") wrap_table /<>/doc/cookbook/tables.rst:192: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data=dict(a=list(range(10)), b=list(range(10)))) table.head() /<>/doc/cookbook/tables.rst:199: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.head(2) /<>/doc/cookbook/tables.rst:208: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.tail() /<>/doc/cookbook/tables.rst:214: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.tail(1) /<>/doc/cookbook/tables.rst:221: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.set_repr_policy(random=3) table /<>/doc/cookbook/tables.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.set_repr_policy(head=2, tail=3) table /<>/doc/cookbook/tables.rst:241: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.header) table = table.with_new_header("Ratio", "Stat") print(table.header) /<>/doc/cookbook/tables.rst:251: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table /<>/doc/cookbook/tables.rst:258: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["a"] = [1, 3, 5] table.columns["b"] = [2, 4, 6] table /<>/doc/cookbook/tables.rst:269: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table = table.with_new_column( "LargeCon", lambda r_v: r_v[0] == "Con" and r_v[1] > 10.0, columns=["Region", "Ratio"], ) table /<>/doc/cookbook/tables.rst:282: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.array /<>/doc/cookbook/tables.rst:292: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") locus = table.tolist("Locus") locus /<>/doc/cookbook/tables.rst:300: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Locus"].tolist() /<>/doc/cookbook/tables.rst:309: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") rows = table.tolist(["Region", "Locus"]) rows /<>/doc/cookbook/tables.rst:322: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.to_dict() /<>/doc/cookbook/tables.rst:332: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.columns.to_dict() /<>/doc/cookbook/tables.rst:340: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") df = table.to_dataframe() df /<>/doc/cookbook/tables.rst:348: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: df = table.to_dataframe(categories="Region") /<>/doc/cookbook/tables.rst:357: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data={"Ts": [31, 58], "Tv": [36, 138], "": ["syn", "nsyn"]}, index_name="") table /<>/doc/cookbook/tables.rst:362: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: contingency = table.to_categorical(["Ts", "Tv"]) contingency /<>/doc/cookbook/tables.rst:367: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: g_test = contingency.G_independence() g_test /<>/doc/cookbook/tables.rst:374: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data={"Ts": [31, 58], "Tv": [36, 138], "": ["syn", "nsyn"]}) contingency = table.to_categorical(["Ts", "Tv"], index_name="") /<>/doc/cookbook/tables.rst:386: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table1 = load_table("data/stats.tsv") table2 = load_table("data/stats.tsv") table = table1.appended(None, table2) table /<>/doc/cookbook/tables.rst:395: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table1.title = "Data1" table2.title = "Data2" table = table1.appended("Data#", table2, title="") table /<>/doc/cookbook/tables.rst:407: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.summed("Ratio") /<>/doc/cookbook/tables.rst:414: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Ratio"].sum() /<>/doc/cookbook/tables.rst:423: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table all_numeric = make_table( header=["A", "B", "C"], data=[range(3), range(3, 6), range(6, 9), range(9, 12)] ) all_numeric /<>/doc/cookbook/tables.rst:434: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_numeric.summed() /<>/doc/cookbook/tables.rst:440: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_numeric.summed(col_sum=False) /<>/doc/cookbook/tables.rst:449: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed = make_table( header=["A", "B", "C"], data=[["*", 1, 2], [3, "*", 5], [6, 7, "*"]] ) mixed /<>/doc/cookbook/tables.rst:458: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed.summed(strict=False) /<>/doc/cookbook/tables.rst:464: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed.summed(col_sum=False, strict=False) /<>/doc/cookbook/tables.rst:473: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") sub_table = table.filtered(lambda x: x < 10.0, columns="Ratio") sub_table /<>/doc/cookbook/tables.rst:481: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sub_table = table.filtered("Ratio < 10.0") sub_table /<>/doc/cookbook/tables.rst:488: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sub_table = table.filtered("Ratio < 10.0 and Region == 'NonCon'") sub_table /<>/doc/cookbook/tables.rst:498: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: big_numeric = all_numeric.filtered_by_column(lambda x: sum(x) > 20) big_numeric /<>/doc/cookbook/tables.rst:506: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.sorted(columns="Ratio") /<>/doc/cookbook/tables.rst:514: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.sorted(columns="Ratio", reverse="Ratio") /<>/doc/cookbook/tables.rst:521: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.sorted(columns=["Region", "Ratio"], reverse="Ratio") /<>/doc/cookbook/tables.rst:528: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") raw = table.tolist("Region") raw /<>/doc/cookbook/tables.rst:537: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") raw = table.tolist(["Locus", "Region"]) raw /<>/doc/cookbook/tables.rst:546: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") assert table.distinct_values("Region") == set(["NonCon", "Con"]) /<>/doc/cookbook/tables.rst:554: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") assert table.count("Region == 'NonCon' and Ratio > 1") == 1 /<>/doc/cookbook/tables.rst:564: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( data=dict(A=["a", "b", "b", "b", "a"], B=["c", "c", "c", "c", "d"]) ) unique = table.count_unique("A") type(unique) /<>/doc/cookbook/tables.rst:574: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unique /<>/doc/cookbook/tables.rst:580: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unique = table.count_unique(["A", "B"]) unique /<>/doc/cookbook/tables.rst:585: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: r = unique.to_table() r /<>/doc/cookbook/tables.rst:595: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rows = [ ["NP_004893", True], ["NP_005079", True], ["NP_005500", False], ["NP_055852", False], ] region_type = make_table(header=["Locus", "LargeCon"], data=rows) stats_table = load_table("data/stats.tsv") new = stats_table.joined(region_type, columns_self="Locus") new /<>/doc/cookbook/tables.rst:615: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["#OTU ID", "14SK041", "14SK802"] rows = [ [-2920, "332", 294], [-1606, "302", 229], [-393, 141, 125], [-2109, 138, 120], ] table = make_table(header=header, rows=rows) table /<>/doc/cookbook/tables.rst:631: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tp = table.transposed(new_column_name="sample", select_as_header="#OTU ID") tp /<>/doc/cookbook/tables.rst:641: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", format="md") print(table) /<>/doc/cookbook/tables.rst:653: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", format="tex") print(table) /<>/doc/cookbook/tables.rst:665: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.to_markdown(justify="ccr")) /<>/doc/cookbook/tables.rst:673: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table( "data/stats.tsv", title="Some stats.", legend="Derived from something." ) print(table.to_latex(justify="ccr", label="tab:table1")) /<>/doc/cookbook/tables.rst:683: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table( "data/stats.tsv", title="Some stats.", legend="Derived from something." ) print(table.to_rst(csv_table=True)) /<>/doc/cookbook/tables.rst:693: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table( "data/stats.tsv", title="Some stats.", legend="Derived from something." ) print(table.to_rst()) /<>/doc/cookbook/tables.rst:705: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.to_string(format="latex")) /<>/doc/cookbook/tables.rst:715: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: rows = [ ["1", 100, 101, 1.123], ["1", 101, 102, 1.123], ["1", 102, 103, 1.123], ["1", 103, 104, 1.123], ["1", 104, 105, 1.123], ["1", 105, 106, 1.123], ["1", 106, 107, 1.123], ["1", 107, 108, 1.123], ["1", 108, 109, 1], ["1", 109, 110, 1], ["1", 110, 111, 1], ["1", 111, 112, 1], ["1", 112, 113, 1], ["1", 113, 114, 1], ["1", 114, 115, 1], ["1", 115, 116, 1], ["1", 116, 117, 1], ["1", 117, 118, 1], ["1", 118, 119, 2], ["1", 119, 120, 2], ["1", 120, 121, 2], ["1", 150, 151, 2], ["1", 151, 152, 2], ["1", 152, 153, 2], ["1", 153, 154, 2], ["1", 154, 155, 2], ["1", 155, 156, 2], ["1", 156, 157, 2], ["1", 157, 158, 2], ["1", 158, 159, 2], ["1", 159, 160, 2], ["1", 160, 161, 2], ] bgraph = make_table(header=["chrom", "start", "end", "value"], rows=rows) /<>/doc/cookbook/tables.rst:754: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bgraph.head() /<>/doc/cookbook/tables.rst:760: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print( bgraph.to_string( format="bedgraph", name="test track", description="test of bedgraph", color=(255, 0, 0), digits=0, ) ) /<>/doc/cookbook/tables.rst:775: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") straight_html = table.to_html() /<>/doc/cookbook/tables.rst:787: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.format.table import known_formats known_formats /<>/doc/cookbook/tables.rst:796: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.write("stats_tab.tex", justify="ccr", label="tab:table1") /<>/doc/cookbook/tables.rst:805: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.write("stats_tab.txt", sep="\t") /<>/doc/cookbook/tables.rst:812: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pathlib for name in ("stats_tab.txt", "stats_tab.tex"): p = pathlib.Path(name) if p.exists(): p.unlink() cookbook/union_dict.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.a cookbook/union_dict.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data["a"] cookbook/union_dict.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.d cookbook/union_dict.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.b |= {"d": 25} data.b cookbook/union_dict.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.union({"d": [25]}) cookbook/union_dict.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b {"c": 24, "d": [25]} cookbook/union_dict.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: KeyError from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data["k"] cookbook/union_dict.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AttributeError data.k /<>/doc/cookbook/useful_utilities.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import numpy def DiffOmega(omega): def omega_from_S(S): omega_est = S / (1 - numpy.e ** (-1 * S)) return abs(omega - omega_est) ** 2 return omega_from_S omega = 0.1 f = DiffOmega(omega) /<>/doc/cookbook/useful_utilities.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.optimisers import maximise, minimise S = minimise( f, # the function xinit=1.0, # the initial value bounds=(-100, 100), # [lower,upper] bounds for the parameter local=True, # just local optimisation, not Simulated Annealing show_progress=False, ) assert 0.0 <= f(S) < 1e-6 print("S=%.4f" % S) /<>/doc/cookbook/useful_utilities.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: TypeError from cogent3.util.misc import iterable my_var = 10 for i in my_var: print("will not work") for i in iterable(my_var): print(i) /<>/doc/cookbook/useful_utilities.rst:75: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import curry def foo(x, y): """Some function""" return x + y bar = curry(foo, 5) print(bar.__doc__) bar(10) /<>/doc/cookbook/useful_utilities.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import is_iterable can_iter = [1, 2, 3, 4] cannot_iter = 1.234 is_iterable(can_iter) /<>/doc/cookbook/useful_utilities.rst:100: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_iterable(cannot_iter) /<>/doc/cookbook/useful_utilities.rst:109: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import is_char class foo: pass is_char("a") /<>/doc/cookbook/useful_utilities.rst:118: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_char("ab") /<>/doc/cookbook/useful_utilities.rst:122: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_char(foo()) /<>/doc/cookbook/useful_utilities.rst:131: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import recursive_flatten l = [[[[1, 2], "abcde"], [5, 6]], [7, 8], [9, 10]] /<>/doc/cookbook/useful_utilities.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: recursive_flatten(l) /<>/doc/cookbook/useful_utilities.rst:146: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import not_list_tuple not_list_tuple(1) /<>/doc/cookbook/useful_utilities.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_list_tuple([1]) /<>/doc/cookbook/useful_utilities.rst:156: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_list_tuple("ab") /<>/doc/cookbook/useful_utilities.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import add_lowercase d = {"A": 5, "B": 6, "C": 7, "foo": 8, 42: "life"} add_lowercase(d) /<>/doc/cookbook/useful_utilities.rst:177: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from numpy import array from cogent3.util.misc import DistanceFromMatrix m = array([[1, 2, 3], [4, 5, 6], [7, 8, 9]]) f = DistanceFromMatrix(m) f(0, 0) /<>/doc/cookbook/useful_utilities.rst:187: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: f(1, 2) /<>/doc/cookbook/useful_utilities.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import ClassChecker class not_okay(object): pass no = not_okay() class okay(object): pass o = okay() class my_dict(dict): pass md = my_dict() cc = ClassChecker(str, okay, dict) o in cc /<>/doc/cookbook/useful_utilities.rst:217: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: no in cc /<>/doc/cookbook/useful_utilities.rst:221: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: 5 in cc /<>/doc/cookbook/useful_utilities.rst:225: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: {"a": 5} in cc /<>/doc/cookbook/useful_utilities.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: "asasas" in cc /<>/doc/cookbook/useful_utilities.rst:233: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: md in cc /<>/doc/cookbook/useful_utilities.rst:242: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import Delegator class ListAndString(list, Delegator): def __init__(self, items, string): Delegator.__init__(self, string) for i in items: self.append(i) ls = ListAndString([1, 2, 3], "ab_cd") len(ls) /<>/doc/cookbook/useful_utilities.rst:255: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls[0] /<>/doc/cookbook/useful_utilities.rst:259: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.upper() /<>/doc/cookbook/useful_utilities.rst:263: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.split("_") /<>/doc/cookbook/useful_utilities.rst:272: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import FunctionWrapper f = FunctionWrapper(str) f /<>/doc/cookbook/useful_utilities.rst:279: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: f(123) /<>/doc/cookbook/useful_utilities.rst:290: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.util.misc import ConstraintError /<>/doc/cookbook/useful_utilities.rst:295: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import ConstrainedDict d = ConstrainedDict({"a": 1, "b": 2, "c": 3}, constraint="abc") d /<>/doc/cookbook/useful_utilities.rst:302: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ConstraintError d["d"] = 5 /<>/doc/cookbook/what_codes.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/what_codes.rst:10: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_codes available_codes() /<>/doc/cookbook/what_codes.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs nt_seqs = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna") nt_seqs[:21] /<>/doc/cookbook/what_codes.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aa_seqs = nt_seqs.get_translation(gc=1, incomplete_ok=True) aa_seqs[:20] /<>/doc/cookbook/what_codes.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code gc = get_code(4) gc /<>/doc/draw/aln/plot_aln-coevolution.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/draw/aln/plot_aln-coevolution.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/brca1.fasta", moltype="dna") aln = aln.no_degenerates(motif_length=3) aln = aln.get_translation() aln = aln[:100] # for compute speed in testing the documentation coevo = aln.coevolution(show_progress=False, drawable="heatmap") coevo.drawable.show() /<>/doc/draw/aln/plot_aln-coevolution.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-coevolution.png" coevo.drawable.write(outpath) /<>/doc/draw/aln/plot_aln-coevolution.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: coevo = aln.coevolution(show_progress=False, drawable="violin") coevo.drawable.show(width=300) /<>/doc/draw/aln/plot_aln-coevolution.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: coevo = aln.coevolution(show_progress=False, drawable="box") coevo.drawable.show(width=300) /<>/doc/draw/aln/plot_aln-dotplot-1.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/draw/aln/plot_aln-dotplot-1.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import os from cogent3 import load_unaligned_seqs seqs = load_unaligned_seqs("data/SCA1-cds.fasta", moltype="dna") draw = seqs.dotplot() draw.show() /<>/doc/draw/aln/plot_aln-dotplot-1.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-dotplot-1.png" draw.write(outpath) /<>/doc/draw/aln/plot_aln-dotplot-1.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: draw = seqs.dotplot(name1="Human", name2="Mouse", window=8, threshold=8) draw.show() /<>/doc/draw/aln/plot_aln-dotplot-1.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: draw = seqs.dotplot(name1="Human", name2="Mouse", rc=True) draw.show() /<>/doc/draw/aln/plot_aln-dotplot-1.rst:59: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: draw = seqs.dotplot(name1="Human", name2="Mouse", rc=True, title="SCA1", width=400) draw.show() /<>/doc/draw/aln/plot_aln-dotplot-2.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/draw/aln/plot_aln-dotplot-2.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app.io import get_data_store, load_json loader = load_json() seqs = loader("data/tp53.json") dp = seqs.dotplot(name1="Macaque", name2="Marmoset", width=600) dp.show() /<>/doc/draw/aln/plot_aln-dotplot-2.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-dotplot-2.png" dp.write(outpath) /<>/doc/draw/aln/plot_aln-dotplot-2.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: help(dp.remove_track) /<>/doc/draw/aln/plot_aln-dotplot-2.rst:41: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dp.remove_track(left_track=True) dp.show() /<>/doc/draw/aln/plot_aln-gaps-per-seq.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/draw/aln/plot_aln-gaps-per-seq.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/brca1.fasta", moltype="dna") counts = aln.count_gaps_per_seq(unique=True) counts[10: 20] # limiting the width of the displayed output /<>/doc/draw/aln/plot_aln-gaps-per-seq.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.count_gaps_per_seq(unique=True, drawable="bar") counts.drawable.show(width=500) /<>/doc/draw/aln/plot_aln-gaps-per-seq.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-gaps-per-seq.png" counts.drawable.write(outpath) /<>/doc/draw/aln/plot_aln-gaps-per-seq.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.count_gaps_per_seq(unique=True, drawable="violin") counts.drawable.show(width=300, height=500) /<>/doc/draw/aln/plot_aln-gaps-per-seq.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.count_gaps_per_seq(unique=True, drawable="box") counts.drawable.show(width=300, height=500) /<>/doc/draw/aln/plot_aln-info-plot.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/draw/aln/plot_aln-info-plot.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_aligned_seqs, make_seq s1 = make_seq("TGATGTAAGGTAGTT", name="s1", moltype="dna") s2 = make_seq("--CTGGAAGGGT---", name="s2", moltype="dna") seqs = make_aligned_seqs(data=[s1, s2], array_align=False, moltype="dna") draw = seqs.information_plot(window=2, include_gap=True) draw.show(width=500, height=400) /<>/doc/draw/aln/plot_aln-info-plot.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/brca1.fasta", moltype="protein") fig = aln.information_plot(stat="median") fig.show(width=500, height=400) /<>/doc/draw/aln/plot_aln-info-plot.rst:37: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-info-plot.png" fig.write(outpath) /<>/doc/draw/aln/plot_aln-seqlogo.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/draw/aln/plot_aln-seqlogo.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.parse import jaspar _, pwm = jaspar.read("data/tbp.jaspar") freqarr = pwm.to_freq_array() freqarr[:5] # illustrating the contents of the MotifFreqsArray /<>/doc/draw/aln/plot_aln-seqlogo.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: logo = freqarr.logo() logo.show(height=250, width=500) /<>/doc/draw/aln/plot_aln-seqlogo.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-seqlogo.png" logo.write(outpath) /<>/doc/draw/aln/plot_aln-seqlogo.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna") l = aln[:311].seqlogo(height=300, width=500, wrap=60, vspace=0.05) l.show() /<>/doc/draw/aln/plot_aln-seqlogo.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aa = aln.get_translation(incomplete_ok=True)[:120] logo = aa.seqlogo(width=500, height=300, wrap=50, vspace=0.1) logo.show() /<>/doc/draw/tree/plot_tree-angular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/draw/tree/plot_tree-angular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure(style="angular", width=600, height=600) fig.show() /<>/doc/draw/tree/plot_tree-angular.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.show() /<>/doc/draw/tree/plot_tree-angular.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-angular.png" fig.write(outpath) /<>/doc/draw/tree/plot_tree-circular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/draw/tree/plot_tree-circular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure("circular", width=600, height=600) fig.scale_bar = "top right" fig.label_pad = 0.1 fig.show() /<>/doc/draw/tree/plot_tree-circular.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.style_edges( "AfricanEl", tip2="Manatee", legendgroup="Afrotheria", line=dict(color="magenta", width=2), ) fig.show(width=650, height=600) /<>/doc/draw/tree/plot_tree-circular.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.label_pad = 0.3 fig.show(width=650, height=600) /<>/doc/draw/tree/plot_tree-circular.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-circular.png" fig.write(outpath) /<>/doc/draw/tree/plot_tree-radial.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/draw/tree/plot_tree-radial.rst:9: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure("radial", width=600, height=600) fig.show() /<>/doc/draw/tree/plot_tree-radial.rst:19: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-radial.png" fig.write(outpath) /<>/doc/draw/tree/plot_tree-radial.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.label_pad = 0.23 fig.show() /<>/doc/draw/tree/plot_tree-square.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/draw/tree/plot_tree-square.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure(width=600, height=600) fig.scale_bar = "top right" fig.show() /<>/doc/draw/tree/plot_tree-square.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-square.png" fig.write(outpath) /<>/doc/draw/tree/plot_tree-square.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.style_edges( "AfricanEl", tip2="Manatee", legendgroup="Afrotheria", line=dict(color="magenta"), ) fig.show() /<>/doc/draw/tree/plot_tree-square.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.show() /<>/doc/draw/tree/plot_tree-support.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/draw/tree/plot_tree-support.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() tree = reader("data/tree-with-support.json") fig = tree.get_figure(show_support=True, threshold=0.8) fig.scale_bar = None fig.show(width=500, height=400) /<>/doc/draw/tree/plot_tree-support.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.support_xshift = 15 fig.support_yshift = 0 fig.show(width=500, height=400) /<>/doc/draw/tree/plot_tree-support.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-support.png" fig.write(outpath) /<>/doc/examples/align_codons_to_protein.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs, make_unaligned_seqs /<>/doc/examples/align_codons_to_protein.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = { "hum": "AAGCAGATCCAGGAAAGCAGCGAGAATGGCAGCCTGGCCGCGCGCCAGGAGAGGCAGGCCCAGGTCAACCTCACT", "mus": "AAGCAGATCCAGGAGAGCGGCGAGAGCGGCAGCCTGGCCGCGCGGCAGGAGAGGCAGGCCCAAGTCAACCTCACG", "rat": "CTGAACAAGCAGCCACTTTCAAACAAGAAA", } unaligned_DNA = make_unaligned_seqs(seqs, moltype="dna") print(unaligned_DNA.to_fasta()) /<>/doc/examples/align_codons_to_protein.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unaligned_aa = unaligned_DNA.get_translation() print(unaligned_aa.to_fasta()) /<>/doc/examples/align_codons_to_protein.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned_aa_seqs = { "hum": "KQIQESSENGSLAARQERQAQVNLT", "mus": "KQIQESGESGSLAARQERQAQVNLT", "rat": "LNKQ------PLS---------NKK", } aligned_aa = make_aligned_seqs(aligned_aa_seqs, moltype="protein") aligned_DNA = aligned_aa.replace_seqs(unaligned_DNA) aligned_DNA /<>/doc/examples/calculate_UPGMA_cluster.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/calculate_UPGMA_cluster.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.cluster.UPGMA import upgma from cogent3.evolve import distance /<>/doc/examples/calculate_UPGMA_cluster.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import HKY85 /<>/doc/examples/calculate_UPGMA_cluster.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/test.paml") /<>/doc/examples/calculate_UPGMA_cluster.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) /<>/doc/examples/calculate_UPGMA_cluster.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mycluster = upgma(d.get_pairwise_distances()) print(mycluster.ascii_art()) /<>/doc/examples/calculate_UPGMA_cluster.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mycluster.write("test_upgma.tree") /<>/doc/examples/calculate_UPGMA_cluster.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("test_upgma.tree") /<>/doc/examples/calculate_neigbourjoining_tree.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/calculate_neigbourjoining_tree.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve import distance from cogent3.phylo import nj /<>/doc/examples/calculate_neigbourjoining_tree.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model /<>/doc/examples/calculate_neigbourjoining_tree.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") /<>/doc/examples/calculate_neigbourjoining_tree.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=get_model("HKY85")) d.run(show_progress=False) /<>/doc/examples/calculate_neigbourjoining_tree.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mytree = nj.nj(d.get_pairwise_distances(), show_progress=False) print(mytree.ascii_art()) /<>/doc/examples/calculate_neigbourjoining_tree.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mytree.write("test_nj.tree") /<>/doc/examples/calculate_neigbourjoining_tree.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("test_nj.tree") /<>/doc/examples/calculate_pairwise_distances.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/calculate_pairwise_distances.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve import distance /<>/doc/examples/calculate_pairwise_distances.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import HKY85 /<>/doc/examples/calculate_pairwise_distances.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") /<>/doc/examples/calculate_pairwise_distances.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) d.get_pairwise_distances() /<>/doc/examples/calculate_pairwise_distances.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d.write("dists_for_phylo.phylip", format="phylip") /<>/doc/examples/calculate_pairwise_distances.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import pickle with open("dists_for_phylo.pickle", "wb") as f: pickle.dump(d.get_pairwise_distances(), f) /<>/doc/examples/calculate_pairwise_distances.rst:61: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os for file_name in "dists_for_phylo.phylip", "dists_for_phylo.pickle": os.remove(file_name) /<>/doc/examples/codon_models.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/codon_models.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model /<>/doc/examples/codon_models.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tf = get_model("GY94") nf = get_model("MG94GTR") cnf = get_model("CNFGTR") /<>/doc/examples/codon_models.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") tree = load_tree("data/primate_brca1.tree") /<>/doc/examples/codon_models.rst:64: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = cnf.make_likelihood_function(tree, digits=2, space=3) lf.set_param_rule("omega", is_constant=True, value=1.0) /<>/doc/examples/codon_models.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: optimiser_args = dict( local=True, max_restarts=5, tolerance=1e-8, show_progress=False ) lf.set_alignment(aln) lf.optimise(**optimiser_args) lf /<>/doc/examples/codon_models.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: neutral_lnL = lf.get_log_likelihood() neutral_nfp = lf.get_num_free_params() lf.set_param_rule("omega", is_constant=False) lf.optimise(**optimiser_args) non_neutral_lnL = lf.get_log_likelihood() non_neutral_nfp = lf.get_num_free_params() lf /<>/doc/examples/codon_models.rst:104: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from scipy.stats.distributions import chi2 LR = 2 * (non_neutral_lnL - neutral_lnL) df = non_neutral_nfp - neutral_nfp print(chi2.sf(LR, df)) /<>/doc/examples/codon_models.rst:114: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Chimpanzee", "Human"], outgroup_name="Galago", clade=True ) lf.optimise(**optimiser_args) lf chimp_human_clade_lnL = lf.get_log_likelihood() chimp_human_clade_nfp = lf.get_num_free_params() /<>/doc/examples/codon_models.rst:124: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (chimp_human_clade_lnL - non_neutral_lnL) df = chimp_human_clade_nfp - non_neutral_nfp print(chi2.sf(LR, df)) /<>/doc/examples/codon_models.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = cnf.make_likelihood_function(tree, digits=2, space=3) lf.set_alignment(aln) lf.optimise(**optimiser_args) non_neutral_lnL = lf.get_log_likelihood() non_neutral_nfp = lf.get_num_free_params() /<>/doc/examples/codon_models.rst:149: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: annot_tree = lf.get_annotated_tree() omega_mle = lf.get_param_value("omega") /<>/doc/examples/codon_models.rst:156: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf = cnf.make_likelihood_function( annot_tree, bins=["neutral", "adaptive"], digits=2, space=3 ) /<>/doc/examples/codon_models.rst:164: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: epsilon = 1e-6 /<>/doc/examples/codon_models.rst:170: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_param_rule("omega", bin="neutral", upper=1, init=omega_mle) rate_lf.set_param_rule( "omega", bin="adaptive", lower=1 + epsilon, upper=100, init=1 + 2 * epsilon ) /<>/doc/examples/codon_models.rst:179: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_param_rule("bprobs", init=[1 - epsilon, epsilon]) /<>/doc/examples/codon_models.rst:185: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_alignment(aln) rate_lf.optimise(**optimiser_args) rate_lnL = rate_lf.get_log_likelihood() rate_nfp = rate_lf.get_num_free_params() LR = 2 * (rate_lnL - non_neutral_lnL) df = rate_nfp - non_neutral_nfp rate_lf /<>/doc/examples/codon_models.rst:195: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(chi2.sf(LR, df)) /<>/doc/examples/codon_models.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pp = rate_lf.get_bin_probs() /<>/doc/examples/codon_models.rst:212: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from IPython.core.display import HTML from numpy import array from cogent3 import make_table header = ['Site Class', 'Proportion', 'Background Edges', 'Foreground Edges'] data = {'Site Class': array(['0', '1', '2a', '2b'], dtype=' 1', '0 < omega0 < 1'], dtype='>/doc/examples/codon_models.rst:232: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf = cnf.make_likelihood_function(tree, bins=["0", "1"], digits=2, space=3) rate_lf.set_param_rule("omega", bin="0", upper=1.0 - epsilon, init=1 - epsilon) rate_lf.set_param_rule("omega", bins="1", is_constant=True, value=1.0) rate_lf.set_alignment(aln) rate_lf.optimise(**optimiser_args) tables = rate_lf.get_statistics(with_titles=True) for table in tables: if "bin" in table.title: print(table) /<>/doc/examples/codon_models.rst:246: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: globals = [t for t in tables if "global" in t.title][0] globals = dict(zip(globals.header, globals.tolist()[0])) bin_params = [t for t in tables if "bin" in t.title][0] rate_class_omegas = dict(bin_params.tolist(["bin", "omega"])) rate_class_probs = dict(bin_params.tolist(["bin", "bprobs"])) lengths = [t for t in tables if "edge" in t.title][0] lengths = dict(lengths.tolist(["edge", "length"])) /<>/doc/examples/codon_models.rst:258: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_branch_lf = cnf.make_likelihood_function( tree, bins=["0", "1", "2a", "2b"], digits=2, space=3 ) /<>/doc/examples/codon_models.rst:266: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for branch, length in lengths.items(): rate_branch_lf.set_param_rule("length", edge=branch, init=length) /<>/doc/examples/codon_models.rst:273: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for param, mle in globals.items(): rate_branch_lf.set_param_rule(param, init=mle) /<>/doc/examples/codon_models.rst:280: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_branch_lf.set_param_rule( "omega", bins=["0", "2a"], upper=1.0, init=rate_class_omegas["0"] ) rate_branch_lf.set_param_rule( "omega", bins=["1", "2b"], is_constant=True, value=1.0 ) rate_branch_lf.set_param_rule( "omega", bins=["2a", "2b"], edges=["Chimpanzee", "Human"], init=99, lower=1.0, upper=100.0, is_constant=False, ) /<>/doc/examples/codon_models.rst:300: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_branch_lf.set_param_rule( "bprobs", init=[ rate_class_probs["0"] - epsilon, rate_class_probs["1"] - epsilon, epsilon, epsilon, ], ) /<>/doc/examples/codon_models.rst:314: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_branch_lf.set_alignment(aln) /<>/doc/examples/coevolution.rst:10: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs from cogent3.core.alignment import ArrayAlignment from cogent3.evolve.coevolution import validate_alignment aln = make_aligned_seqs( {"1": "GAA", "2": "CTA", "3": "CTC", "4": "-TC"}, moltype="protein", array_align=True, ) validate_alignment(aln) /<>/doc/examples/coevolution.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs from cogent3.core.alignment import ArrayAlignment aln = make_aligned_seqs( {"1": "AAA", "2": "CTA", "3": "CTC", "4": "-TC"}, moltype="protein", array_align=True, ) /<>/doc/examples/coevolution.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.coevolution import ( coevolve_pair, coevolve_pair_functions, ) coevolve_pair(coevolve_pair_functions["mi"], aln, pos1=1, pos2=2) /<>/doc/examples/coevolution.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.coevolution import ( coevolve_pair, coevolve_pair_functions, ) coevolve_pair(coevolve_pair_functions["sca"], aln, pos1=1, pos2=2, cutoff=0.5) /<>/doc/examples/coevolution.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.coevolution import ( coevolve_position, coevolve_position_functions, ) coevolve_position(coevolve_position_functions["mi"], aln, position=1) /<>/doc/examples/coevolution.rst:71: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.coevolution import ( coevolve_alignment, coevolve_alignment_functions, ) coevolve_alignment(coevolve_alignment_functions["mi"], aln) /<>/doc/examples/coevolution.rst:82: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(coevolve_pair_functions.keys()) /<>/doc/examples/coevolution.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.coevolution import ( coevolve_alignment_functions, coevolve_alignments, ) aln1 = make_aligned_seqs( { "human+protein1": "AAA", "pig+protein1": "CTA", "chicken+protein1": "CTC", "echidna+weird_db_identifier": "-TC", }, moltype="protein", array_align=True, ) aln2 = make_aligned_seqs( { "pig+protein2": "AAAY", "chicken+protein2": "CTAY", "echidna+protein2": "CTCF", "human+protein2": "-TCF", }, moltype="protein", array_align=True, ) coevolve_alignments(coevolve_alignment_functions["mi"], aln1, aln2) /<>/doc/examples/complete_seq_features.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA from cogent3.core.annotation import Feature s = DNA.make_seq("AAGAAGAAGACCCCCAAAAAAAAAATTTTTTTTTTAAAAAAAAAAAAA", name="Orig") exon1 = s.add_annotation(Feature, "exon", "fred", [(10, 15)]) exon2 = s.add_annotation(Feature, "exon", "trev", [(30, 40)]) /<>/doc/examples/complete_seq_features.rst:19: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: s[exon1] exon1.get_slice() /<>/doc/examples/complete_seq_features.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: exons = s.get_annotations_matching("exon") print(exons) /<>/doc/examples/complete_seq_features.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dont_exist = s.get_annotations_matching("dont_exist") dont_exist s[dont_exist] /<>/doc/examples/complete_seq_features.rst:41: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s.get_region_covering_all(exons)) print(s.get_region_covering_all(exons).get_shadow()) /<>/doc/examples/complete_seq_features.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: s.get_region_covering_all(exons).get_slice() /<>/doc/examples/complete_seq_features.rst:54: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: s[exon1, exon2] /<>/doc/examples/complete_seq_features.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError print(s.get_region_covering_all(exons + exons)) s[exon1, exon1, exon1, exon1, exon1] /<>/doc/examples/complete_seq_features.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError s[15:20, 5:16] /<>/doc/examples/complete_seq_features.rst:75: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: exon1[0:3].get_slice() /<>/doc/examples/complete_seq_features.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: c = s[exon1[4:]] + s print(len(c)) for feat in c.annotations: print(feat) /<>/doc/examples/complete_seq_features.rst:90: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError print(c[exon1]) /<>/doc/examples/complete_seq_features.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: len(s.annotations) region = s.get_region_covering_all(exons) len(s.annotations) region.attach() len(s.annotations) region.detach() len(s.annotations) /<>/doc/examples/complete_seq_features.rst:109: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: plus = DNA.make_seq("AAGGGGAAAACCCCCAAAAAAAAAATTTTTTTTTTAAA", name="plus") plus_cds = plus.add_annotation(Feature, "CDS", "gene", [(2, 6), (10, 15), (25, 35)]) print(plus_cds.get_slice()) minus = plus.rc() minus_cds = minus.get_annotations_matching("CDS")[0] print(minus_cds.get_slice()) /<>/doc/examples/complete_seq_features.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) print(aln) exon = aln.get_seq("x").add_annotation(Feature, "exon", "fred", [(3, 8)]) aln_exons = aln.get_annotations_from_seq("x", "exon") aln_exons = aln.get_annotations_from_any_seq("exon") /<>/doc/examples/complete_seq_features.rst:134: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(exon) print(aln_exons[0]) print(aln_exons[0].get_slice()) aln_exons[0].attach() len(aln.annotations) /<>/doc/examples/complete_seq_features.rst:144: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: exons = aln.get_projected_annotations("y", "exon") print(exons) print(aln.get_seq("y")[exons[0].map.without_gaps()]) /<>/doc/examples/complete_seq_features.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( [["x", "-AAAAAAAAA"], ["y", "TTTT--CCCC"]], array_align=False ) s = DNA.make_seq("AAAAAAAAA", name="x") exon = s.add_annotation(Feature, "exon", "fred", [(3, 8)]) exon = aln.get_seq("x").copy_annotations(s) aln_exons = list(aln.get_annotations_from_seq("x", "exon")) print(aln_exons) /<>/doc/examples/complete_seq_features.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: exon = aln.get_seq("y").copy_annotations(s) aln_exons = list(aln.get_annotations_from_seq("y", "exon")) print(aln_exons) print(aln[aln_exons]) /<>/doc/examples/complete_seq_features.rst:174: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs([["x", "-AAAA"], ["y", "TTTTT"]], array_align=False) seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x") exon = seq.add_feature("exon", "A", [(5, 8)]) aln.get_seq("x").copy_annotations(seq) copied = list(aln.get_annotations_from_seq("x", "exon")) copied copied[0].get_slice() /<>/doc/examples/complete_seq_features.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( [["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x") match_exon = seq.add_feature("exon", "A", [(5, 8)]) aln.get_seq("y").copy_annotations(seq) copied = list(aln.get_annotations_from_seq("y", "exon")) copied /<>/doc/examples/complete_seq_features.rst:199: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( [["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) diff_len_seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCCCCCCCCCC", "x") nonmatch = diff_len_seq.add_feature("repeat", "A", [(12, 14)]) aln.get_seq("y").copy_annotations(diff_len_seq) copied = list(aln.get_annotations_from_seq("y", "repeat")) copied /<>/doc/examples/complete_seq_features.rst:212: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( [["x", "-AAAAAAAAA"], ["y", "------TTTT"]], array_align=False ) exon = aln.get_seq("x").add_feature("exon", "fred", [(3, 8)]) aln_exons = list(aln.get_annotations_from_seq("x", "exon")) print(aln_exons) print(aln_exons[0].get_slice()) aln = make_aligned_seqs( [["x", "-AAAAAAAAA"], ["y", "TTTT--T---"]], array_align=False ) exon = aln.get_seq("x").add_feature("exon", "fred", [(3, 8)]) aln_exons = list(aln.get_annotations_from_seq("x", "exon")) print(aln_exons[0].get_slice()) /<>/doc/examples/complete_seq_features.rst:230: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( [["x", "C-CCCAAAAA"], ["y", "-T----TTTT"]], moltype="dna", array_align=False ) print(aln) exon = aln.get_seq("x").add_feature("exon", "ex1", [(0, 4)]) print(exon) print(exon.get_slice()) aln_exons = list(aln.get_annotations_from_seq("x", "exon")) print(aln_exons) print(aln_exons[0].get_slice()) /<>/doc/examples/complete_seq_features.rst:245: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(aln_exons[0].as_one_span().get_slice()) /<>/doc/examples/complete_seq_features.rst:251: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln_rc = aln.rc() rc_exons = list(aln_rc.get_annotations_from_any_seq("exon")) print(aln_rc[rc_exons]) # not using as_one_span, so gap removed from x print(aln_rc[rc_exons[0].as_one_span()]) /<>/doc/examples/complete_seq_features.rst:260: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_exons = aln.get_region_covering_all(aln_exons) coords = all_exons.get_coordinates() assert coords == [(0, 1), (2, 5)] /<>/doc/examples/complete_seq_features.rst:270: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( [["x", "C-CCCAAAAAGGGAA"], ["y", "-T----TTTTG-GTT"]], array_align=False ) print(aln) exon = aln.get_seq("x").add_feature("exon", "norwegian", [(0, 4)]) print(exon.get_slice()) repeat = aln.get_seq("x").add_feature("repeat", "blue", [(9, 12)]) print(repeat.get_slice()) repeat = aln.get_seq("y").add_feature("repeat", "frog", [(5, 7)]) print(repeat.get_slice()) /<>/doc/examples/complete_seq_features.rst:285: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(aln.get_seq("x").with_masked_annotations("exon", mask_char="?")) print(aln.get_seq("x").with_masked_annotations("exon", mask_char="?", shadow=True)) print(aln.get_seq("x").with_masked_annotations(["exon", "repeat"], mask_char="?")) print( aln.get_seq("x").with_masked_annotations( ["exon", "repeat"], mask_char="?", shadow=True ) ) print(aln.get_seq("y").with_masked_annotations("exon", mask_char="?")) print(aln.get_seq("y").with_masked_annotations("repeat", mask_char="?")) print( aln.get_seq("y").with_masked_annotations("repeat", mask_char="?", shadow=True) ) /<>/doc/examples/complete_seq_features.rst:303: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(aln.with_masked_annotations("exon", mask_char="?")) print(aln.with_masked_annotations("exon", mask_char="?", shadow=True)) print(aln.with_masked_annotations("repeat", mask_char="?")) print(aln.with_masked_annotations("repeat", mask_char="?", shadow=True)) print(aln.with_masked_annotations(["repeat", "exon"], mask_char="?")) print(aln.with_masked_annotations(["repeat", "exon"], shadow=True)) /<>/doc/examples/complete_seq_features.rst:314: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data = [["human", "CGAAACGTTT"], ["mouse", "CTAAACGTCG"]] as_series = make_aligned_seqs(data, array_align=False) as_items = make_aligned_seqs(data, array_align=False) /<>/doc/examples/complete_seq_features.rst:322: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: as_series.get_seq("human").add_feature("cpgsite", "cpg", [(0, 2), (5, 7)]) as_series.get_seq("mouse").add_feature("cpgsite", "cpg", [(5, 7), (8, 10)]) /<>/doc/examples/complete_seq_features.rst:329: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: as_items.get_seq("human").add_feature("cpgsite", "cpg", [(0, 2)]) as_items.get_seq("human").add_feature("cpgsite", "cpg", [(5, 7)]) as_items.get_seq("mouse").add_feature("cpgsite", "cpg", [(5, 7)]) as_items.get_seq("mouse").add_feature("cpgsite", "cpg", [(8, 10)]) /<>/doc/examples/complete_seq_features.rst:338: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: serial = as_series.with_masked_annotations(["cpgsite"]) print(serial) itemwise = as_items.with_masked_annotations(["cpgsite"]) print(itemwise) /<>/doc/examples/complete_seq_features.rst:347: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(plus.with_masked_annotations("CDS")) print(minus.with_masked_annotations("CDS")) /<>/doc/examples/empirical_protein_models.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/empirical_protein_models.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_tree from cogent3.evolve.substitution_model import EmpiricalProteinMatrix from cogent3.parse.paml_matrix import PamlMatrixParser /<>/doc/examples/empirical_protein_models.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: treestring = "(((rabbit,rat),human),goat-cow,marsupial);" t = make_tree(treestring) /<>/doc/examples/empirical_protein_models.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/abglobin_aa.phylip", moltype="protein") /<>/doc/examples/empirical_protein_models.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: matrix_file = open("data/dayhoff.dat") /<>/doc/examples/empirical_protein_models.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: empirical_matrix, empirical_frequencies = PamlMatrixParser(matrix_file) /<>/doc/examples/empirical_protein_models.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = EmpiricalProteinMatrix(empirical_matrix, empirical_frequencies) /<>/doc/examples/empirical_protein_models.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = sm.make_likelihood_function(t) lf.set_alignment(al) lf.optimise(show_progress=False) lf /<>/doc/examples/hmm_par_heterogeneity.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/hmm_par_heterogeneity.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.substitution_model import ( TimeReversibleNucleotide, predicate, ) from scipy.stats.distributions import chi2 /<>/doc/examples/hmm_par_heterogeneity.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/long_testseqs.fasta") tree = load_tree("data/test.tree") /<>/doc/examples/hmm_par_heterogeneity.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: MotifChange = predicate.MotifChange treat_gap = dict(recode_gaps=True, model_gaps=False) kappa = (~MotifChange("R", "Y")).aliased("kappa") model = TimeReversibleNucleotide(predicates=[kappa], **treat_gap) /<>/doc/examples/hmm_par_heterogeneity.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf_one = model.make_likelihood_function(tree, digits=2, space=3) lf_one.set_alignment(aln) lf_one.optimise(show_progress=False) lnL_one = lf_one.get_log_likelihood() df_one = lf_one.get_num_free_params() lf_one /<>/doc/examples/hmm_par_heterogeneity.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bin_submod = TimeReversibleNucleotide( predicates=[kappa], ordered_param="rate", distribution="gamma", **treat_gap ) lf_bins = bin_submod.make_likelihood_function( tree, bins=2, sites_independent=True, digits=2, space=3 ) lf_bins.set_param_rule("bprobs", is_constant=True) lf_bins.set_alignment(aln) lf_bins.optimise(local=True, show_progress=False) lnL_bins = lf_bins.get_log_likelihood() df_bins = lf_bins.get_num_free_params() assert df_bins == 9 lf_bins /<>/doc/examples/hmm_par_heterogeneity.rst:86: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf_patches = bin_submod.make_likelihood_function( tree, bins=2, sites_independent=False, digits=2, space=3 ) lf_patches.set_param_rule("bprobs", is_constant=True) lf_patches.set_alignment(aln) lf_patches.optimise(local=True, show_progress=False) lnL_patches = lf_patches.get_log_likelihood() df_patches = lf_patches.get_num_free_params() lf_patches /<>/doc/examples/hmm_par_heterogeneity.rst:100: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = lambda alt, null: 2 * (alt - null) /<>/doc/examples/hmm_par_heterogeneity.rst:106: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lr = LR(lnL_bins, lnL_one) lr /<>/doc/examples/hmm_par_heterogeneity.rst:111: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print("%.4f" % chi2.sf(lr, df_patches - df_bins)) /<>/doc/examples/hmm_par_heterogeneity.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = lf_patches.get_param_value("bprobs") print("%.1f : %.1f" % tuple(bprobs)) /<>/doc/examples/hmm_par_heterogeneity.rst:124: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pp = lf_patches.get_bin_probs() /<>/doc/examples/hmm_par_heterogeneity.rst:130: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(pp["bin0"][20]) /<>/doc/examples/hmm_par_heterogeneity.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from numpy import array single_kappa = lf_one.get_param_value("kappa") /<>/doc/examples/hmm_par_heterogeneity.rst:151: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: kappa_bin_submod = TimeReversibleNucleotide(predicates=[kappa], **treat_gap) lf_kappa = kappa_bin_submod.make_likelihood_function( tree, bins=["slow", "fast"], sites_independent=False, digits=1, space=3 ) /<>/doc/examples/hmm_par_heterogeneity.rst:160: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: epsilon = 1e-6 lf_kappa.set_param_rule( kappa, init=single_kappa - epsilon, upper=single_kappa, bin="slow" ) lf_kappa.set_param_rule( kappa, init=single_kappa + epsilon, lower=single_kappa, bin="fast" ) /<>/doc/examples/hmm_par_heterogeneity.rst:172: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf_kappa.set_param_rule("bprobs", init=array([1.0 - epsilon, 0.0 + epsilon])) lf_kappa.set_alignment(aln) lf_kappa.optimise(local=True, show_progress=False) lf_kappa /<>/doc/examples/manipulating_tree_nodes.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree, make_tree from cogent3.core.tree import PhyloNode from cogent3.parse.tree import DndParser /<>/doc/examples/manipulating_tree_nodes.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree_string = "(B:0.2,(C:0.3,D:0.4)E:0.5)F;" complex_tree_string = "(((363564 AB294167.1 Alkalibacterium putridalgicola:0.0028006,55874 AB083411.1 Marinilactibacillus psychrotolerans:0.0022089):0.40998,(15050 Y10772.1 Facklamia hominis:0.32304,(132509 AY707780.1 Aerococcus viridans:0.58815,((143063 AY879307.1 Abiotrophia defectiva:0.5807,83619 AB042060.1 Bacillus schlegelii:0.23569):0.03586,169722 AB275483.1 Fibrobacter succinogenes:0.38272):0.06516):0.03492):0.14265):0.63594,(3589 M62687.1 Fibrobacter intestinalis:0.65866,314063 CP001146.1 Dictyoglomus thermophilum:0.38791):0.32147,276579 EU652053.1 Thermus scotoductus:0.57336);" simple_tree = make_tree(simple_tree_string) complex_tree = DndParser(complex_tree_string, PhyloNode) /<>/doc/examples/manipulating_tree_nodes.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(simple_tree.ascii_art()) /<>/doc/examples/manipulating_tree_nodes.rst:41: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: A_node = PhyloNode(name="A", Length=0.1) /<>/doc/examples/manipulating_tree_nodes.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(simple_tree.children) /<>/doc/examples/manipulating_tree_nodes.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree.children[1].remove("C") /<>/doc/examples/manipulating_tree_nodes.rst:59: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree.children[1].insert(0, A_node) /<>/doc/examples/manipulating_tree_nodes.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(simple_tree.ascii_art()) /<>/doc/examples/manipulating_tree_nodes.rst:71: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree.children[1].remove("A") print(simple_tree.ascii_art()) /<>/doc/examples/manipulating_tree_nodes.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree.prune() print(simple_tree.ascii_art()) /<>/doc/examples/manipulating_tree_nodes.rst:90: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for n in complex_tree.iter_tips(): n.name = n.name.split()[2] + " " + n.name.split()[3] /<>/doc/examples/manipulating_tree_nodes.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(complex_tree.ascii_art(show_internal=False)) /<>/doc/examples/manipulating_tree_nodes.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tips = complex_tree.tips() /<>/doc/examples/manipulating_tree_nodes.rst:111: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tips_to_delete = [] AEROCOCCUS_INDEX = 3 for n in tips: if tips[AEROCOCCUS_INDEX].distance(n) > 1.8: tips_to_delete.append(n) /<>/doc/examples/manipulating_tree_nodes.rst:121: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for n in tips_to_delete: n.parent.remove(n) complex_tree.prune() /<>/doc/examples/manipulating_tree_nodes.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(complex_tree.ascii_art(show_internal=False)) /<>/doc/examples/neutral_test.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/neutral_test.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model from scipy.stats.distributions import chi2 /<>/doc/examples/neutral_test.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") t = load_tree("data/test.tree") /<>/doc/examples/neutral_test.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("MG94GTR") /<>/doc/examples/neutral_test.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = sm.make_likelihood_function(t, digits=2, space=2) /<>/doc/examples/neutral_test.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_alignment(al) /<>/doc/examples/neutral_test.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(global_tolerance=1.0, show_progress=False) /<>/doc/examples/neutral_test.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /<>/doc/examples/neutral_test.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: null_lnL = lf.get_log_likelihood() null_nfp = lf.get_num_free_params() /<>/doc/examples/neutral_test.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", is_independent=True) /<>/doc/examples/neutral_test.rst:71: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=True, show_progress=False) /<>/doc/examples/neutral_test.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /<>/doc/examples/neutral_test.rst:83: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: at = lf.get_annotated_tree() /<>/doc/examples/neutral_test.rst:89: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (lf.get_log_likelihood() - null_lnL) df = lf.get_num_free_params() - null_nfp P = chi2.sf(LR, df) /<>/doc/examples/neutral_test.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(f"Likelihood ratio statistic = {LR}") print(f"degrees-of-freedom = {df}") print(f"probability = {P}") /<>/doc/examples/parametric_bootstrap.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/parametric_bootstrap.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve import bootstrap from cogent3.evolve.models import HKY85 /<>/doc/examples/parametric_bootstrap.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: def create_alt_function(): t = load_tree("data/test.tree") sm = HKY85() return sm.make_likelihood_function(t) /<>/doc/examples/parametric_bootstrap.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: def create_null_function(): lf = create_alt_function() # set the local clock for humans & howler monkey lf.set_local_clock("Human", "HowlerMon") return lf /<>/doc/examples/parametric_bootstrap.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/long_testseqs.fasta") /<>/doc/examples/parametric_bootstrap.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP = bootstrap.EstimateProbability( create_null_function(), create_alt_function(), aln ) /<>/doc/examples/parametric_bootstrap.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP.set_num_replicates(5) /<>/doc/examples/parametric_bootstrap.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP.run(show_progress=False) /<>/doc/examples/parametric_bootstrap.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: p = estimateP.get_estimated_prob() /<>/doc/examples/parametric_bootstrap.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print("%.2f, %.2f" % estimateP.get_observed_lnL()) /<>/doc/examples/period_estimation.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import numpy numpy.random.seed(11) /<>/doc/examples/period_estimation.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import numpy t = numpy.arange(0, 10, 0.1) n = numpy.random.randn(len(t)) nse = numpy.convolve(n, numpy.exp(-t / 0.05)) * 0.1 nse = nse[: len(t)] sig = numpy.sin(2 * numpy.pi * t) + nse /<>/doc/examples/period_estimation.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import dft pwr, period = dft(sig) print(period) print(pwr) /<>/doc/examples/period_estimation.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pwr = abs(pwr) max_pwr, max_period = sorted(zip(pwr, period))[-1] print(max_pwr, max_period) /<>/doc/examples/period_estimation.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import auto_corr pwr, period = auto_corr(sig) print(period) print(pwr) /<>/doc/examples/period_estimation.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: max_pwr, max_period = sorted(zip(pwr, period))[-1] print(max_pwr, max_period) /<>/doc/examples/period_estimation.rst:89: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: s = ( "ATCGTTGGGACCGGTTCAAGTTTTGGAACTCGCAAGGGGTGAATGGTCTTCGTCTAACGCTGG" "GGAACCCTGAATCGTTGTAACGCTGGGGTCTTTAACCGTTCTAATTTAACGCTGGGGGGTTCT" "AATTTTTAACCGCGGAATTGCGTC" ) /<>/doc/examples/period_estimation.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import SeqToSymbols seq_to_symbols = SeqToSymbols(["AA", "TT", "AT"]) symbols = seq_to_symbols(s) len(symbols) == len(s) symbols /<>/doc/examples/period_estimation.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import ipdft powers, periods = ipdft(symbols) powers /<>/doc/examples/period_estimation.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /<>/doc/examples/period_estimation.rst:123: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import auto_corr, hybrid powers, periods = auto_corr(symbols) powers /<>/doc/examples/period_estimation.rst:130: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /<>/doc/examples/period_estimation.rst:134: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers, periods = hybrid(symbols) powers /<>/doc/examples/period_estimation.rst:139: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /<>/doc/examples/period_estimation.rst:151: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import goertzel pwr = goertzel(sig, 10) print(pwr) /<>/doc/examples/period_estimation.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers, periods = auto_corr(symbols) llim = 2 period5 = 5 - llim periods[period5] /<>/doc/examples/period_estimation.rst:172: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers[period5] /<>/doc/examples/period_estimation.rst:178: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import goertzel period = 4 power = goertzel(symbols, period) ipdft_powers, periods = ipdft(symbols) ipdft_power = abs(ipdft_powers[period - llim]) round(power, 6) == round(ipdft_power, 6) power /<>/doc/examples/period_estimation.rst:191: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: power = hybrid(symbols, period=period) power /<>/doc/examples/period_estimation.rst:204: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import Goertzel goertzel_calc = Goertzel(len(sig), period=10) /<>/doc/examples/period_estimation.rst:212: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import blockwise_bootstrap obs_stat, p = blockwise_bootstrap( sig, calc=goertzel_calc, block_size=10, num_reps=1000 ) print(obs_stat) print(p) /<>/doc/examples/period_estimation.rst:230: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import Hybrid hybrid_calculator = Hybrid(len(s), period=4) /<>/doc/examples/period_estimation.rst:240: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import SeqToSymbols seq_to_symbols = SeqToSymbols(["AA", "TT", "AT"], length=len(s)) /<>/doc/examples/period_estimation.rst:248: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import blockwise_bootstrap stat, p = blockwise_bootstrap( s, calc=hybrid_calculator, block_size=10, num_reps=1000, seq_to_symbols=seq_to_symbols, ) print(stat) p < 0.1 /<>/doc/examples/phylo_by_ls.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/phylo_by_ls.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pickle from cogent3 import load_aligned_seqs from cogent3.evolve import distance from cogent3.evolve.fast_distance import DistanceMatrix from cogent3.evolve.models import HKY85 al = load_aligned_seqs("data/long_testseqs.fasta") d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) with open("dists_for_phylo.pickle", "wb") as f: pickle.dump(d.get_pairwise_distances(), f) /<>/doc/examples/phylo_by_ls.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import pickle from cogent3.phylo import least_squares /<>/doc/examples/phylo_by_ls.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: with open("dists_for_phylo.pickle", "rb") as f: dists = pickle.load(f) /<>/doc/examples/phylo_by_ls.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls = least_squares.WLS(dists) /<>/doc/examples/phylo_by_ls.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls_distance_matrix = least_squares.WLS(DistanceMatrix(dists)) ls_pairwise_matrix = least_squares.WLS(dists.to_dict()) /<>/doc/examples/phylo_by_ls.rst:67: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: score, tree = ls.trex(a=5, k=1, show_progress=False) assert score < 1e-4 /<>/doc/examples/phylo_by_ls.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: trees = ls.trex(a=5, k=5, return_all=True, show_progress=False) /<>/doc/examples/phylo_by_ls.rst:85: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(len(trees)) /<>/doc/examples/phylo_by_ls.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: wls_stats = [tree[0] for tree in trees] /<>/doc/examples/phylo_by_ls.rst:103: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: t1 = trees[0][1].balanced() t2 = trees[1][1].balanced() print(t1.ascii_art()) /<>/doc/examples/phylo_by_ls.rst:109: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(t2.ascii_art()) /<>/doc/examples/phylo_by_ls.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree query_tree = make_tree( "((Human:.2,DogFaced:.2):.3,(NineBande:.1, Mouse:.5):.2,HowlerMon:.1)" ) /<>/doc/examples/phylo_by_ls.rst:130: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.evaluate_tree(query_tree) /<>/doc/examples/phylo_by_ls.rst:136: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: wls, t = ls.evaluate_topology(query_tree) assert "%.4f" % wls == "0.0084" /<>/doc/examples/phylo_by_ls.rst:148: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("dists_for_phylo.pickle") /<>/doc/examples/rate_heterogeneity.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/rate_heterogeneity.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.substitution_model import TimeReversibleNucleotide /<>/doc/examples/rate_heterogeneity.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide(equal_motif_probs=True) tree = load_tree("data/test.tree") lf = model.make_likelihood_function(tree) lf.set_param_rule("length", value=0.6, is_constant=True) aln1 = lf.simulate_alignment(sequence_length=10000) lf.set_param_rule("length", value=0.2, is_constant=True) aln2 = lf.simulate_alignment(sequence_length=10000) aln3 = aln1 + aln2 /<>/doc/examples/rate_heterogeneity.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide( equal_motif_probs=True, ordered_param="rate", distribution="free" ) lf = model.make_likelihood_function(tree, bins=2, digits=2, space=3) lf.set_alignment(aln3) lf.optimise(local=True, max_restarts=2, show_progress=False) /<>/doc/examples/rate_heterogeneity.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = [t for t in lf.get_statistics() if "bin" in t.title][0] bprobs /<>/doc/examples/rate_heterogeneity.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide( equal_motif_probs=True, ordered_param="rate", distribution="gamma" ) lf = model.make_likelihood_function(tree, bins=4) lf.set_param_rule("bprobs", is_constant=True) lf.set_alignment(aln3) lf.optimise(local=True, max_restarts=2, show_progress=False) /<>/doc/examples/relative_rate.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/relative_rate.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model from scipy.stats.distributions import chi2 /<>/doc/examples/relative_rate.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/long_testseqs.fasta") t = load_tree(filename="data/test.tree") /<>/doc/examples/relative_rate.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("HKY85") /<>/doc/examples/relative_rate.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = sm.make_likelihood_function(t, digits=2, space=3) /<>/doc/examples/relative_rate.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_local_clock("Human", "HowlerMon") /<>/doc/examples/relative_rate.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_alignment(aln) /<>/doc/examples/relative_rate.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False) /<>/doc/examples/relative_rate.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_name("clock") lf /<>/doc/examples/relative_rate.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: null_lnL = lf.get_log_likelihood() null_nfp = lf.get_num_free_params() /<>/doc/examples/relative_rate.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("length", is_independent=True) /<>/doc/examples/relative_rate.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False) /<>/doc/examples/relative_rate.rst:84: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_name("non clock") lf /<>/doc/examples/relative_rate.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (lf.get_log_likelihood() - null_lnL) df = lf.get_num_free_params() - null_nfp P = chi2.sf(LR, df) /<>/doc/examples/relative_rate.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print("Likelihood ratio statistic = ", LR) print("degrees-of-freedom = ", df) print("probability = ", P) /<>/doc/examples/scope_model_params_on_trees.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/scope_model_params_on_trees.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import MG94HKY aln = load_aligned_seqs("data/long_testseqs.fasta") tree = load_tree("data/test.tree") /<>/doc/examples/scope_model_params_on_trees.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = MG94HKY() lf = sm.make_likelihood_function(tree, digits=2, space=3) lf.set_alignment(aln) /<>/doc/examples/scope_model_params_on_trees.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tree.ascii_art()) /<>/doc/examples/scope_model_params_on_trees.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["DogFaced", "Mouse"], outgroup_name="Human", init=2.0, clade=True, ) lf /<>/doc/examples/scope_model_params_on_trees.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", init=1.0) lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", init=2.0, stem=True, clade=False, ) lf /<>/doc/examples/scope_model_params_on_trees.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: lf.set_param_rule("omega", init=1.0) /<>/doc/examples/scope_model_params_on_trees.rst:96: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", init=2.0, stem=True, clade=True, ) lf /<>/doc/examples/scope_model_params_on_trees.rst:160: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: lf.set_param_rule("omega", init=1.0) /<>/doc/examples/scope_model_params_on_trees.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, value=1.0, is_constant=True, ) lf.optimise(local=True, show_progress=False) lf /<>/doc/examples/scope_model_params_on_trees.rst:180: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, is_constant=False, ) lf.optimise(local=True, show_progress=False) lf /<>/doc/examples/scope_model_params_on_trees.rst:194: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, is_independent=True, ) lf.optimise(local=True, show_progress=False) lf /<>/doc/examples/scope_model_params_on_trees.rst:208: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", is_independent=True) lf.optimise(local=True, show_progress=False) lf /<>/doc/examples/seq_features.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s = DNA.make_seq("aagaagaagacccccaaaaaaaaaattttttttttaaaaaaaaaaaaa", name="Orig") exon1 = s.add_feature("exon", "exon1", [(10, 15)]) exon2 = s.add_feature("exon", "exon2", [(30, 40)]) /<>/doc/examples/seq_features.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core.annotation import Feature s2 = DNA.make_seq("aagaagaagacccccaaaaaaaaaattttttttttaaaaaaaaaaaaa", name="Orig2") exon3 = s2.add_annotation(Feature, "exon", "exon1", [(35, 40)]) /<>/doc/examples/seq_features.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: s[exon1] /<>/doc/examples/seq_features.rst:41: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: exons = s.get_annotations_matching("exon") print(exons) /<>/doc/examples/seq_features.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s.get_region_covering_all(exons)) s.get_region_covering_all(exons).get_slice() /<>/doc/examples/seq_features.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s.get_region_covering_all(exons).get_shadow().get_slice()) /<>/doc/examples/seq_features.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: exon1[0:3].get_slice() /<>/doc/examples/simple.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/simple.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_tree from cogent3.evolve.models import get_model model = get_model("HKY85") aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") tree = make_tree(tip_names=aln.names) lf = model.make_likelihood_function(tree) lf.set_alignment(aln) lf.optimise(show_progress=False) lf /<>/doc/examples/simulate_alignment.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import sys from cogent3 import make_tree from cogent3.evolve.models import get_model /<>/doc/examples/simulate_alignment.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: t = make_tree("(a:0.4,b:0.3,(c:0.15,d:0.2)edge.0:0.1);") /<>/doc/examples/simulate_alignment.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("F81") lf = sm.make_likelihood_function(t) lf.set_constant_lengths() lf.set_motif_probs(dict(A=0.1, C=0.2, G=0.3, T=0.4)) lf /<>/doc/examples/simulate_alignment.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simulated = lf.simulate_alignment(sequence_length=1000) simulated /<>/doc/examples/testing_multi_loci.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/testing_multi_loci.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_table, make_tree from cogent3.evolve.models import HKY85 from scipy.stats.distributions import chi2 from cogent3.recalculation.scope import ALL, EACH aln = load_aligned_seqs("data/long_testseqs.fasta") half = len(aln) // 2 aln1 = aln[:half] aln2 = aln[half:] /<>/doc/examples/testing_multi_loci.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: loci_names = ["1st-half", "2nd-half"] loci = [aln1, aln2] tree = make_tree(tip_names=aln.names) mod = HKY85() /<>/doc/examples/testing_multi_loci.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = mod.make_likelihood_function(tree, loci=loci_names, digits=2, space=3) lf.set_param_rule("length", is_independent=False) lf.set_param_rule("kappa", loci=ALL) lf.set_alignment(loci) lf.optimise(show_progress=False) lf /<>/doc/examples/testing_multi_loci.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_lnL = lf.lnL all_nfp = lf.nfp lf.set_param_rule("kappa", loci=EACH) lf.optimise(show_progress=False) lf /<>/doc/examples/testing_multi_loci.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: each_lnL = lf.lnL each_nfp = lf.nfp LR = 2 * (each_lnL - all_lnL) df = each_nfp - all_nfp /<>/doc/examples/testing_multi_loci.rst:62: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: make_table( header=["LR", "df", "p"], rows=[[LR, df, chi2.sf(LR, df)]], digits=2, space=3, ) /<>/doc/index.rst:8: ERROR: Unknown directive type "dropdown". .. dropdown:: Click to see an animation showing testing a hypothesis involving a non-stationary nucleotide process. .. raw:: html /<>/doc/index.rst:16: ERROR: Unknown directive type "dropdown". .. dropdown:: Click to see an animation showing defining and using sequence annotations. .. raw:: html /<>/doc/index.rst:22: ERROR: Unknown directive type "panels". .. panels:: :header: bg-primary :footer: text-right --- ``cogent3`` apps ^^^^^^^^^^^^^^^^ ``cogent3`` comes with pre-defined "apps" that simplify otherwise complex tasks. They provide capabilities that can be used by themselves, or added together to define a pipeline. They also simplify parallel execution of pipelines. +++++++++++ .. link-button:: app/index :type: ref :text: … :classes: stretched-link --- Cookbook ^^^^^^^^ The cookbook presents short code recipes targeted at specific problems. +++++++++++ .. link-button:: cookbook/index :type: ref :text: … :classes: stretched-link --- Tutorials ^^^^^^^^^ The tutorials present code for solving more extensive problems. +++++++++++ .. link-button:: examples/index :type: ref :text: … :classes: stretched-link --- API ^^^ The API for major ``cogent3`` objects +++++++++++ .. link-button:: api/index :type: ref :text: … :classes: stretched-link looking for now-outdated files... none found pickling environment... done checking consistency... /<>/doc/data_file_links.rst: WARNING: document isn't included in any toctree /<>/doc/draw/index.rst: WARNING: document isn't included in any toctree /<>/doc/general.rst: WARNING: document isn't included in any toctree /<>/doc/install.rst: WARNING: document isn't included in any toctree /<>/doc/licenses.rst: WARNING: document isn't included in any toctree /<>/doc/pycogent.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 0%] api/__init__/cogent3.__init__.available_apps writing output... [ 1%] api/__init__/cogent3.__init__.available_codes writing output... [ 2%] api/__init__/cogent3.__init__.available_models writing output... [ 3%] api/__init__/cogent3.__init__.available_moltypes writing output... [ 4%] api/__init__/cogent3.__init__.get_code writing output... [ 4%] api/__init__/cogent3.__init__.get_model writing output... [ 5%] api/__init__/cogent3.__init__.get_moltype writing output... [ 6%] api/__init__/cogent3.__init__.load_aligned_seqs writing output... [ 7%] api/__init__/cogent3.__init__.load_delimited writing output... [ 8%] api/__init__/cogent3.__init__.load_seq writing output... [ 8%] api/__init__/cogent3.__init__.load_table writing output... [ 9%] api/__init__/cogent3.__init__.load_tree writing output... [ 10%] api/__init__/cogent3.__init__.load_unaligned_seqs writing output... [ 11%] api/__init__/cogent3.__init__.make_aligned_seqs writing output... [ 12%] api/__init__/cogent3.__init__.make_seq writing output... [ 12%] api/__init__/cogent3.__init__.make_table writing output... [ 13%] api/__init__/cogent3.__init__.make_tree writing output... [ 14%] api/__init__/cogent3.__init__.make_unaligned_seqs writing output... [ 15%] api/alignment/alignment writing output... [ 16%] api/alignment/classes/cogent3.core.alignment.Alignment writing output... [ 16%] api/alignment/classes/cogent3.core.alignment.ArrayAlignment writing output... [ 17%] api/alignment/classes/cogent3.core.alignment.SequenceCollection writing output... [ 18%] api/alphabet/alphabet writing output... [ 19%] api/alphabet/classes/cogent3.core.alphabet.Alphabet writing output... [ 20%] api/apps/composable.define_app writing output... [ 20%] api/genetic_code/classes/cogent3.core.genetic_code.GeneticCode writing output... [ 21%] api/genetic_code/genetic_code writing output... [ 22%] api/index writing output... [ 23%] api/moltype/classes/cogent3.core.moltype.MolType writing output... [ 24%] api/moltype/moltype writing output... [ 24%] api/sequence/classes/cogent3.core.sequence.DnaSequence writing output... [ 25%] api/sequence/classes/cogent3.core.sequence.ProteinSequence writing output... [ 26%] api/sequence/classes/cogent3.core.sequence.RnaSequence writing output... [ 27%] api/sequence/sequence writing output... [ 28%] api/table/classes/cogent3.parse.table.FilteringParser writing output... [ 28%] api/table/classes/cogent3.util.table.Columns writing output... [ 29%] api/table/classes/cogent3.util.table.Table writing output... [ 30%] api/table/table writing output... [ 31%] api/tree/classes/cogent3.core.tree.PhyloNode writing output... [ 32%] api/tree/tree writing output... [ 32%] app/align-codon writing output... [ 33%] app/align-nucleotide writing output... [ 34%] app/align-protein writing output... [ 35%] app/app-get writing output... [ 36%] app/app-help writing output... [ 36%] app/app-overview writing output... [ 37%] app/available-apps writing output... [ 38%] app/dstore writing output... [ 39%] app/evo-ancestral-states writing output... [ 40%] app/evo-dt-nuc-model writing output... [ 40%] app/evo-extract-model-stats writing output... [ 41%] app/evo-hypothesis writing output... [ 42%] app/evo-model writing output... [ 43%] app/evo-model-timehet writing output... [ 44%] app/evo-model-with-tree writing output... [ 44%] app/evo-natsel_neutral writing output... [ 45%] app/evo-natsel_sitehet writing output... [ 46%] app/evo-natsel_timehet writing output... [ 47%] app/evo-natsel_zhang writing output... [ 48%] app/evo-nstat-codon-model writing output... [ 48%] app/evo-tr-codon-model writing output... [ 49%] app/evo-tr-nuc-model writing output... [ 50%] app/index writing output... [ 51%] app/not-completed writing output... [ 52%] app/user_function writing output... [ 52%] cookbook/DNA_and_RNA_sequences writing output... [ 53%] cookbook/alignments writing output... [ 54%] cookbook/alphabet writing output... [ 55%] cookbook/annotations writing output... [ 56%] cookbook/building_alignments writing output... [ 56%] cookbook/building_phylogenies writing output... [ 57%] cookbook/calc_genetic_distance writing output... [ 58%] cookbook/evo_modelling writing output... [ 59%] cookbook/genetic_code writing output... [ 60%] cookbook/index writing output... [ 60%] cookbook/loading_sequences writing output... [ 61%] cookbook/loading_tabular writing output... [ 62%] cookbook/manipulating_biological_data writing output... [ 63%] cookbook/moltypes writing output... [ 64%] cookbook/protein_sequences writing output... [ 64%] cookbook/simple_trees writing output... [ 65%] cookbook/tables writing output... [ 66%] cookbook/useful_utilities writing output... [ 67%] cookbook/what_codes writing output... [ 68%] data_file_links writing output... [ 68%] draw/aln/plot_aln-coevolution writing output... [ 69%] draw/aln/plot_aln-dotplot-1 writing output... [ 70%] draw/aln/plot_aln-dotplot-2 writing output... [ 71%] draw/aln/plot_aln-gaps-per-seq writing output... [ 72%] draw/aln/plot_aln-info-plot writing output... [ 72%] draw/aln/plot_aln-seqlogo writing output... [ 73%] draw/index writing output... [ 74%] draw/tree/plot_tree-angular writing output... [ 75%] draw/tree/plot_tree-circular writing output... [ 76%] draw/tree/plot_tree-radial writing output... [ 76%] draw/tree/plot_tree-square writing output... [ 77%] draw/tree/plot_tree-support writing output... [ 78%] examples/align_codons_to_protein writing output... [ 79%] examples/calculate_UPGMA_cluster writing output... [ 80%] examples/calculate_neigbourjoining_tree writing output... [ 80%] examples/calculate_pairwise_distances writing output... [ 81%] examples/codon_models writing output... [ 82%] examples/coevolution writing output... [ 83%] examples/complete_seq_features writing output... [ 84%] examples/empirical_protein_models writing output... [ 84%] examples/hmm_par_heterogeneity writing output... [ 85%] examples/index writing output... [ 86%] examples/manipulating_tree_nodes writing output... [ 87%] examples/neutral_test writing output... [ 88%] examples/parallel writing output... [ 88%] examples/parametric_bootstrap writing output... [ 89%] examples/period_estimation writing output... [ 90%] examples/phylo_by_ls writing output... [ 91%] examples/rate_heterogeneity writing output... [ 92%] examples/relative_rate writing output... [ 92%] examples/scope_model_params_on_trees writing output... [ 93%] examples/seq_features writing output... [ 94%] examples/simple writing output... [ 95%] examples/simulate_alignment writing output... [ 96%] examples/testing_multi_loci writing output... [ 96%] general writing output... [ 97%] index writing output... [ 98%] install writing output... [ 99%] licenses writing output... [100%] pycogent generating indices... genindex done writing additional pages... search done copying downloadable files... [ 4%] data/abglobin_aa.phylip copying downloadable files... [ 8%] data/dists_for_phylo.json copying downloadable files... [ 12%] data/long_testseqs.fasta copying downloadable files... [ 16%] data/primate_brca1.fasta copying downloadable files... [ 20%] data/primate_brca1.tree copying downloadable files... [ 24%] data/primate_cdx2_promoter.fasta copying downloadable files... [ 28%] data/test.paml copying downloadable files... [ 32%] data/test.tree copying downloadable files... [ 36%] data/test2.fasta copying downloadable files... [ 40%] data/trna_profile.fasta copying downloadable files... [ 44%] data/refseqs.fasta copying downloadable files... [ 48%] data/refseqs_protein.fasta copying downloadable files... [ 52%] data/inseqs.fasta copying downloadable files... [ 56%] data/inseqs_protein.fasta copying downloadable files... [ 60%] data/SCA1-cds.fasta copying downloadable files... [ 64%] data/tp53.json copying downloadable files... [ 68%] data/brca1-bats.fasta copying downloadable files... [ 72%] data/brca1.fasta copying downloadable files... [ 76%] data/GN-tree.json copying downloadable files... [ 80%] data/tree-with-support.json copying downloadable files... [ 84%] data/F9-demo.fa copying downloadable files... [ 88%] data/BRCA1-demo.fasta copying downloadable files... [ 92%] data/tbp.jaspar copying downloadable files... [ 96%] data/stats.tsv copying downloadable files... [100%] data/CerebellumDukeDNaseSeq.pk copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 925 warnings. The HTML pages are in _build/html. Build finished. The HTML pages are in _build/html. make[2]: Leaving directory '/<>/doc' # remove superfluous files and dirs find doc/_build -name "*.doctree*" -delete rm -f doc/_build/html/_sources/COGENT_LICENSE.txt rm -f doc/_build/html/_static/jquery.js rm -f doc/_build/html/_static/underscore.js rm -rf doc/_build/html/_images/math/ make[1]: Leaving directory '/<>' dh_auto_test -a -O--buildsystem=pybuild I: pybuild pybuild:307: cp -r /<>/tests/data /<>/.pybuild/cpython3_3.11_cogent3/build I: pybuild base:240: cd /<>/.pybuild/cpython3_3.11_cogent3/build; python3.11 -m pytest -k 'not test_pickleable_member_roundtrip and not test_pickleable_roundtrip' ============================= test session starts ============================== platform linux -- Python 3.11.2, pytest-7.2.1, pluggy-1.0.0+repack rootdir: /<>, configfile: pyproject.toml plugins: anyio-3.6.2, cov-4.0.0, xdist-3.1.0 collected 2873 items / 4 deselected / 2869 selected tests/test_phylo.py ................ [ 0%] tests/test_recalculation.py . [ 0%] tests/test_align/test_align.py ............................... [ 1%] tests/test_align/test_compare.py ....................................... [ 3%] .... [ 3%] tests/test_app/test_align.py ....................... [ 3%] tests/test_app/test_app_mpi.py s [ 4%] tests/test_app/test_composable.py .............xX....................... [ 5%] ........................................... [ 6%] tests/test_app/test_data_store_new.py .................................. [ 8%] ....................... [ 8%] tests/test_app/test_dist.py ....... [ 9%] tests/test_app/test_evo.py ........................................s [ 10%] tests/test_app/test_init.py ............. [ 10%] tests/test_app/test_io_new.py .......................................... [ 12%] ...... [ 12%] tests/test_app/test_result.py ............................ [ 13%] tests/test_app/test_sample.py ................. [ 14%] tests/test_app/test_sqlite_data_store.py ............................... [ 15%] .................. [ 15%] tests/test_app/test_translate.py ...... [ 16%] tests/test_app/test_tree.py ..... [ 16%] tests/test_app/test_typing.py ..................... [ 17%] tests/test_cluster/test_UPGMA.py ....... [ 17%] tests/test_core/test_alignment.py ...................................... [ 18%] ........................................................................ [ 21%] ........................................................................ [ 23%] ........................................................................ [ 26%] ........................................................................ [ 28%] ................................................................... [ 30%] tests/test_core/test_alphabet.py ........................ [ 31%] tests/test_core/test_annotation.py ......... [ 32%] tests/test_core/test_core_standalone.py ................................ [ 33%] .......................... [ 34%] tests/test_core/test_features.py ............................. [ 35%] tests/test_core/test_genetic_code.py ................... [ 35%] tests/test_core/test_info.py ............ [ 36%] tests/test_core/test_location.py ................................... [ 37%] tests/test_core/test_maps.py .... [ 37%] tests/test_core/test_moltype.py ........................................ [ 38%] ......................... [ 39%] tests/test_core/test_profile.py ................................ [ 40%] tests/test_core/test_seq_aln_integration.py .............. [ 41%] tests/test_core/test_sequence.py ....................................... [ 42%] ........................................................................ [ 45%] ........................................................................ [ 47%] ........................................... [ 49%] tests/test_core/test_tree.py ........................................... [ 50%] ........................................................................ [ 53%] ......................... [ 54%] tests/test_data/test_molecular_weight.py . [ 54%] tests/test_draw/test_dendrogram.py .......... [ 54%] tests/test_draw/test_dotplot.py ........... [ 54%] tests/test_draw/test_draw_integration.py ........................ [ 55%] tests/test_draw/test_logo.py ..... [ 55%] tests/test_draw/test_shapes.py ... [ 56%] tests/test_evolve/test_best_likelihood.py ....... [ 56%] tests/test_evolve/test_bootstrap.py .. [ 56%] tests/test_evolve/test_coevolution.py .................................. [ 57%] ........................................................................ [ 60%] .............. [ 60%] tests/test_evolve/test_distance.py ..................................... [ 61%] ..... [ 62%] tests/test_evolve/test_likelihood_function.py .......................... [ 62%] .............................................. [ 64%] tests/test_evolve/test_models.py ........... [ 64%] tests/test_evolve/test_motifchange.py ............. [ 65%] tests/test_evolve/test_newq.py ............. [ 65%] tests/test_evolve/test_ns_substitution_model.py .............. [ 66%] tests/test_evolve/test_parameter_controller.py .......... [ 66%] tests/test_evolve/test_scale_rules.py .... [ 66%] tests/test_evolve/test_substitution_model.py ...................... [ 67%] tests/test_format/test_bedgraph.py ........ [ 67%] tests/test_format/test_clustal.py ... [ 67%] tests/test_format/test_fasta.py . [ 68%] tests/test_maths/test_distance_transform.py ............................ [ 68%] ....... [ 69%] tests/test_maths/test_geometry.py .......... [ 69%] tests/test_maths/test_matrix_exponential_integration.py .... [ 69%] tests/test_maths/test_matrix_logarithm.py ... [ 69%] tests/test_maths/test_measure.py ........ [ 70%] tests/test_maths/test_optimisers.py ...... [ 70%] tests/test_maths/test_period.py ....... [ 70%] tests/test_maths/test_util.py ....... [ 70%] tests/test_maths/test_stats/test_contingency.py .................... [ 71%] tests/test_maths/test_stats/test_distribution.py ....................... [ 72%] . [ 72%] tests/test_maths/test_stats/test_information_criteria.py ... [ 72%] tests/test_maths/test_stats/test_jackknife.py .... [ 72%] tests/test_maths/test_stats/test_ks.py ...... [ 72%] tests/test_maths/test_stats/test_number.py ...................... [ 73%] tests/test_maths/test_stats/test_period.py .......... [ 73%] tests/test_maths/test_stats/test_special.py ....................... [ 74%] tests/test_maths/test_stats/test_test.py ............................... [ 75%] ...................................................................... [ 78%] tests/test_parse/test_blast.py .............. [ 78%] tests/test_parse/test_blast_xml.py ............... [ 79%] tests/test_parse/test_cigar.py ..... [ 79%] tests/test_parse/test_clustal.py ......... [ 79%] tests/test_parse/test_dialign.py ... [ 79%] tests/test_parse/test_ebi.py ........................................... [ 81%] ............ [ 81%] tests/test_parse/test_fasta.py ..................... [ 82%] tests/test_parse/test_gbseq.py . [ 82%] tests/test_parse/test_genbank.py ................ [ 83%] tests/test_parse/test_gff.py ...... [ 83%] tests/test_parse/test_greengenes.py .... [ 83%] tests/test_parse/test_locuslink.py ............. [ 83%] tests/test_parse/test_ncbi_taxonomy.py .................. [ 84%] tests/test_parse/test_nexus.py ............... [ 85%] tests/test_parse/test_pamlmatrix.py . [ 85%] tests/test_parse/test_phylip.py ... [ 85%] tests/test_parse/test_psl.py ... [ 85%] tests/test_parse/test_pwm_parsers.py .. [ 85%] tests/test_parse/test_rdb.py .................. [ 85%] tests/test_parse/test_record.py ........................................ [ 87%] .. [ 87%] tests/test_parse/test_record_finder.py ................. [ 88%] tests/test_parse/test_tinyseq.py . [ 88%] tests/test_parse/test_tree.py ............... [ 88%] tests/test_parse/test_unigene.py .... [ 88%] tests/test_util/test_deserialise.py ............................ [ 89%] tests/test_util/test_dictarray.py ............................... [ 90%] tests/test_util/test_io.py ...................................ssss.sss [ 92%] tests/test_util/test_misc.py ........................................... [ 93%] .......................................... [ 95%] tests/test_util/test_parallel.py sss [ 95%] tests/test_util/test_recode_alignment.py ............... [ 95%] tests/test_util/test_table.py .......................................... [ 97%] ............................................................. [ 99%] tests/test_util/test_transform.py ..... [ 99%] tests/test_util/test_union_dict.py ........... [100%] =============================== warnings summary =============================== ../../../../../../usr/lib/python3/dist-packages/llvmlite/binding/ffi.py:159 /usr/lib/python3/dist-packages/llvmlite/binding/ffi.py:159: DeprecationWarning: path is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice. _lib_handle = importlib.resources.path(pkgname, _lib_name) .pybuild/cpython3_3.11_cogent3/build/tests/test_app/test_evo.py::TestHypothesisResult::test_alt_hyp_fail_error /<>/.pybuild/cpython3_3.11_cogent3/build/cogent3/core/sequence.py:1123: UserWarning: Dropped remainder "GA" from end of sequence warnings.warn( .pybuild/cpython3_3.11_cogent3/build/tests/test_core/test_alignment.py::SequenceCollectionTests::test_set_repr_policy_valid_input /usr/lib/python3.11/unittest/case.py:678: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) return self.run(*args, **kwds) .pybuild/cpython3_3.11_cogent3/build/tests/test_core/test_alignment.py::SequenceCollectionTests::test_set_wrap_affects_repr_html /usr/lib/python3.11/unittest/case.py:678: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) return self.run(*args, **kwds) .pybuild/cpython3_3.11_cogent3/build/tests/test_core/test_core_standalone.py::TestConstructorFunctions::test_load_seq /<>/.pybuild/cpython3_3.11_cogent3/build/cogent3/core/info.py:208: UserWarning: Keys overwritten by other sequence: source warn("Keys overwritten by other sequence: " + "".join(overwrites)) .pybuild/cpython3_3.11_cogent3/build/tests/test_evolve/test_likelihood_function.py::LikelihoodFunctionTests::test_get_param_rules_multilocus .pybuild/cpython3_3.11_cogent3/build/tests/test_util/test_deserialise.py::TestDeserialising::test_deserialise_likelihood_function_multilocus /<>/.pybuild/cpython3_3.11_cogent3/build/cogent3/evolve/parameter_controller.py:414: UserWarning: Used mean of 12 mprobs values .pybuild/cpython3_3.11_cogent3/build/tests/test_evolve/test_likelihood_function.py::LikelihoodFunctionTests::test_make_discrete_markov /<>/.pybuild/cpython3_3.11_cogent3/build/tests/test_evolve/test_likelihood_function.py:808: UserWarning: Ignoring tree edge lengths .pybuild/cpython3_3.11_cogent3/build/tests/test_evolve/test_likelihood_function.py::LikelihoodFunctionTests::test_set_param_rule_adjust_bounds /<>/.pybuild/cpython3_3.11_cogent3/build/cogent3/evolve/parameter_controller.py:414: UserWarning: Used mean of 7 beta values .pybuild/cpython3_3.11_cogent3/build/tests/test_evolve/test_ns_substitution_model.py::NonStatMarkov::test_general_vs_constructed_general /<>/.pybuild/cpython3_3.11_cogent3/build/cogent3/maths/optimisers.py:189: UserWarning: Unused arg for local alignment: results .pybuild/cpython3_3.11_cogent3/build/tests/test_maths/test_stats/test_test.py::StatTests::test_t_two_sample_switch /usr/lib/python3/dist-packages/numpy/core/_methods.py:269: RuntimeWarning: Degrees of freedom <= 0 for slice .pybuild/cpython3_3.11_cogent3/build/tests/test_util/test_misc.py::UtilsTests::test_get_setting_from_environ /<>/.pybuild/cpython3_3.11_cogent3/build/cogent3/util/misc.py:1034: UserWarning: could not cast name=blah to type , skipping -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ SKIPPED [1] tests/test_app/test_app_mpi.py:26: Not using MPI SKIPPED [1] tests/test_app/test_evo.py:857: Does not work on single-cpu systems SKIPPED [4] tests/test_util/test_io.py:320: Do not test in Debian since offline SKIPPED [1] tests/test_util/test_io.py:361: Do not test in Debian since offline SKIPPED [1] tests/test_util/test_io.py:378: Do not test in Debian since offline SKIPPED [1] tests/test_util/test_io.py:388: Do not test in Debian since offline SKIPPED [1] tests/test_util/test_parallel.py:38: Does not work on single-cpu systems SKIPPED [1] tests/test_util/test_parallel.py:61: Does not work on single-cpu systems SKIPPED [1] tests/test_util/test_parallel.py:49: Does not work on single-cpu systems XFAIL tests/test_app/test_composable.py::test_as_completed_progress[True] - passes except when run in full test suite XPASS tests/test_app/test_composable.py::test_as_completed_progress[False] passes except when run in full test suite = 2855 passed, 12 skipped, 4 deselected, 1 xfailed, 1 xpassed, 12 warnings in 120.62s (0:02:00) = create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild I: pybuild plugin_pyproject:161: Copying package built for python3.11 to destdir dh_install -a -O--buildsystem=pybuild debian/rules override_dh_installdocs make[1]: Entering directory '/<>' dh_installdocs rm -rf debian/python-cogent/usr/share/doc/python-cogent/html/_sources find debian -name doctrees -type d | xargs rm -rf make[1]: Leaving directory '/<>' dh_installchangelogs -a -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/<>' dh_python3 --shebang=/usr/bin/python3 make[1]: Leaving directory '/<>' dh_installsystemduser -a -O--buildsystem=pybuild dh_lintian -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress --exclude=.js --exclude=.fasta --exclude=.txt --exclude=.pdb make[1]: Leaving directory '/<>' dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild debian/rules override_dh_shlibdeps make[1]: Entering directory '/<>' dh_shlibdeps dh_numpy3 make[1]: Leaving directory '/<>' dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package python3-cogent3: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 152 pkgstriptranslations: processing python3-cogent3 (in debian/python3-cogent3); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python3-cogent3/DEBIAN/control, package python3-cogent3, directory debian/python3-cogent3 pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-cogent3 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-cogent3' in '../python3-cogent3_2023.2.12a1+dfsg-1_ppc64el.deb'. dpkg-genbuildinfo --build=any -O../python-cogent_2023.2.12a1+dfsg-1_ppc64el.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../python-cogent_2023.2.12a1+dfsg-1_ppc64el.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-02-22T17:19:22Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ python-cogent_2023.2.12a1+dfsg-1_ppc64el.changes: ------------------------------------------------- Format: 1.8 Date: Wed, 22 Feb 2023 08:07:42 +0100 Source: python-cogent Binary: python3-cogent3 Built-For-Profiles: noudeb Architecture: ppc64el Version: 2023.2.12a1+dfsg-1 Distribution: lunar-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: python3-cogent3 - framework for genomic biology Changes: python-cogent (2023.2.12a1+dfsg-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: 46fba5376dde52eb065a3b0d07b10aa8eb07bcfc 13811 python-cogent_2023.2.12a1+dfsg-1_ppc64el.buildinfo a80f0218a7c4d4072530ba39deb01aab2aa58597 1954644 python3-cogent3_2023.2.12a1+dfsg-1_ppc64el.deb Checksums-Sha256: 9132749fa492658b6627fafa25f397b97cdbfc6c8888997596231bd97750cb88 13811 python-cogent_2023.2.12a1+dfsg-1_ppc64el.buildinfo 50c189afddfc4a3fb7b5706dd4b2bd01b1462ec511487c096c9f7003daf9bba5 1954644 python3-cogent3_2023.2.12a1+dfsg-1_ppc64el.deb Files: af59c997637642389c6d677b9ebad234 13811 python optional python-cogent_2023.2.12a1+dfsg-1_ppc64el.buildinfo 2e825289c9c73adfa08ec884da05a864 1954644 python optional python3-cogent3_2023.2.12a1+dfsg-1_ppc64el.deb /<>/python-cogent_2023.2.12a1+dfsg-1_ppc64el.changes.new could not be renamed to /<>/python-cogent_2023.2.12a1+dfsg-1_ppc64el.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: python-cogent Binary: python3-cogent3 Architecture: ppc64el Version: 2023.2.12a1+dfsg-1 Checksums-Md5: 2e825289c9c73adfa08ec884da05a864 1954644 python3-cogent3_2023.2.12a1+dfsg-1_ppc64el.deb Checksums-Sha1: a80f0218a7c4d4072530ba39deb01aab2aa58597 1954644 python3-cogent3_2023.2.12a1+dfsg-1_ppc64el.deb Checksums-Sha256: 50c189afddfc4a3fb7b5706dd4b2bd01b1462ec511487c096c9f7003daf9bba5 1954644 python3-cogent3_2023.2.12a1+dfsg-1_ppc64el.deb Build-Origin: Ubuntu Build-Architecture: ppc64el Build-Date: Wed, 22 Feb 2023 17:19:22 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-11), autotools-dev (= 20220109.1), base-files (= 12.3ubuntu1), base-passwd (= 3.6.1), bash (= 5.2.15-2ubuntu1), binutils (= 2.40-2ubuntu2), binutils-common (= 2.40-2ubuntu2), binutils-powerpc64le-linux-gnu (= 2.40-2ubuntu2), blt (= 2.5.3+dfsg-4.1build2), bsdextrautils (= 2.38.1-4ubuntu1), bsdutils (= 1:2.38.1-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), ca-certificates (= 20211016ubuntu1), coreutils (= 9.1-1ubuntu2), cpp (= 4:12.2.0-3ubuntu1), cpp-12 (= 12.2.0-14ubuntu2), cython3 (= 0.29.32-2ubuntu1), dash (= 0.5.12-2ubuntu1), debconf (= 1.5.82), debhelper (= 13.11.4ubuntu3), debianutils (= 5.7-0.4), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-python (= 5.20230130), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.8-4), docutils-common (= 0.19+dfsg-6), dpkg (= 1.21.20ubuntu2), dpkg-dev (= 1.21.20ubuntu2), dwz (= 0.15-1), file (= 1:5.44-3), findutils (= 4.9.0-3ubuntu1), flit (= 3.8.0-3), fontconfig-config (= 2.14.1-3ubuntu2), fonts-dejavu-core (= 2.37-4), fonts-glyphicons-halflings (= 1.009~3.4.1+dfsg-3), fonts-lyx (= 2.3.7-1), g++ (= 4:12.2.0-3ubuntu1), g++-12 (= 12.2.0-14ubuntu2), gcc (= 4:12.2.0-3ubuntu1), gcc-12 (= 12.2.0-14ubuntu2), gcc-12-base (= 12.2.0-14ubuntu2), gcc-13-base (= 13-20230215-1ubuntu2), gettext (= 0.21-11), gettext-base (= 0.21-11), grep (= 3.8-5), groff-base (= 1.22.4-9), gzip (= 1.12-1ubuntu1), hostname (= 3.23+nmu1ubuntu1), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), jupyter-sphinx-theme-common (= 0.0.6+ds1-11), libacl1 (= 2.3.1-3), libarchive-zip-perl (= 1.68-1), libargon2-1 (= 0~20171227-0.3), libasan8 (= 13-20230215-1ubuntu2), libatomic1 (= 13-20230215-1ubuntu2), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.0.9-1), libaudit1 (= 1:3.0.9-1), libbinutils (= 2.40-2ubuntu2), libblas3 (= 3.11.0-2), libblkid1 (= 2.38.1-4ubuntu1), libboost-dev (= 1.74.0.3ubuntu7), libboost1.74-dev (= 1.74.0-18.1ubuntu3), libbrotli1 (= 1.0.9-2build7), libbsd0 (= 0.11.7-2), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.37-0ubuntu1), libc-dev-bin (= 2.37-0ubuntu1), libc6 (= 2.37-0ubuntu1), libc6-dev (= 2.37-0ubuntu1), libcap-ng0 (= 0.8.3-1build1), libcap2 (= 1:2.66-3ubuntu2), libcc1-0 (= 13-20230215-1ubuntu2), libcom-err2 (= 1.47.0-1ubuntu1), libcrypt-dev (= 1:4.4.33-2), libcrypt1 (= 1:4.4.33-2), libctf-nobfd0 (= 2.40-2ubuntu2), libctf0 (= 2.40-2ubuntu2), libcurl4 (= 7.87.0-2ubuntu2), libdb5.3 (= 5.3.28+dfsg2-1), libdebconfclient0 (= 0.267ubuntu1), libdebhelper-perl (= 13.11.4ubuntu3), libdeflate0 (= 1.15-1), libdpkg-perl (= 1.21.20ubuntu2), libdw1 (= 0.188-2.1), libedit2 (= 3.1-20221030-2), libelf1 (= 0.188-2.1), libexpat1 (= 2.5.0-1), libexpat1-dev (= 2.5.0-1), libffi8 (= 3.4.4-1), libfile-stripnondeterminism-perl (= 1.13.1-1), libfontconfig1 (= 2.14.1-3ubuntu2), libfreetype6 (= 2.12.1+dfsg-4), libfribidi0 (= 1.0.8-2.1ubuntu1), libgcc-12-dev (= 12.2.0-14ubuntu2), libgcc-s1 (= 13-20230215-1ubuntu2), libgcrypt20 (= 1.10.1-3ubuntu1), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgfortran5 (= 13-20230215-1ubuntu2), libglib2.0-0 (= 2.74.5-1), libgmp10 (= 2:6.2.1+dfsg1-1.1ubuntu1), libgnutls30 (= 3.7.8-5ubuntu1), libgomp1 (= 13-20230215-1ubuntu2), libgpg-error0 (= 1.46-1), libgraphite2-3 (= 1.3.14-1build2), libgssapi-krb5-2 (= 1.20.1-1build1), libharfbuzz0b (= 6.0.0+dfsg-3build1), libhogweed6 (= 3.8.1-2), libicu72 (= 72.1-3ubuntu1), libidn2-0 (= 2.3.3-1build1), libimagequant0 (= 2.17.0-1), libisl23 (= 0.25-1), libitm1 (= 13-20230215-1ubuntu2), libjansson4 (= 2.14-2), libjbig0 (= 2.1-6ubuntu1), libjpeg-turbo8 (= 2.1.5-2ubuntu1), libjpeg8 (= 8c-2ubuntu11), libjs-bootstrap (= 3.4.1+dfsg-3), libjs-bootswatch (= 3.3.7+dfsg2-1.1), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-jquery-hotkeys (= 0~20130707+git2d51e3a9+dfsg-2ubuntu1), libjs-jquery-isonscreen (= 1.2.0-1.1), libjs-jquery-metadata (= 12-4), libjs-jquery-tablesorter (= 1:2.31.3+dfsg1-3), libjs-jquery-throttle-debounce (= 1.1+dfsg.1-2), libjs-jquery-ui (= 1.13.2+dfsg-1), libjs-sphinxdoc (= 5.3.0-3), libjs-underscore (= 1.13.4~dfsg+~1.11.4-3), libjson-perl (= 4.10000-1), libk5crypto3 (= 1.20.1-1build1), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-1build1), libkrb5support0 (= 1.20.1-1build1), liblapack3 (= 3.11.0-2), liblbfgsb0 (= 3.0+dfsg.3-11), liblcms2-2 (= 2.14-2), libldap2 (= 2.6.3+dfsg-1~exp1ubuntu2), liblerc4 (= 4.0.0+ds-2ubuntu2), libllvm14 (= 1:14.0.6-12), liblsan0 (= 13-20230215-1ubuntu2), liblua5.3-0 (= 5.3.6-2), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.4.1-0.2), libmagic-mgc (= 1:5.44-3), libmagic1 (= 1:5.44-3), libmd0 (= 1.0.4-2), libmount1 (= 2.38.1-4ubuntu1), libmpc3 (= 1.3.1-1), libmpdec3 (= 2.5.1-2build2), libmpfr6 (= 4.2.0-1), libncursesw6 (= 6.4-2), libnettle8 (= 3.8.1-2), libnghttp2-14 (= 1.52.0-1), libnorm1 (= 1.5.9+dfsg-2), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libopenblas-dev (= 0.3.21+ds-4), libopenblas-pthread-dev (= 0.3.21+ds-4), libopenblas0 (= 0.3.21+ds-4), libopenblas0-pthread (= 0.3.21+ds-4), libopenjp2-7 (= 2.5.0-1build1), libp11-kit0 (= 0.24.1-2ubuntu1), libpam-modules (= 1.5.2-5ubuntu1), libpam-modules-bin (= 1.5.2-5ubuntu1), libpam-runtime (= 1.5.2-5ubuntu1), libpam0g (= 1.5.2-5ubuntu1), libpcre2-8-0 (= 10.42-1), libperl5.36 (= 5.36.0-7), libpfm4 (= 4.12.1+git12-g678bca9-1), libpgm-5.3-0 (= 5.3.128~dfsg-2), libpipeline1 (= 1.5.7-1), libpng16-16 (= 1.6.39-2), libpsl5 (= 0.21.2-1), libpython3-all-dev (= 3.11.2-1), libpython3-dev (= 3.11.2-1), libpython3-stdlib (= 3.11.2-1), libpython3.10-minimal (= 3.10.9-1), libpython3.10-stdlib (= 3.10.9-1), libpython3.11 (= 3.11.2-4), libpython3.11-dev (= 3.11.2-4), libpython3.11-minimal (= 3.11.2-4), libpython3.11-stdlib (= 3.11.2-4), libqhull-r8.0 (= 2020.2-5), libquadmath0 (= 13-20230215-1ubuntu2), libraqm0 (= 0.7.0-4.1), libreadline8 (= 8.2-1.3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg-10), libsasl2-modules-db (= 2.1.28+dfsg-10), libseccomp2 (= 2.5.4-1ubuntu2), libselinux1 (= 3.4-1build3), libsmartcols1 (= 2.38.1-4ubuntu1), libsodium23 (= 1.0.18-1build2), libsqlite3-0 (= 3.40.1-1), libssh-4 (= 0.10.4-2), libssl3 (= 3.0.8-1ubuntu1), libstdc++-12-dev (= 12.2.0-14ubuntu2), libstdc++6 (= 13-20230215-1ubuntu2), libsub-override-perl (= 0.09-4), libsystemd0 (= 252.5-2ubuntu1), libtasn1-6 (= 4.19.0-2), libtcl8.6 (= 8.6.13+dfsg-2), libtiff6 (= 4.5.0-4ubuntu1), libtinfo6 (= 6.4-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtk8.6 (= 8.6.13-2), libtool (= 2.4.7-5), libtsan2 (= 13-20230215-1ubuntu2), libubsan1 (= 13-20230215-1ubuntu2), libuchardet0 (= 0.0.7-1build2), libudev1 (= 252.5-2ubuntu1), libunistring2 (= 1.0-2), libuuid1 (= 2.38.1-4ubuntu1), libwebp7 (= 1.2.4-0.1build1), libwebpdemux2 (= 1.2.4-0.1build1), libwebpmux3 (= 1.2.4-0.1build1), libx11-6 (= 2:1.8.3-3), libx11-data (= 2:1.8.3-3), libxau6 (= 1:1.0.9-1build5), libxcb1 (= 1.15-1), libxdmcp6 (= 1:1.1.3-0ubuntu5), libxext6 (= 2:1.3.4-1build1), libxft2 (= 2.3.6-1), libxml2 (= 2.9.14+dfsg-1.1build1), libxrender1 (= 1:0.9.10-1.1), libxsimd-dev (= 8.1.0-7), libxslt1.1 (= 1.1.35-1), libxss1 (= 1:1.2.3-1build2), libyaml-0-2 (= 0.2.5-1), libzmq5 (= 4.3.4-6), libzstd1 (= 1.5.4+dfsg2-3), linux-libc-dev (= 6.1.0-14.14), llvm-14 (= 1:14.0.6-12), llvm-14-linker-tools (= 1:14.0.6-12), llvm-14-runtime (= 1:14.0.6-12), login (= 1:4.13+dfsg1-1ubuntu1), lsb-base (= 11.6), lto-disabled-list (= 38), m4 (= 1.4.19-3), make (= 4.3-4.1build1), man-db (= 2.11.2-1), mawk (= 1.3.4.20200120-3.1), media-types (= 10.0.0), ncurses-base (= 6.4-2), ncurses-bin (= 6.4-2), openssl (= 3.0.8-1ubuntu1), pandoc (= 2.17.1.1-1.1ubuntu1), pandoc-data (= 2.17.1.1-1.1ubuntu1), patch (= 2.7.6-7build2), perl (= 5.36.0-7), perl-base (= 5.36.0-7), perl-modules-5.36 (= 5.36.0-7), po-debconf (= 1.0.21+nmu1), pybuild-plugin-pyproject (= 5.20230130), python-babel-localedata (= 2.10.3-1), python-matplotlib-data (= 3.5.2-4), python-tinycss2-common (= 1.2.1-2), python3 (= 3.11.2-1), python3-alabaster (= 0.7.12-1), python3-all (= 3.11.2-1), python3-all-dev (= 3.11.2-1), python3-anyio (= 3.6.2-1), python3-appdirs (= 1.4.4-3), python3-argon2 (= 21.1.0-2), python3-attr (= 22.2.0-1), python3-babel (= 2.10.3-1), python3-beniget (= 0.4.1-3), python3-bleach (= 5.0.1-2), python3-brotli (= 1.0.9-2build7), python3-bs4 (= 4.11.2-2), python3-build (= 0.9.0-1), python3-certifi (= 2022.9.24-1), python3-cffi-backend (= 1.15.1-5), python3-chardet (= 5.1.0+dfsg-2), python3-commonmark (= 0.9.1-4), python3-coverage (= 6.5.0+dfsg1-2), python3-cycler (= 0.11.0-1), python3-dateutil (= 2.8.2-1), python3-decorator (= 5.1.1-3), python3-defusedxml (= 0.7.1-2), python3-dev (= 3.11.2-1), python3-distutils (= 3.11.2-2), python3-docutils (= 0.19+dfsg-6), python3-entrypoints (= 0.4-2), python3-execnet (= 1.9.0-1), python3-fastjsonschema (= 2.16.2-1), python3-fonttools (= 4.38.0-1), python3-fs (= 2.4.16-2), python3-gast (= 0.5.2-2), python3-html5lib (= 1.1-3), python3-idna (= 3.3-1), python3-imagesize (= 1.4.1-1), python3-importlib-metadata (= 4.12.0-1), python3-iniconfig (= 1.1.1-2), python3-installer (= 0.6.0+dfsg1-1), python3-isort (= 5.6.4-1), python3-jinja2 (= 3.0.3-2), python3-json5 (= 0.9.10-1), python3-jsonschema (= 4.6.0-3ubuntu1), python3-jupyter-client (= 7.4.9-2), python3-jupyter-core (= 4.12.0-1), python3-jupyter-server (= 1.23.3-1), python3-jupyter-sphinx-theme (= 0.0.6+ds1-11), python3-jupyterlab-pygments (= 0.2.2-3), python3-jupyterlab-server (= 2.16.5-1), python3-kiwisolver (= 1.4.4-1), python3-lib2to3 (= 3.11.2-2), python3-llvmlite (= 0.39.1-2), python3-lxml (= 4.9.2-1), python3-lz4 (= 4.0.2+dfsg-1), python3-markupsafe (= 2.1.2-1), python3-matplotlib (= 3.5.2-4), python3-minimal (= 3.11.2-1), python3-more-itertools (= 8.10.0-2), python3-mpmath (= 1.2.1-2), python3-nbclient (= 0.7.2-1), python3-nbconvert (= 6.5.3-3), python3-nbformat (= 5.5.0-1), python3-nbsphinx (= 0.8.11+ds-1), python3-nest-asyncio (= 1.5.4-1), python3-numba (= 0.56.4+dfsg-2), python3-numpy (= 1:1.24.2-1), python3-numpydoc (= 1.5.0-1), python3-packaging (= 23.0-1), python3-pandas (= 1.5.3+dfsg-2), python3-pandas-lib (= 1.5.3+dfsg-2), python3-pandocfilters (= 1.5.0-1), python3-pbr (= 5.11.0-0ubuntu1), python3-pep517 (= 0.13.0-2), python3-pil (= 9.4.0-1.1build1), python3-pil.imagetk (= 9.4.0-1.1build1), python3-pkg-resources (= 66.1.1-1), python3-plotly (= 5.4.1+dfsg-1), python3-pluggy (= 1.0.0+repack-1), python3-ply (= 3.11-5), python3-prometheus-client (= 0.16.0-0.1), python3-ptyprocess (= 0.7.0-5), python3-py (= 1.11.0-1), python3-pygments (= 2.14.0+dfsg-1), python3-pyparsing (= 3.0.9-1), python3-pyrsistent (= 0.18.1-1build2), python3-pytest (= 7.2.1-2), python3-pytest-cov (= 4.0.0-1), python3-pytest-xdist (= 3.1.0-1), python3-pythran (= 0.11.0+ds-7), python3-recommonmark (= 0.7.1+ds-5), python3-requests (= 2.28.1+dfsg-1ubuntu1), python3-roman (= 3.3-3), python3-scipy (= 1.10.0-12), python3-scitrack (= 2021.5.3-3), python3-send2trash (= 1.8.1~b0-2), python3-setuptools (= 66.1.1-1), python3-six (= 1.16.0-4), python3-sniffio (= 1.2.0-1), python3-snowballstemmer (= 2.2.0-2), python3-soupsieve (= 2.4-1), python3-sphinx (= 5.3.0-3), python3-sphinx-bootstrap-theme (= 0.8.1-1), python3-sphinx-gallery (= 0.10.1-3), python3-sympy (= 1.11.1-1), python3-tenacity (= 8.2.1-1), python3-terminado (= 0.17.0-1), python3-tinycss2 (= 1.2.1-2), python3-tinydb (= 3.15.2-4), python3-tk (= 3.11.2-2), python3-toml (= 0.10.2-1), python3-tomli (= 2.0.1-2), python3-tomli-w (= 1.0.0-2), python3-tornado (= 6.2.0-3), python3-tqdm (= 4.64.1-1), python3-traitlets (= 5.5.0-1), python3-typing-extensions (= 4.4.0-1), python3-tz (= 2022.7.1-1), python3-ufolib2 (= 0.14.0+dfsg1-1), python3-urllib3 (= 1.26.12-1), python3-webencodings (= 0.5.1-5), python3-websocket (= 1.2.3-1), python3-wheel (= 0.38.4-1), python3-zipp (= 1.0.0-6), python3-zmq (= 24.0.1-4), python3.10 (= 3.10.9-1), python3.10-minimal (= 3.10.9-1), python3.11 (= 3.11.2-4), python3.11-dev (= 3.11.2-4), python3.11-minimal (= 3.11.2-4), readline-common (= 8.2-1.3), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-1), sensible-utils (= 0.0.17+nmu1), sgml-base (= 1.31), sphinx-common (= 5.3.0-3), sysvinit-utils (= 3.05-7ubuntu2), tar (= 1.34+dfsg-1.1), tk8.6-blt2.5 (= 2.5.3+dfsg-4.1build2), tzdata (= 2022g-2ubuntu1), unicode-data (= 15.0.0-1), usrmerge (= 33ubuntu1), util-linux (= 2.38.1-4ubuntu1), util-linux-extra (= 2.38.1-4ubuntu1), x11-common (= 1:7.7+23ubuntu2), xml-core (= 0.18+nmu1), xz-utils (= 5.4.1-0.2), zlib1g (= 1:1.2.13.dfsg-1ubuntu4), zlib1g-dev (= 1:1.2.13.dfsg-1ubuntu4) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1677049662" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ python3-cogent3_2023.2.12a1+dfsg-1_ppc64el.deb ---------------------------------------------- new Debian package, version 2.0. size 1954644 bytes: control archive=10610 bytes. 1295 bytes, 27 lines control 36575 bytes, 390 lines md5sums 281 bytes, 12 lines * postinst #!/bin/sh 394 bytes, 12 lines * prerm #!/bin/sh Package: python3-cogent3 Source: python-cogent Version: 2023.2.12a1+dfsg-1 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 6638 Depends: python3-chardet, python3-numba, python3-numpy (>= 1:1.22.0), python3-numpy-abi9, python3-scipy, python3-scitrack, python3-tinydb, python3-tqdm, python3-typing-extensions, python3:any, python3-matplotlib, python3-pandas, python3-plotly Recommends: ncbi-blast+-legacy, dialign Suggests: python-cogent-doc Breaks: python-cogent Replaces: python-cogent Provides: python-cogent Section: python Priority: optional Homepage: https://github.com/cogent3/cogent3 Description: framework for genomic biology PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: * controlling third-party applications, * devising workflows; querying databases, * conducting novel probabilistic analyses of biological sequence evolution, and * generating publication quality graphics. It is distinguished by many unique built-in capabilities (such as true codon alignment) and the frequent addition of entirely new methods for the analysis of genomic data. drwxr-xr-x root/root 0 2023-02-22 07:07 ./ drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/ drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/lib/ drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/lib/python3/ drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3-2023.2.12a1.dist-info/ -rw-r--r-- root/root 9955 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3-2023.2.12a1.dist-info/METADATA -rw-r--r-- root/root 14436 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3-2023.2.12a1.dist-info/RECORD -rw-r--r-- root/root 81 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3-2023.2.12a1.dist-info/WHEEL drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/ -rw-r--r-- root/root 18604 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/__init__.py drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/align/ -rw-r--r-- root/root 660 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/align/__init__.py -rw-r--r-- root/root 3442 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/align/align.py -rw-r--r-- root/root 1564 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/align/compare_numba.py -rw-r--r-- root/root 6137 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/align/dp_calculation.py -rw-r--r-- root/root 3814 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/align/indel_model.py -rw-r--r-- root/root 8114 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/align/indel_positions.py -rw-r--r-- root/root 39249 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/align/pairwise.py -rw-r--r-- root/root 11346 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/align/pairwise_pogs_numba.py -rw-r--r-- root/root 9151 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/align/pairwise_seqs_numba.py -rw-r--r-- root/root 4546 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/align/progressive.py -rw-r--r-- root/root 17981 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/align/pycompare.py -rw-r--r-- root/root 2894 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/align/traceback.py drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/app/ -rw-r--r-- root/root 6813 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/app/__init__.py -rw-r--r-- root/root 17248 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/app/align.py -rw-r--r-- root/root 48905 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/app/composable.py -rw-r--r-- root/root 36059 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/app/data_store.py -rw-r--r-- root/root 21841 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/app/data_store_new.py -rw-r--r-- root/root 4391 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/app/dist.py -rw-r--r-- root/root 36480 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/app/evo.py -rw-r--r-- root/root 19992 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/app/io.py -rw-r--r-- root/root 18894 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/app/io_new.py -rw-r--r-- root/root 19914 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/app/result.py -rw-r--r-- root/root 21786 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/app/sample.py -rw-r--r-- root/root 13792 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/app/sqlite_data_store.py -rw-r--r-- root/root 8530 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/app/translate.py -rw-r--r-- root/root 4123 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/app/tree.py -rw-r--r-- root/root 4728 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/app/typing.py drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/cluster/ -rw-r--r-- root/root 6007 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/cluster/UPGMA.py -rw-r--r-- root/root 403 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/cluster/__init__.py drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/core/ -rw-r--r-- root/root 582 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/core/__init__.py -rw-r--r-- root/root 167754 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/core/alignment.py -rw-r--r-- root/root 33272 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/core/alphabet.py -rw-r--r-- root/root 17308 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/core/annotation.py -rw-r--r-- root/root 19906 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/core/genetic_code.py -rw-r--r-- root/root 5859 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/core/info.py -rw-r--r-- root/root 34951 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/core/location.py -rw-r--r-- root/root 47778 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/core/moltype.py -rw-r--r-- root/root 18310 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/core/profile.py -rw-r--r-- root/root 70388 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/core/sequence.py -rw-r--r-- root/root 89974 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/core/tree.py drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/data/ -rw-r--r-- root/root 344 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/data/__init__.py -rw-r--r-- root/root 3311 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/data/energy_params.py -rw-r--r-- root/root 1841 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/data/molecular_weight.py drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/draw/ -rw-r--r-- root/root 423 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/draw/__init__.py -rw-r--r-- root/root 31233 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/draw/dendrogram.py -rw-r--r-- root/root 10680 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/draw/dotplot.py -rw-r--r-- root/root 24919 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/draw/drawable.py -rw-r--r-- root/root 49215 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/draw/letter.py -rw-r--r-- root/root 4281 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/draw/logo.py drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/ -rw-r--r-- root/root 743 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/__init__.py -rw-r--r-- root/root 4796 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/best_likelihood.py -rw-r--r-- root/root 7165 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/bootstrap.py -rwxr-xr-x root/root 95145 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/coevolution.py -rw-r--r-- root/root 3493 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/discrete_markov.py -rw-r--r-- root/root 13332 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/distance.py -rw-r--r-- root/root 25382 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/fast_distance.py -rw-r--r-- root/root 9977 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/likelihood_calculation.py -rw-r--r-- root/root 42635 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/likelihood_function.py -rw-r--r-- root/root 10908 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/likelihood_tree.py -rw-r--r-- root/root 1630 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/likelihood_tree_numba.py -rw-r--r-- root/root 65908 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/models.py -rw-r--r-- root/root 10851 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/motif_prob_model.py -rw-r--r-- root/root 7522 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/ns_substitution_model.py -rw-r--r-- root/root 936 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/pairwise_distance_numba.py -rw-r--r-- root/root 20738 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/parameter_controller.py -rw-r--r-- root/root 9210 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/predicate.py -rw-r--r-- root/root 5038 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/simulate.py -rw-r--r-- root/root 2486 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/solved_models.py -rw-r--r-- root/root 1758 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/solved_models_numba.py -rw-r--r-- root/root 2390 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/substitution_calculation.py -rw-r--r-- root/root 37764 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/evolve/substitution_model.py drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/format/ -rw-r--r-- root/root 730 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/format/__init__.py -rw-r--r-- root/root 1903 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/format/alignment.py -rw-r--r-- root/root 5082 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/format/bedgraph.py -rw-r--r-- root/root 2069 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/format/clustal.py -rw-r--r-- root/root 1726 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/format/fasta.py -rw-r--r-- root/root 1618 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/format/gde.py -rw-r--r-- root/root 1335 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/format/nexus.py -rw-r--r-- root/root 1694 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/format/paml.py -rw-r--r-- root/root 2215 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/format/phylip.py -rw-r--r-- root/root 31829 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/format/table.py -rw-r--r-- root/root 3225 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/format/util.py drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/ -rw-r--r-- root/root 703 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/__init__.py -rw-r--r-- root/root 53729 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/distance_transform.py -rw-r--r-- root/root 6771 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/geometry.py -rw-r--r-- root/root 7217 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/markov.py -rw-r--r-- root/root 3460 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/matrix_exponential_integration.py -rw-r--r-- root/root 4738 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/matrix_exponentiation.py -rw-r--r-- root/root 3906 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/matrix_logarithm.py -rw-r--r-- root/root 4100 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/measure.py -rw-r--r-- root/root 6543 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/optimisers.py -rw-r--r-- root/root 9277 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/period.py -rw-r--r-- root/root 1613 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/period_numba.py -rw-r--r-- root/root 3578 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/scipy_optimisers.py -rw-r--r-- root/root 16786 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/scipy_optimize.py -rw-r--r-- root/root 9364 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/simannealingoptimiser.py -rw-r--r-- root/root 4148 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/solve.py drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/stats/ -rw-r--r-- root/root 656 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/stats/__init__.py -rw-r--r-- root/root 13501 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/stats/contingency.py -rw-r--r-- root/root 17879 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/stats/distribution.py -rw-r--r-- root/root 1104 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/stats/information_criteria.py -rw-r--r-- root/root 6209 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/stats/jackknife.py -rw-r--r-- root/root 3718 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/stats/kendall.py -rw-r--r-- root/root 3796 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/stats/ks.py -rw-r--r-- root/root 11720 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/stats/number.py -rw-r--r-- root/root 7115 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/stats/period.py -rw-r--r-- root/root 33120 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/stats/special.py -rw-r--r-- root/root 63171 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/stats/test.py -rw-r--r-- root/root 8181 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/maths/util.py drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/ -rw-r--r-- root/root 956 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/__init__.py -rw-r--r-- root/root 11642 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/blast.py -rw-r--r-- root/root 10001 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/blast_xml.py -rw-r--r-- root/root 4904 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/cigar.py -rw-r--r-- root/root 1128 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/cisbp.py -rw-r--r-- root/root 3455 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/clustal.py -rw-r--r-- root/root 1665 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/cogent3_json.py -rw-r--r-- root/root 2163 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/dialign.py -rw-r--r-- root/root 58727 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/ebi.py -rw-r--r-- root/root 9896 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/fasta.py -rw-r--r-- root/root 4446 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/gbseq.py -rw-r--r-- root/root 1739 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/gcg.py -rw-r--r-- root/root 22640 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/genbank.py -rw-r--r-- root/root 3618 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/gff.py -rw-r--r-- root/root 2845 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/greengenes.py -rw-r--r-- root/root 1255 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/jaspar.py -rw-r--r-- root/root 10509 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/locuslink.py -rw-r--r-- root/root 9226 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/ncbi_taxonomy.py -rw-r--r-- root/root 7130 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/newick.py -rw-r--r-- root/root 7281 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/nexus.py -rw-r--r-- root/root 1063 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/paml.py -rw-r--r-- root/root 1516 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/paml_matrix.py -rw-r--r-- root/root 3944 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/phylip.py -rw-r--r-- root/root 2058 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/psl.py -rw-r--r-- root/root 5315 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/rdb.py -rw-r--r-- root/root 20438 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/record.py -rw-r--r-- root/root 6816 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/record_finder.py -rw-r--r-- root/root 3158 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/sequence.py -rw-r--r-- root/root 5187 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/table.py -rw-r--r-- root/root 2484 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/tinyseq.py -rw-r--r-- root/root 6341 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/tree.py -rw-r--r-- root/root 2657 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/tree_xml.py -rw-r--r-- root/root 4253 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/parse/unigene.py drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/phylo/ -rw-r--r-- root/root 411 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/phylo/__init__.py -rw-r--r-- root/root 10615 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/phylo/consensus.py -rw-r--r-- root/root 3357 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/phylo/least_squares.py -rw-r--r-- root/root 2546 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/phylo/maximum_likelihood.py -rw-r--r-- root/root 9796 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/phylo/nj.py -rw-r--r-- root/root 5409 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/phylo/tree_collection.py -rw-r--r-- root/root 9840 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/phylo/tree_space.py -rw-r--r-- root/root 2857 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/phylo/util.py drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/recalculation/ -rw-r--r-- root/root 356 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/recalculation/__init__.py -rw-r--r-- root/root 23431 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/recalculation/calculation.py -rw-r--r-- root/root 22851 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/recalculation/definition.py -rw-r--r-- root/root 30532 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/recalculation/scope.py -rw-r--r-- root/root 2944 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/recalculation/setting.py drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/util/ -rw-r--r-- root/root 684 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/util/__init__.py -rw-r--r-- root/root 1515 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/util/checkpointing.py -rw-r--r-- root/root 11192 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/util/deserialise.py -rw-r--r-- root/root 19907 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/util/dict_array.py -rw-r--r-- root/root 10334 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/util/io.py -rw-r--r-- root/root 33482 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/util/misc.py -rw-r--r-- root/root 7650 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/util/parallel.py -rw-r--r-- root/root 6678 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/util/progress_display.py -rwxr-xr-x root/root 16571 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/util/recode_alignment.py -rw-r--r-- root/root 70023 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/util/table.py -rw-r--r-- root/root 3677 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/util/transform.py -rw-r--r-- root/root 3420 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/util/union_dict.py -rw-r--r-- root/root 1934 2023-02-22 07:07 ./usr/lib/python3/dist-packages/cogent3/util/warning.py drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/ -rw-r--r-- root/root 99549 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/1A1X.pdb -rw-r--r-- root/root 83673 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/1LJO.pdb -rw-r--r-- root/root 163053 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/2E12.pdb -rw-r--r-- root/root 2102 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/ENSG00000198712.fa -rw-r--r-- root/root 34368 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/F6AVWTA01.sff -rw-r--r-- root/root 461873 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/Homo_sapiens_codon_usage.pri -rw-r--r-- root/root 682 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/M0926_1.02.txt -rw-r--r-- root/root 14989 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/annotated_seq.gb -rw-r--r-- root/root 854 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/bowtie_output.map -rw-r--r-- root/root 168104 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/brca1.fasta -rw-r--r-- root/root 1323 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/brca1_5.250.paml -rw-r--r-- root/root 352 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/brca1_5.paml -rw-r--r-- root/root 47 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/brca1_5.tree -rw-r--r-- root/root 104 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/c_elegans_WS199_dna_shortened.fasta -rw-r--r-- root/root 1296 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/c_elegans_WS199_shortened_gff.gff3 -rw-r--r-- root/root 1323 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/ensembl_sample.gff3 -rw-r--r-- root/root 1312 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/fastq.txt -rw-r--r-- root/root 5411 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/formattest.aln -rw-r--r-- root/root 3122 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/formattest.fasta -rw-r--r-- root/root 790 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/formattest.fasta.bz2 -rw-r--r-- root/root 719 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/formattest.fasta.gz -rw-r--r-- root/root 3105 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/formattest.gde -rw-r--r-- root/root 3499 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/formattest.msf -rw-r--r-- root/root 3103 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/formattest.paml -rw-r--r-- root/root 3528 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/formattest.phylip -rw-r--r-- root/root 514 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/gff2_test.gff -rw-r--r-- root/root 7042 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/interleaved.phylip -rw-r--r-- root/root 12921 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/long_testseqs.fasta -rw-r--r-- root/root 157 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/long_testseqs.tree -rw-r--r-- root/root 579 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/murphy.tree -rw-r--r-- root/root 2813 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/nexus_aa.nxs -rw-r--r-- root/root 478 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/nexus_comments.nex -rw-r--r-- root/root 8290 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/nexus_dna.nex -rw-r--r-- root/root 401 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/nexus_mixed.nex -rw-r--r-- root/root 20093 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/primate_brca1.fasta -rw-r--r-- root/root 69 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/primate_brca1.tree -rw-r--r-- root/root 29415 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/primates_brca1.fasta -rw-r--r-- root/root 101 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/primates_brca1.tree -rw-r--r-- root/root 244 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/sample.jaspar -rw-r--r-- root/root 251 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/sample.tsv -rw-r--r-- root/root 240815 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/sample_locked.tinydb -rw-r--r-- root/root 1105324 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/sample_locked_w_log.tinydb -rw-r--r-- root/root 5389 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/scitrack.log -rw-r--r-- root/root 9918 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/site-het-param-rules.json -rw-r--r-- root/root 767 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/test.psl -rw-r--r-- root/root 2216 2023-02-22 07:07 ./usr/lib/python3/dist-packages/data/test.sff drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/share/ drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/ -rw-r--r-- root/root 364 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/README.test -rw-r--r-- root/root 1971 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/changelog.Debian.gz -rw-r--r-- root/root 1987 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/copyright -rw-r--r-- root/root 478 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/run-unit-test drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/tests/ -rw-r--r-- root/root 584 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/__init__.py -rw-r--r-- root/root 1912 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/benchmark.py.gz -rw-r--r-- root/root 1449 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/benchmark_aligning.py drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/tests/data/ -rw-r--r-- root/root 99549 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/1A1X.pdb -rw-r--r-- root/root 83673 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/1LJO.pdb -rw-r--r-- root/root 163053 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/2E12.pdb -rw-r--r-- root/root 2102 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/ENSG00000198712.fa -rw-r--r-- root/root 12006 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/F6AVWTA01.sff.gz -rw-r--r-- root/root 146765 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/Homo_sapiens_codon_usage.pri.gz -rw-r--r-- root/root 682 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/M0926_1.02.txt -rw-r--r-- root/root 5905 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/annotated_seq.gb.gz -rw-r--r-- root/root 854 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/bowtie_output.map -rw-r--r-- root/root 168104 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/brca1.fasta -rw-r--r-- root/root 1323 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/brca1_5.250.paml -rw-r--r-- root/root 352 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/brca1_5.paml -rw-r--r-- root/root 47 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/brca1_5.tree -rw-r--r-- root/root 104 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/c_elegans_WS199_dna_shortened.fasta -rw-r--r-- root/root 1296 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/c_elegans_WS199_shortened_gff.gff3 -rw-r--r-- root/root 1323 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/ensembl_sample.gff3 -rw-r--r-- root/root 1312 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/fastq.txt -rw-r--r-- root/root 1357 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/formattest.aln.gz -rw-r--r-- root/root 3122 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/formattest.fasta -rw-r--r-- root/root 790 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/formattest.fasta.bz2 -rw-r--r-- root/root 719 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/tests/data/formattest.fasta.gz -rw-r--r-- root/root 3105 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/formattest.gde -rw-r--r-- root/root 3499 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/formattest.msf -rw-r--r-- root/root 3103 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/formattest.paml -rw-r--r-- root/root 3528 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/formattest.phylip -rw-r--r-- root/root 514 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/gff2_test.gff -rw-r--r-- root/root 1321 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/interleaved.phylip.gz -rw-r--r-- root/root 12921 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/long_testseqs.fasta -rw-r--r-- root/root 157 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/long_testseqs.tree -rw-r--r-- root/root 579 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/murphy.tree -rw-r--r-- root/root 2813 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/nexus_aa.nxs -rw-r--r-- root/root 478 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/nexus_comments.nex -rw-r--r-- root/root 2387 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/nexus_dna.nex.gz -rw-r--r-- root/root 401 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/nexus_mixed.nex -rw-r--r-- root/root 20093 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/primate_brca1.fasta -rw-r--r-- root/root 69 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/primate_brca1.tree -rw-r--r-- root/root 29415 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/primates_brca1.fasta -rw-r--r-- root/root 101 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/primates_brca1.tree -rw-r--r-- root/root 244 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/sample.jaspar -rw-r--r-- root/root 251 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/sample.tsv -rw-r--r-- root/root 42127 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/sample_locked.tinydb.gz -rw-r--r-- root/root 239318 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/sample_locked_w_log.tinydb.gz -rw-r--r-- root/root 1272 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/scitrack.log.gz -rw-r--r-- root/root 9918 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/site-het-param-rules.json -rw-r--r-- root/root 767 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/test.psl -rw-r--r-- root/root 2216 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/data/test.sff drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/tests/test_align/ -rw-r--r-- root/root 338 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_align/__init__.py -rw-r--r-- root/root 3012 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_align/test_align.py.gz -rw-r--r-- root/root 3664 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_align/test_compare.py.gz drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/tests/test_app/ -rw-r--r-- root/root 22 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/tests/test_app/data.zip -rw-r--r-- root/root 4649 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_app/test_align.py.gz -rw-r--r-- root/root 1431 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_app/test_app_mpi.py -rw-r--r-- root/root 7131 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_app/test_composable.py.gz -rw-r--r-- root/root 4600 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_app/test_data_store_new.py.gz -rw-r--r-- root/root 1995 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_app/test_dist.py.gz -rw-r--r-- root/root 5933 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/tests/test_app/test_evo.py.gz -rw-r--r-- root/root 2050 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_app/test_init.py.gz -rw-r--r-- root/root 5010 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_app/test_io_new.py.gz -rw-r--r-- root/root 2633 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_app/test_result.py.gz -rw-r--r-- root/root 3835 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_app/test_sample.py.gz -rw-r--r-- root/root 4175 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_app/test_sqlite_data_store.py.gz -rw-r--r-- root/root 1594 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_app/test_translate.py.gz -rw-r--r-- root/root 1979 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_app/test_tree.py.gz -rw-r--r-- root/root 1195 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_app/test_typing.py.gz drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/tests/test_cluster/ -rw-r--r-- root/root 359 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_cluster/__init__.py -rw-r--r-- root/root 1634 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_cluster/test_UPGMA.py.gz drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/tests/test_core/ -rw-r--r-- root/root 723 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_core/__init__.py -rw-r--r-- root/root 25944 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_core/test_alignment.py.gz -rw-r--r-- root/root 2827 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_core/test_alphabet.py.gz -rw-r--r-- root/root 2406 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_core/test_annotation.py.gz -rw-r--r-- root/root 6834 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_core/test_core_standalone.py.gz -rw-r--r-- root/root 6244 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_core/test_features.py.gz -rw-r--r-- root/root 3752 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_core/test_genetic_code.py.gz -rw-r--r-- root/root 1724 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_core/test_info.py.gz -rw-r--r-- root/root 4164 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_core/test_location.py.gz -rw-r--r-- root/root 1550 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_core/test_maps.py.gz -rw-r--r-- root/root 7819 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_core/test_moltype.py.gz -rw-r--r-- root/root 3715 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_core/test_profile.py.gz -rw-r--r-- root/root 2729 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_core/test_seq_aln_integration.py.gz -rw-r--r-- root/root 10995 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_core/test_sequence.py.gz -rw-r--r-- root/root 17185 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_core/test_tree.py.gz drwxr-xr-x root/root 0 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_data/ -rw-r--r-- root/root 310 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_data/__init__.py -rw-r--r-- root/root 1793 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_data/test_molecular_weight.py drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/tests/test_draw/ -rw-r--r-- root/root 403 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_draw/__init__.py -rw-r--r-- root/root 2347 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_draw/test_dendrogram.py.gz -rw-r--r-- root/root 1733 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_draw/test_dotplot.py.gz -rw-r--r-- root/root 3319 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_draw/test_draw_integration.py.gz -rw-r--r-- root/root 3061 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_draw/test_logo.py -rw-r--r-- root/root 1499 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_draw/test_shapes.py drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/tests/test_evolve/ -rw-r--r-- root/root 603 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_evolve/__init__.py -rw-r--r-- root/root 1366 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_best_likelihood.py.gz -rw-r--r-- root/root 1701 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_bootstrap.py.gz -rw-r--r-- root/root 166620 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_coevolution.py.gz -rw-r--r-- root/root 5983 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_distance.py.gz -rw-r--r-- root/root 14031 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_likelihood_function.py.gz -rw-r--r-- root/root 1525 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_models.py.gz -rw-r--r-- root/root 1293 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_motifchange.py.gz -rw-r--r-- root/root 3768 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_newq.py.gz -rw-r--r-- root/root 14985 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_ns_substitution_model.py.gz -rw-r--r-- root/root 2434 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_parameter_controller.py.gz -rw-r--r-- root/root 2152 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_scale_rules.py.gz -rw-r--r-- root/root 2651 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_simulation.py -rw-r--r-- root/root 2682 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_evolve/test_substitution_model.py.gz drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/tests/test_format/ -rw-r--r-- root/root 423 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_format/__init__.py -rw-r--r-- root/root 1039 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_format/test_bedgraph.py.gz -rw-r--r-- root/root 2674 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_format/test_clustal.py -rw-r--r-- root/root 2419 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_format/test_fasta.py drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/tests/test_maths/ -rw-r--r-- root/root 561 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_maths/__init__.py -rw-r--r-- root/root 3804 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_maths/test_distance_transform.py.gz -rw-r--r-- root/root 1821 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_maths/test_geometry.py.gz -rw-r--r-- root/root 1574 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_maths/test_matrix_exponential_integration.py.gz -rw-r--r-- root/root 1362 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_maths/test_matrix_logarithm.py.gz -rw-r--r-- root/root 2116 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_maths/test_measure.py.gz -rw-r--r-- root/root 3343 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_maths/test_optimisers.py -rw-r--r-- root/root 2950 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_maths/test_period.py.gz drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/ -rw-r--r-- root/root 400 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/__init__.py -rw-r--r-- root/root 2235 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/test_contingency.py.gz -rw-r--r-- root/root 8079 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/test_distribution.py.gz -rw-r--r-- root/root 1080 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/test_information_criteria.py -rw-r--r-- root/root 1796 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/test_jackknife.py.gz -rw-r--r-- root/root 1515 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/test_ks.py.gz -rw-r--r-- root/root 2895 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/test_number.py.gz -rw-r--r-- root/root 1512 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/test_period.py.gz -rw-r--r-- root/root 4452 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/test_special.py.gz -rw-r--r-- root/root 16939 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_maths/test_stats/test_test.py.gz -rw-r--r-- root/root 1624 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_maths/test_util.py.gz drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/tests/test_parse/ -rw-r--r-- root/root 864 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/__init__.py -rw-r--r-- root/root 3103 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_blast.py.gz -rw-r--r-- root/root 3260 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_blast_xml.py.gz -rw-r--r-- root/root 3287 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_cigar.py -rw-r--r-- root/root 1592 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_clustal.py.gz -rw-r--r-- root/root 1727 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_dialign.py.gz -rw-r--r-- root/root 8805 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_ebi.py.gz -rw-r--r-- root/root 4409 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_fasta.py.gz -rw-r--r-- root/root 1914 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_gbseq.py.gz -rw-r--r-- root/root 6232 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_genbank.py.gz -rw-r--r-- root/root 1489 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_gff.py.gz -rw-r--r-- root/root 2142 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_greengenes.py.gz -rw-r--r-- root/root 3772 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_locuslink.py.gz -rw-r--r-- root/root 3442 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_ncbi_taxonomy.py.gz -rw-r--r-- root/root 4093 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_nexus.py.gz -rw-r--r-- root/root 2496 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_pamlmatrix.py -rw-r--r-- root/root 4160 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_phylip.py.gz -rw-r--r-- root/root 1737 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_psl.py -rw-r--r-- root/root 1809 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_pwm_parsers.py -rw-r--r-- root/root 2808 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_rdb.py.gz -rw-r--r-- root/root 4576 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_record.py.gz -rw-r--r-- root/root 1768 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_record_finder.py.gz -rw-r--r-- root/root 1740 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_tinyseq.py -rw-r--r-- root/root 2125 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_tree.py.gz -rw-r--r-- root/root 2202 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_parse/test_unigene.py.gz -rw-r--r-- root/root 4098 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_phylo.py.gz -rw-r--r-- root/root 2312 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_recalculation.py.gz drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/tests/test_util/ -rw-r--r-- root/root 553 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_util/__init__.py -rw-r--r-- root/root 3924 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_util/test_deserialise.py.gz -rw-r--r-- root/root 4013 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_util/test_dictarray.py.gz -rw-r--r-- root/root 2954 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/tests/test_util/test_io.py.gz -rw-r--r-- root/root 8790 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_util/test_misc.py.gz -rw-r--r-- root/root 2606 2023-02-22 07:07 ./usr/share/doc/python3-cogent3/tests/test_util/test_parallel.py -rw-r--r-- root/root 2654 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_util/test_recode_alignment.py.gz -rw-r--r-- root/root 14557 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_util/test_table.py.gz -rw-r--r-- root/root 1912 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_util/test_transform.py.gz -rw-r--r-- root/root 1176 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/test_util/test_union_dict.py.gz -rw-r--r-- root/root 3332 2023-02-12 07:36 ./usr/share/doc/python3-cogent3/tests/timetrial.py drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/share/lintian/ drwxr-xr-x root/root 0 2023-02-22 07:07 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 75 2023-02-22 07:07 ./usr/share/lintian/overrides/python3-cogent3 +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: ppc64el Build Type: any Build-Space: 47704 Build-Time: 168 Distribution: lunar-proposed Host Architecture: ppc64el Install-Time: 149 Job: python-cogent_2023.2.12a1+dfsg-1.dsc Machine Architecture: ppc64el Package: python-cogent Package-Time: 319 Source-Version: 2023.2.12a1+dfsg-1 Space: 47704 Status: successful Version: 2023.2.12a1+dfsg-1 -------------------------------------------------------------------------------- Finished at 2023-02-22T17:19:22Z Build needed 00:05:19, 47704k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=lunar --arch=ppc64el PACKAGEBUILD-25612566 Scanning for processes to kill in build PACKAGEBUILD-25612566