https://launchpad.net/ubuntu/+source/python-cogent/2023.12.15a1+dfsg-1/+build/27687842 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-073 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:53:38 UTC 2023 aarch64 Buildd toolchain package versions: launchpad-buildd_235~645~ubuntu20.04.1 python3-lpbuildd_235~645~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 26 Jan 23:14:58 ntpdate[2694]: adjust time server 10.211.37.1 offset -0.000290 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27687842 --image-type chroot /home/buildd/filecache-default/0aaa0d191106d33e51979a9c6a062e50b7f5b3b2 Creating target for build PACKAGEBUILD-27687842 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27687842 Starting target for build PACKAGEBUILD-27687842 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27687842 'deb http://ftpmaster.internal/ubuntu noble main universe' 'deb http://ftpmaster.internal/ubuntu noble-security main universe' 'deb http://ftpmaster.internal/ubuntu noble-updates main universe' 'deb http://ftpmaster.internal/ubuntu noble-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-27687842 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27687842 Updating target for build PACKAGEBUILD-27687842 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [256 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 Packages [1395 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [517 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 Packages [14.7 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6021 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [241 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [89.8 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [1144 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [398 kB] Fetched 25.1 MB in 1min 3s (400 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.36 libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-13-aarch64-linux-gnu gcc-14-base gcc-aarch64-linux-gnu libperl5.38 libunistring5 perl-modules-5.38 The following packages will be upgraded: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-aarch64-linux-gnu binutils-common bsdextrautils bsdutils coreutils cpp cpp-13 debconf debconf-i18n debianutils diffutils dpkg dpkg-dev fakeroot g++ g++-13 gcc gcc-13 gcc-13-base grep init init-system-helpers krb5-locales libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error-l10n libgpg-error0 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libitm1 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblsan0 liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libpng16-16 libproc2-0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libssl3 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login lto-disabled-list mawk mount ncurses-base ncurses-bin openssl optipng passwd perl perl-base perl-modules-5.36 pinentry-curses procps psmisc readline-common sed systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring usrmerge util-linux uuid-runtime xz-utils zlib1g 149 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. Need to get 116 MB of archives. After this operation, 60.0 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3 [71.9 kB] Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.38-3ubuntu1 [1573 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.38-3ubuntu1 [19.4 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc-common all 1.3.4+ds-1build1 [8566 B] Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc-dev arm64 1.3.4+ds-1build1 [232 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libgssapi-krb5-2 arm64 1.20.1-5build1 [139 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libkrb5-3 arm64 1.20.1-5build1 [347 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libk5crypto3 arm64 1.20.1-5build1 [85.5 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libkrb5support0 arm64 1.20.1-5build1 [33.5 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libssl3 arm64 3.0.10-1ubuntu3 [1752 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc3 arm64 1.3.4+ds-1build1 [99.3 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl2 arm64 1.3.0-3 [40.9 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcrypt1 arm64 1:4.4.36-4 [100 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.6.0-14.14 [1554 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gcc-14-base arm64 14-20240126-2ubuntu1 [46.0 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgcc-s1 arm64 14-20240126-2ubuntu1 [49.9 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libc6 arm64 2.38-3ubuntu1 [2740 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 base-files arm64 13ubuntu6 [84.1 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 debianutils arm64 5.16 [93.7 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 bash arm64 5.2.21-2ubuntu1 [777 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 bsdutils arm64 1:2.39.2-6ubuntu1 [96.9 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 coreutils arm64 9.4-2ubuntu2 [1715 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 diffutils arm64 1:3.10-1 [174 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libgpg-error-l10n all 1.47-3build1 [8024 B] Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libgpg-error0 arm64 1.47-3build1 [69.9 kB] Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgcrypt20 arm64 1.10.3-2 [472 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma5 arm64 5.4.5-0.3 [140 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libstdc++6 arm64 14-20240126-2ubuntu1 [749 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libacl1 arm64 2.3.1-4ubuntu1 [19.4 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libapparmor1 arm64 4.0.0~alpha2-0ubuntu8 [48.8 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libaudit-common all 1:3.1.2-2 [5594 B] Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libcap-ng0 arm64 0.8.4-1 [16.4 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libaudit1 arm64 1:3.1.2-2 [47.4 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libblkid1 arm64 2.39.2-6ubuntu1 [121 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libzstd1 arm64 1.5.5+dfsg2-2 [270 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libkmod2 arm64 30+20230601-2ubuntu1 [49.8 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-8-0 arm64 10.42-4ubuntu1 [211 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libselinux1 arm64 3.5-2 [79.4 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libmount1 arm64 2.39.2-6ubuntu1 [132 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtext-iconv-perl arm64 1.7-8build1 [13.0 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtext-charwidth-perl arm64 0.04-11build1 [9316 B] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-modules-5.38 all 5.38.2-3 [3110 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libperl5.38 arm64 5.38.2-3 [4772 kB] Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl arm64 5.38.2-3 [231 kB] Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-base arm64 5.38.2-3 [1777 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 liblocale-gettext-perl arm64 1.07-6build1 [15.0 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 perl-modules-5.36 all 5.36.0-10ubuntu1 [2984 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libperl5.36 arm64 5.36.0-10ubuntu1 [4673 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libdb5.3 arm64 5.3.28+dfsg2-4 [718 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libgdbm6 arm64 1.23-5 [33.8 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libgdbm-compat4 arm64 1.23-5 [6302 B] Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g arm64 1:1.3.dfsg-3ubuntu1 [61.6 kB] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 debconf-i18n all 1.5.85 [205 kB] Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 debconf all 1.5.85 [124 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libpam0g arm64 1.5.2-9.1ubuntu2 [65.8 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libseccomp2 arm64 2.5.4-2ubuntu1 [50.1 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd-sysv arm64 255.2-3ubuntu2 [11.9 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd-dev all 255.2-3ubuntu2 [101 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd arm64 255.2-3ubuntu2 [3397 kB] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsystemd-shared arm64 255.2-3ubuntu2 [2012 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libargon2-1 arm64 0~20190702+dfsg-4 [20.5 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libuuid1 arm64 2.39.2-6ubuntu1 [34.3 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libcryptsetup12 arm64 2:2.6.1-6ubuntu1 [240 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libfdisk1 arm64 2.39.2-6ubuntu1 [141 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 mount arm64 2.39.2-6ubuntu1 [116 kB] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsystemd0 arm64 255.2-3ubuntu2 [421 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libudev1 arm64 255.2-3ubuntu2 [170 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 libxxhash0 arm64 0.8.2-2 [21.2 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libapt-pkg6.0 arm64 2.7.10 [929 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 tar arm64 1.35+dfsg-3 [248 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 dpkg arm64 1.22.2ubuntu2 [1290 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 grep arm64 3.11-4 [174 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 login arm64 1:4.13+dfsg1-3ubuntu1 [200 kB] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 ncurses-bin arm64 6.4+20240113-1 [186 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 sed arm64 4.9-2 [201 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 util-linux arm64 2.39.2-6ubuntu1 [1113 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 libdebconfclient0 arm64 0.271ubuntu1 [11.2 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 base-passwd arm64 3.6.3 [51.1 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libc-bin arm64 2.38-3ubuntu1 [590 kB] Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 ncurses-base all 6.4+20240113-1 [25.4 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 sysvinit-utils arm64 3.08-3ubuntu1 [33.3 kB] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 apt arm64 2.7.10 [1333 kB] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 apt-utils arm64 2.7.10 [205 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 libffi8 arm64 3.4.4-2 [22.2 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 libp11-kit0 arm64 0.25.3-2ubuntu2 [274 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 libunistring5 arm64 1.1-2 [528 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 libidn2-0 arm64 2.3.4-1build1 [65.3 kB] Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgnutls30 arm64 3.8.3-1ubuntu1 [942 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main arm64 libpam-modules-bin arm64 1.5.2-9.1ubuntu2 [47.0 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 libpam-modules arm64 1.5.2-9.1ubuntu2 [284 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 init arm64 1.66ubuntu1 [6186 B] Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 libsmartcols1 arm64 2.39.2-6ubuntu1 [62.9 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 uuid-runtime arm64 2.39.2-6ubuntu1 [32.3 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 libattr1 arm64 1:2.5.2-1 [11.0 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 libmd0 arm64 1.1.0-2 [24.7 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main arm64 libpam-runtime all 1.5.2-9.1ubuntu2 [40.6 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 libsemanage-common all 3.5-1build1 [9982 B] Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 libsepol2 arm64 3.5-2 [289 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main arm64 libsemanage2 arm64 3.5-1build1 [90.0 kB] Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libncursesw6 arm64 6.4+20240113-1 [145 kB] Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtinfo6 arm64 6.4+20240113-1 [104 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main arm64 passwd arm64 1:4.13+dfsg1-3ubuntu1 [837 kB] Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 g++-13 arm64 13.2.0-11ubuntu1 [13.9 kB] Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gcc-13 arm64 13.2.0-11ubuntu1 [463 kB] Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 cpp-13 arm64 13.2.0-11ubuntu1 [1030 B] Get:109 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-11ubuntu1 [9539 kB] Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcc1-0 arm64 14-20240126-2ubuntu1 [44.8 kB] Get:111 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgprofng0 arm64 2.41.90.20240122-1ubuntu1 [777 kB] Get:112 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libctf0 arm64 2.41.90.20240122-1ubuntu1 [95.8 kB] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libctf-nobfd0 arm64 2.41.90.20240122-1ubuntu1 [99.4 kB] Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsframe1 arm64 2.41.90.20240122-1ubuntu1 [14.0 kB] Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 binutils-aarch64-linux-gnu arm64 2.41.90.20240122-1ubuntu1 [3298 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libbinutils arm64 2.41.90.20240122-1ubuntu1 [768 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 binutils arm64 2.41.90.20240122-1ubuntu1 [18.1 kB] Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 binutils-common arm64 2.41.90.20240122-1ubuntu1 [238 kB] Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libstdc++-13-dev arm64 13.2.0-11ubuntu1 [2319 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgomp1 arm64 14-20240126-2ubuntu1 [144 kB] Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libitm1 arm64 14-20240126-2ubuntu1 [27.6 kB] Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libatomic1 arm64 14-20240126-2ubuntu1 [11.1 kB] Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libasan8 arm64 14-20240126-2ubuntu1 [2923 kB] Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 liblsan0 arm64 14-20240126-2ubuntu1 [1282 kB] Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgcc-13-dev arm64 13.2.0-11ubuntu1 [2464 kB] Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtsan2 arm64 14-20240126-2ubuntu1 [2689 kB] Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libubsan1 arm64 14-20240126-2ubuntu1 [1151 kB] Get:128 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libhwasan0 arm64 14-20240126-2ubuntu1 [1546 kB] Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-11ubuntu1 [18.7 MB] Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-11ubuntu1 [10.9 MB] Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gcc-13-base arm64 13.2.0-11ubuntu1 [46.4 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main arm64 libproc2-0 arm64 2:4.0.4-2ubuntu1 [56.5 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main arm64 mawk arm64 1.3.4.20231126-1 [123 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main arm64 procps arm64 2:4.0.4-2ubuntu1 [706 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main arm64 usrmerge all 38ubuntu1 [58.8 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main arm64 krb5-locales all 1.20.1-5build1 [13.7 kB] Get:137 http://ftpmaster.internal/ubuntu noble/main arm64 readline-common all 8.2-3 [56.2 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main arm64 libreadline8 arm64 8.2-3 [152 kB] Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsqlite3-0 arm64 3.45.0-1 [703 kB] Get:140 http://ftpmaster.internal/ubuntu noble/main arm64 openssl arm64 3.0.10-1ubuntu3 [1168 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main arm64 tzdata all 2023d-1ubuntu2 [321 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main arm64 bash-completion all 1:2.11-8 [180 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main arm64 bsdextrautils arm64 2.39.2-6ubuntu1 [71.4 kB] Get:144 http://ftpmaster.internal/ubuntu noble/main arm64 libpng16-16 arm64 1.6.40-3 [203 kB] Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 psmisc arm64 23.6-2 [178 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main arm64 xz-utils arm64 5.4.5-0.3 [277 kB] Get:147 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 g++ arm64 4:13.2.0-3ubuntu1 [1080 B] Get:148 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gcc arm64 4:13.2.0-3ubuntu1 [5012 B] Get:149 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 cpp arm64 4:13.2.0-3ubuntu1 [22.4 kB] Get:150 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-3ubuntu1 [5156 B] Get:151 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-3ubuntu1 [1198 B] Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-3ubuntu1 [958 B] Get:153 http://ftpmaster.internal/ubuntu noble/main arm64 dpkg-dev all 1.22.2ubuntu2 [1168 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main arm64 libdpkg-perl all 1.22.2ubuntu2 [321 kB] Get:155 http://ftpmaster.internal/ubuntu noble/main arm64 lto-disabled-list all 46 [12.3 kB] Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libfakeroot arm64 1.33-1 [32.5 kB] Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 fakeroot arm64 1.33-1 [66.9 kB] Get:158 http://ftpmaster.internal/ubuntu noble/main arm64 optipng arm64 0.7.7-3 [82.1 kB] Get:159 http://ftpmaster.internal/ubuntu noble/main arm64 pinentry-curses arm64 1.2.1-3ubuntu1 [34.0 kB] Preconfiguring packages ... 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Setting up libperl5.38:arm64 (5.38.2-3) ... Setting up binutils (2.41.90.20240122-1ubuntu1) ... Setting up gcc-13-aarch64-linux-gnu (13.2.0-11ubuntu1) ... Setting up perl (5.38.2-3) ... Setting up libtirpc-dev:arm64 (1.3.4+ds-1build1) ... Setting up gcc-13 (13.2.0-11ubuntu1) ... Setting up libdpkg-perl (1.22.2ubuntu2) ... Setting up cpp (4:13.2.0-3ubuntu1) ... Setting up libnsl2:arm64 (1.3.0-3) ... Setting up gcc-aarch64-linux-gnu (4:13.2.0-3ubuntu1) ... Setting up gcc (4:13.2.0-3ubuntu1) ... Setting up dpkg-dev (1.22.2ubuntu2) ... Setting up libnsl-dev:arm64 (1.3.0-3) ... Setting up libc6-dev:arm64 (2.38-3ubuntu1) ... Setting up libstdc++-13-dev:arm64 (13.2.0-11ubuntu1) ... Setting up g++-13-aarch64-linux-gnu (13.2.0-11ubuntu1) ... Setting up g++-13 (13.2.0-11ubuntu1) ... Setting up g++-aarch64-linux-gnu (4:13.2.0-3ubuntu1) ... Setting up g++ (4:13.2.0-3ubuntu1) ... Processing triggers for libc-bin (2.38-3ubuntu1) ... Processing triggers for debianutils (5.16) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-27687842 arm64 noble-proposed -c chroot:build-PACKAGEBUILD-27687842 --arch=arm64 --dist=noble-proposed --nolog python-cogent_2023.12.15a1+dfsg-1.dsc Initiating build PACKAGEBUILD-27687842 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:53:38 UTC 2023 aarch64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-arm64-073.buildd +==============================================================================+ | python-cogent 2023.12.15a1+dfsg-1 (arm64) Fri, 26 Jan 2024 23:26:01 +0000 | +==============================================================================+ Package: python-cogent Version: 2023.12.15a1+dfsg-1 Source Version: 2023.12.15a1+dfsg-1 Distribution: noble-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27687842/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/python-cogent-vNYFjo/resolver-EDJ2me' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-cogent_2023.12.15a1+dfsg-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/python-cogent-vNYFjo/python-cogent-2023.12.15a1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/python-cogent-vNYFjo' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-sequence-python3, 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, python3-sphinxcontrib.bibtex, python3-sphinx-design, python3-pydata-sphinx-theme, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-sequence-python3, 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, python3-sphinxcontrib.bibtex, python3-sphinx-design, python3-pydata-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 [590 B] Get:5 copy:/<>/apt_archive ./ Packages [667 B] Fetched 2220 B in 0s (11.7 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 packages were automatically installed and are no longer required: apt-utils bash-completion debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 liblocale-gettext-perl libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libunistring2 perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev blt cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file flit fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-glyphicons-halflings fonts-lyx gettext gettext-base groff-base intltool-debian jupyter-sphinx-theme-common libarchive-zip-perl libblas3 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 libhwloc15 libicu74 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 liblua5.4-0 libmagic-mgc libmagic1 libnghttp2-14 libnorm1 libopenjp2-7 libpfm4 libpgm-5.3-0 libpipeline1 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libpython3.12 libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libqhull-r8.0 libraqm0 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsodium23 libssh-4 libsub-override-perl libtbb12 libtbbbind-2-5 libtbbmalloc2 libtcl8.6 libtiff6 libtk8.6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 libyaml-0-2 libzmq5 llvm-14 llvm-14-linker-tools llvm-14-runtime m4 man-db media-types netbase 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-bleach python3-brotli python3-bs4 python3-build python3-certifi python3-cffi-backend python3-chardet python3-commonmark python3-contourpy 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-html5lib python3-idna python3-imagesize 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-latexcodec python3-lib2to3 python3-llvmlite python3-lxml python3-lz4 python3-markupsafe python3-matplotlib python3-minimal python3-mpmath python3-nbclient python3-nbconvert python3-nbformat python3-nbsphinx python3-numba python3-numpy python3-numpydoc python3-packaging python3-pandas python3-pandas-lib python3-pandocfilters python3-pil python3-pil.imagetk python3-pkg-resources python3-platformdirs python3-plotly python3-pluggy python3-prometheus-client python3-ptyprocess python3-py python3-pybtex python3-pybtex-docutils python3-pydata-sphinx-theme python3-pygments python3-pyparsing python3-pyproject-hooks python3-pyrsistent python3-pytest python3-pytest-cov python3-pytest-xdist 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-design python3-sphinx-gallery python3-sphinxcontrib.bibtex python3-sympy python3-tabulate python3-tenacity python3-terminado python3-tinycss2 python3-tinydb python3-tk python3-toml 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-yaml python3-zmq python3.11 python3.11-dev python3.11-minimal python3.12 python3.12-dev python3.12-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 low-memory-monitor libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk 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-rfc3987 python3-uritemplate python3-webcolors jupyter-sphinx-theme-doc python-latexcodec-doc llvmlite-doc python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common 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 gfortran python-pandas-doc python3-statsmodels python-pil-doc python3-ipykernel subversion python-pybtex-doc python-pybtex-docutils-doc 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 python-sphinxcontrib.bibtex-doc 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 python3.11-venv python3.11-doc binfmt-support python3.12-venv python3.12-doc sgml-base-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libhwloc-plugins javascript-common libjson-xs-perl libldap-common publicsuffix libsasl2-modules libltdl-dev llvm-14-dev libmail-sendmail-perl libpaper-utils python3-json-pointer python3-cssselect 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 cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file flit fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-glyphicons-halflings fonts-lyx gettext gettext-base groff-base intltool-debian jupyter-sphinx-theme-common libarchive-zip-perl libblas3 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 libhwloc15 libicu74 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 liblua5.4-0 libmagic-mgc libmagic1 libnghttp2-14 libnorm1 libopenjp2-7 libpfm4 libpgm-5.3-0 libpipeline1 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libpython3.12 libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libqhull-r8.0 libraqm0 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsodium23 libssh-4 libsub-override-perl libtbb12 libtbbbind-2-5 libtbbmalloc2 libtcl8.6 libtiff6 libtk8.6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 libyaml-0-2 libzmq5 llvm-14 llvm-14-linker-tools llvm-14-runtime m4 man-db media-types netbase 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-bleach python3-brotli python3-bs4 python3-build python3-certifi python3-cffi-backend python3-chardet python3-commonmark python3-contourpy 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-html5lib python3-idna python3-imagesize 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-latexcodec python3-lib2to3 python3-llvmlite python3-lxml python3-lz4 python3-markupsafe python3-matplotlib python3-minimal python3-mpmath python3-nbclient python3-nbconvert python3-nbformat python3-nbsphinx python3-numba python3-numpy python3-numpydoc python3-packaging python3-pandas python3-pandas-lib python3-pandocfilters python3-pil python3-pil.imagetk python3-pkg-resources python3-platformdirs python3-plotly python3-pluggy python3-prometheus-client python3-ptyprocess python3-py python3-pybtex python3-pybtex-docutils python3-pydata-sphinx-theme python3-pygments python3-pyparsing python3-pyproject-hooks python3-pyrsistent python3-pytest python3-pytest-cov python3-pytest-xdist 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-design python3-sphinx-gallery python3-sphinxcontrib.bibtex python3-sympy python3-tabulate python3-tenacity python3-terminado python3-tinycss2 python3-tinydb python3-tk python3-toml 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-yaml python3-zmq python3.11 python3.11-dev python3.11-minimal python3.12 python3.12-dev python3.12-minimal sbuild-build-depends-main-dummy sgml-base sphinx-common tk8.6-blt2.5 unicode-data x11-common xml-core zlib1g-dev 0 upgraded, 274 newly installed, 0 to remove and 0 not upgraded. Need to get 217 MB of archives. After this operation, 1114 MB of additional disk space will be used. 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arm64 libxdmcp6 arm64 1:1.1.3-0ubuntu5 [10.8 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb1 arm64 1.15-1 [47.6 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libx11-data all 2:1.8.7-1 [115 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libx11-6 arm64 2:1.8.7-1 [645 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libxext6 arm64 2:1.3.4-1build1 [31.1 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 man-db arm64 2.12.0-3 [1226 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 m4 arm64 1.4.19-4 [240 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 autoconf all 2.71-3 [339 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 autotools-dev all 20220109.1 [44.9 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 automake all 1:1.16.5-1.3 [558 kB] Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 autopoint all 0.21-14ubuntu1 [422 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libbrotli1 arm64 1.1.0-2 [339 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libfreetype6 arm64 2.13.2+dfsg-1 [390 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.14.2-6ubuntu1 [36.0 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.14.2-6ubuntu1 [140 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7 [618 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 blt arm64 2.5.3+dfsg-7 [4826 B] Get:66 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 cython3 arm64 3.0.8-1ubuntu1 [6240 kB] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdebhelper-perl all 13.11.10ubuntu1 [86.7 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 libtool all 2.4.7-7 [166 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 dh-autoreconf all 20 [16.1 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 libsub-override-perl all 0.10-1 [10.0 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 libdw1 arm64 0.190-1 [254 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 debugedit arm64 1:5.0-5 [45.9 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 dwz arm64 0.15-1 [110 kB] Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gettext arm64 0.21-14ubuntu1 [846 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 debhelper all 13.11.10ubuntu1 [863 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lib2to3 all 3.11.5-1 [79.0 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 python3-distutils all 3.11.5-1 [131 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 python3-setuptools all 68.1.2-2 [396 kB] Get:84 http://ftpmaster.internal/ubuntu noble/universe arm64 dh-python all 6.20231223 [128 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 xml-core all 0.19 [20.3 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 docutils-common all 0.20.1+dfsg-3 [132 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 python3-roman all 3.3-3 [9632 B] Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 python3-docutils all 0.20.1+dfsg-3 [393 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 python3-certifi all 2023.11.17-1 [165 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 python3-chardet all 5.2.0+dfsg-1 [117 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main arm64 python3-idna all 3.3-2 [45.4 kB] Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-urllib3 all 2.0.7-1 [113 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 python3-requests all 2.31.0+dfsg-1ubuntu1 [50.7 kB] Get:94 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-tomli-w all 1.0.0-2 [7368 B] Get:95 http://ftpmaster.internal/ubuntu noble/universe arm64 flit all 3.9.0-2 [86.3 kB] Get:96 http://ftpmaster.internal/ubuntu noble/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] Get:97 http://ftpmaster.internal/ubuntu noble/universe arm64 fonts-lyx all 2.4.0~RC1-2 [170 kB] Get:98 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] Get:99 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-bootswatch all 3.3.7+dfsg2-1.1 [133 kB] Get:100 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-sphinx-bootstrap-theme all 0.8.1-1 [430 kB] Get:101 http://ftpmaster.internal/ubuntu noble/universe arm64 jupyter-sphinx-theme-common all 0.0.6+ds1-11 [13.6 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.11.0-2build1 [143 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-4 [21.1 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-4 [54.5 kB] Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libldap2 arm64 2.6.6+dfsg-1~exp1ubuntu2 [193 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2build4 [59.2 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main arm64 libssh-4 arm64 0.10.6-2 [226 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main arm64 libcurl4 arm64 8.5.0-2ubuntu1 [394 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.18-1 [42.6 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main arm64 libexpat1-dev arm64 2.5.0-2 [123 kB] Get:111 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgfortran5 arm64 14-20240126-2ubuntu1 [441 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] Get:114 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc15 arm64 2.10.0-1 [158 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] Get:117 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] Get:118 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-metadata all 12-4 [6582 B] Get:119 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-3 [193 kB] Get:120 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.5 kB] Get:121 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-sphinxdoc all 7.2.6-3 [149 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main arm64 libjson-perl all 4.10000-1 [81.9 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.11.0-2build1 [2134 kB] Get:126 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] Get:129 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libllvm14 arm64 1:14.0.6-16build2 [22.8 MB] Get:130 http://ftpmaster.internal/ubuntu noble/main arm64 liblua5.4-0 arm64 5.4.6-2 [118 kB] Get:131 http://ftpmaster.internal/ubuntu noble/universe arm64 libnorm1 arm64 1.5.9+dfsg-3 [176 kB] Get:132 http://ftpmaster.internal/ubuntu noble/universe arm64 libpgm-5.3-0 arm64 5.3.128~dfsg-2 [151 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.12 arm64 3.12.1-2 [2287 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3ubuntu1 [895 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.12-dev arm64 3.12.1-2 [5392 kB] Get:136 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpython3-dev arm64 3.12.1-0ubuntu1 [9924 B] Get:137 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11 arm64 3.11.7-2 [2167 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-dev arm64 3.11.7-2 [5009 kB] Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpython3-all-dev arm64 3.12.1-0ubuntu1 [914 B] Get:140 http://ftpmaster.internal/ubuntu noble/universe arm64 libqhull-r8.0 arm64 2020.2-6 [188 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.3 [14.0 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main arm64 libsodium23 arm64 1.0.18-1build2 [123 kB] Get:144 http://ftpmaster.internal/ubuntu noble/universe arm64 libtbbmalloc2 arm64 2021.11.0-2ubuntu2 [43.8 kB] Get:145 http://ftpmaster.internal/ubuntu noble/universe arm64 libtbbbind-2-5 arm64 2021.11.0-2ubuntu2 [16.4 kB] Get:146 http://ftpmaster.internal/ubuntu noble/universe arm64 libtbb12 arm64 2021.11.0-2ubuntu2 [79.9 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.3 [190 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.3 [12.1 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.3 [25.0 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main arm64 libxslt1.1 arm64 1.1.35-1 [161 kB] Get:153 http://ftpmaster.internal/ubuntu noble/universe arm64 libzmq5 arm64 4.3.5-1 [246 kB] Get:154 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 llvm-14-runtime arm64 1:14.0.6-16build2 [461 kB] Get:155 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 llvm-14-linker-tools arm64 1:14.0.6-16build2 [1248 kB] Get:156 http://ftpmaster.internal/ubuntu noble/universe arm64 libpfm4 arm64 4.13.0+git16-g535c204-1 [69.8 kB] Get:157 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 llvm-14 arm64 1:14.0.6-16build2 [11.6 MB] Get:158 http://ftpmaster.internal/ubuntu noble/universe arm64 pandoc-data all 3.1.3-1 [92.4 kB] Get:159 http://ftpmaster.internal/ubuntu noble/universe arm64 pandoc arm64 3.1.3+ds-2 [27.7 MB] Get:160 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] Get:161 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pyproject-hooks all 1.0.0-2 [9434 B] Get:162 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-toml all 0.10.2-1 [16.5 kB] Get:163 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-wheel all 0.42.0-1 [53.1 kB] Get:164 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-build all 0.10.0-1 [17.6 kB] Get:165 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-installer all 0.7.0+dfsg1-2 [18.1 kB] Get:166 http://ftpmaster.internal/ubuntu noble/universe arm64 pybuild-plugin-pyproject all 6.20231223 [1762 B] Get:167 http://ftpmaster.internal/ubuntu noble/main arm64 python-babel-localedata all 2.10.3-3build1 [6357 kB] Get:168 http://ftpmaster.internal/ubuntu noble/universe arm64 python-matplotlib-data all 3.6.3-1ubuntu3 [2936 kB] Get:169 http://ftpmaster.internal/ubuntu noble/universe arm64 python-tinycss2-common all 1.2.1-2 [33.9 kB] Get:170 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-all arm64 3.12.1-0ubuntu1 [910 B] Get:171 http://ftpmaster.internal/ubuntu noble/main arm64 python3.12-dev arm64 3.12.1-2 [506 kB] Get:172 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-dev arm64 3.12.1-0ubuntu1 [26.7 kB] Get:173 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-dev arm64 3.11.7-2 [508 kB] Get:174 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-all-dev arm64 3.12.1-0ubuntu1 [914 B] Get:175 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-sniffio all 1.3.0-2 [7216 B] Get:176 http://ftpmaster.internal/ubuntu noble/main arm64 python3-typing-extensions all 4.7.1-2 [57.6 kB] Get:177 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-anyio all 4.2.0-1 [56.5 kB] Get:178 http://ftpmaster.internal/ubuntu noble/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] Get:179 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-argon2 arm64 21.1.0-2 [21.2 kB] Get:180 http://ftpmaster.internal/ubuntu noble/main arm64 python3-attr all 23.2.0-1 [57.2 kB] Get:181 http://ftpmaster.internal/ubuntu noble/main arm64 python3-tz all 2023.3.post1-2 [31.4 kB] Get:182 http://ftpmaster.internal/ubuntu noble/main arm64 python3-babel all 2.10.3-3build1 [87.5 kB] Get:183 http://ftpmaster.internal/ubuntu noble/main arm64 python3-six all 1.16.0-4 [12.4 kB] Get:184 http://ftpmaster.internal/ubuntu noble/main arm64 python3-webencodings all 0.5.1-5 [11.5 kB] Get:185 http://ftpmaster.internal/ubuntu noble/main arm64 python3-html5lib all 1.1-3ubuntu1 [88.7 kB] Get:186 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-bleach all 6.1.0-2 [49.6 kB] Get:187 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-brotli arm64 1.1.0-2 [345 kB] Get:188 http://ftpmaster.internal/ubuntu noble/main arm64 python3-soupsieve all 2.5-1 [33.0 kB] Get:189 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-bs4 all 4.12.3-1 [109 kB] Get:190 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-commonmark all 0.9.1-4 [45.8 kB] Get:191 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] Get:192 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-contourpy arm64 1.0.7-1build2 [244 kB] Get:193 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-coverage arm64 7.3.2-0ubuntu1 [147 kB] Get:194 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cycler all 0.11.0-1 [8156 B] Get:195 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] Get:196 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] Get:197 http://ftpmaster.internal/ubuntu noble/main arm64 python3-defusedxml all 0.7.1-2 [42.0 kB] Get:198 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-entrypoints all 0.4-2 [7146 B] Get:199 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-execnet all 2.0.0-2 [33.6 kB] Get:200 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fastjsonschema all 2.19.0-1 [19.6 kB] Get:201 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-scipy arm64 1.10.1-7 [18.7 MB] Get:202 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] Get:203 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mpmath all 1.2.1-2 [419 kB] Get:204 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-sympy all 1.12-7 [3966 kB] Get:205 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fs all 2.4.16-3 [91.1 kB] Get:206 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-lxml arm64 5.1.0-1 [2042 kB] Get:207 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build2 [28.4 kB] Get:208 http://ftpmaster.internal/ubuntu noble/universe arm64 unicode-data all 15.1.0-1 [8878 kB] Get:209 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fonttools arm64 4.46.0-1 [1625 kB] Get:210 http://ftpmaster.internal/ubuntu noble/main arm64 python3-imagesize all 1.4.1-1 [6844 B] Get:211 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] Get:212 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-isort all 5.6.4-1 [63.1 kB] Get:213 http://ftpmaster.internal/ubuntu noble/main arm64 python3-markupsafe arm64 2.1.3-1build1 [13.5 kB] Get:214 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-jinja2 all 3.1.2-1ubuntu1 [107 kB] Get:215 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-json5 all 0.9.14-1 [16.0 kB] Get:216 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pyrsistent arm64 0.18.1-1build5 [59.3 kB] Get:217 http://ftpmaster.internal/ubuntu noble/main arm64 python3-jsonschema all 4.10.3-2ubuntu1 [62.9 kB] Get:218 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-platformdirs all 4.1.0-1 [15.9 kB] Get:219 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-traitlets all 5.5.0-2 [85.0 kB] Get:220 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-jupyter-core all 5.3.2-1 [25.4 kB] Get:221 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-tornado arm64 6.4.0-0ubuntu1 [298 kB] Get:222 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-py all 1.11.0-2 [72.7 kB] Get:223 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-zmq arm64 24.0.1-5 [363 kB] Get:224 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-jupyter-client all 8.6.0-0ubuntu1 [75.6 kB] Get:225 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-jupyterlab-pygments all 0.2.2-3 [6054 B] Get:226 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-nbformat all 5.9.1-1 [41.2 kB] Get:227 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-nbclient all 0.8.0-1 [55.6 kB] Get:228 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandocfilters all 1.5.0-1 [24.0 kB] Get:229 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-tinycss2 all 1.2.1-2 [19.6 kB] Get:230 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-nbconvert all 6.5.3-4 [152 kB] Get:231 http://ftpmaster.internal/ubuntu noble/main arm64 python3-prometheus-client all 0.19.0+ds1-1 [41.7 kB] Get:232 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-send2trash all 1.8.2-1 [15.5 kB] Get:233 http://ftpmaster.internal/ubuntu noble/main arm64 python3-ptyprocess all 0.7.0-5 [15.1 kB] Get:234 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-terminado all 0.18.0-1 [13.1 kB] Get:235 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-websocket all 1.2.3-1 [34.7 kB] Get:236 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-jupyter-server all 1.23.3-2 [186 kB] Get:237 http://ftpmaster.internal/ubuntu noble/main arm64 sphinx-common all 7.2.6-3 [741 kB] Get:238 http://ftpmaster.internal/ubuntu noble/main arm64 python3-alabaster all 0.7.12-1 [17.8 kB] Get:239 http://ftpmaster.internal/ubuntu noble/main arm64 python3-snowballstemmer all 2.2.0-4 [59.7 kB] Get:240 http://ftpmaster.internal/ubuntu noble/main arm64 python3-sphinx all 7.2.6-3 [557 kB] Get:241 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-nbsphinx all 0.8.11+ds-1 [36.9 kB] Get:242 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-recommonmark all 0.7.1+ds-5 [16.9 kB] Get:243 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-jupyter-sphinx-theme all 0.0.6+ds1-11 [2812 B] Get:244 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-jupyterlab-server all 2.25.2-1 [40.5 kB] Get:245 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-kiwisolver arm64 1.4.4-1build2 [65.4 kB] Get:246 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-latexcodec all 2.0.1-2 [17.1 kB] Get:247 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-llvmlite arm64 0.41.1-1 [151 kB] Get:248 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB] Get:249 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-pil arm64 10.2.0-1 [477 kB] Get:250 http://ftpmaster.internal/ubuntu noble/main arm64 python3-tk arm64 3.11.5-1 [112 kB] Get:251 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-pil.imagetk arm64 10.2.0-1 [9708 B] Get:252 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pyparsing all 3.1.1-1 [86.2 kB] Get:253 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-matplotlib arm64 3.6.3-1ubuntu3 [7291 kB] Get:254 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-numba arm64 0.58.1+dfsg-1 [2464 kB] Get:255 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-tabulate all 0.8.10-1 [38.2 kB] Get:256 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-numpydoc all 1.6.0-1 [50.4 kB] Get:257 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-pandas-lib arm64 1.5.3+dfsg-12 [6834 kB] Get:258 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-pandas all 1.5.3+dfsg-12 [2915 kB] Get:259 http://ftpmaster.internal/ubuntu noble/main arm64 python3-tenacity all 8.2.3-2 [14.8 kB] Get:260 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-plotly all 5.15.0+dfsg1-1 [2222 kB] Get:261 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pluggy all 1.3.0-1 [19.6 kB] Get:262 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pybtex all 0.24.0-4 [70.0 kB] Get:263 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pybtex-docutils all 1.0.2-1 [7176 B] Get:264 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pydata-sphinx-theme all 0.7.2-3 [1092 kB] Get:265 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pytest all 7.4.4-1 [305 kB] Get:266 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-isonscreen all 1.2.0-1.1 [3244 B] Get:267 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pytest-cov all 4.1.0-1 [21.5 kB] Get:268 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pytest-xdist all 3.4.0-1 [32.0 kB] Get:269 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scitrack all 2021.5.3-3 [9424 B] Get:270 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-sphinx-design all 0.5.0-2 [866 kB] Get:271 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-sphinx-gallery all 0.10.1-4 [95.3 kB] Get:272 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-sphinxcontrib.bibtex all 2.6.2-1 [25.2 kB] Get:273 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-tinydb all 3.15.2-4 [16.6 kB] Get:274 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-tqdm all 4.64.1-1 [98.9 kB] Preconfiguring packages ... Fetched 217 MB in 54s (4009 kB/s) Selecting previously unselected package libpython3.12-minimal:arm64. (Reading database ... 15813 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.1-2_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.1-2) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-2_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-2) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.1-2_arm64.deb ... Unpacking python3.12-minimal (3.12.1-2) ... Setting up libpython3.12-minimal:arm64 (3.12.1-2) ... Setting up libexpat1:arm64 (2.5.0-2) ... Setting up python3.12-minimal (3.12.1-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 16131 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.1-0ubuntu1_arm64.deb ... 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Setting up libyaml-0-2:arm64 (0.2.5-1) ... Setting up libglib2.0-0:arm64 (2.78.3-2) ... No schema files found: doing nothing. Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Setting up libpgm-5.3-0:arm64 (5.3.128~dfsg-2) ... Setting up fonts-lyx (2.4.0~RC1-2) ... Setting up libdebhelper-perl (13.11.10ubuntu1) ... Setting up libbrotli1:arm64 (1.1.0-2) ... Setting up libnorm1:arm64 (1.5.9+dfsg-3) ... 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:arm64 (1.58.0-1) ... Setting up libmagic1:arm64 (1:5.45-2) ... Setting up libdeflate0:arm64 (1.18-1) ... Setting up gettext-base (0.21-14ubuntu1) ... Setting up m4 (1.4.19-4) ... Setting up libqhull-r8.0:arm64 (2020.2-6) ... Setting up file (1:5.45-2) ... Setting up libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... Setting up python-babel-localedata (2.10.3-3build1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-4) ... Setting up unicode-data (15.1.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.11.0-2build1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libpfm4:arm64 (4.13.0+git16-g535c204-1) ... Setting up libexpat1-dev:arm64 (2.5.0-2) ... Setting up libfreetype6:arm64 (2.13.2+dfsg-1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libjs-bootswatch (3.3.7+dfsg2-1.1) ... Setting up libfribidi0:arm64 (1.0.13-3) ... Setting up libimagequant0:arm64 (2.18.0-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libhwloc15:arm64 (2.10.0-1) ... Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... Setting up autopoint (0.21-14ubuntu1) ... Setting up fonts-dejavu-core (2.37-8) ... 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Setting up python-matplotlib-data (3.6.3-1ubuntu3) ... Setting up libwebpmux3:arm64 (1.3.2-0.3) ... Setting up libbsd0:arm64 (0.11.8-1) ... Setting up libelf1:arm64 (0.190-1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3build3) ... Setting up libldap2:arm64 (2.6.6+dfsg-1~exp1ubuntu2) ... Setting up libjs-bootstrap (3.4.1+dfsg-3) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libjpeg8:arm64 (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-minimal (3.11.7-2) ... Setting up libdw1:arm64 (0.190-1) ... Setting up libxdmcp6:arm64 (1:1.1.3-0ubuntu5) ... Setting up liblapack3:arm64 (3.11.0-2build1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-14ubuntu1) ... Setting up libzmq5:arm64 (4.3.5-1) ... Setting up libpython3.12-stdlib:arm64 (3.12.1-2) ... Setting up libtool (2.4.7-7) ... Setting up fontconfig-config (2.14.2-6ubuntu1) ... Setting up libwebpdemux2:arm64 (1.3.2-0.3) ... Setting up libpython3.11-stdlib:arm64 (3.11.7-2) ... Setting up python3.12 (3.12.1-2) ... Setting up libedit2:arm64 (3.1-20230828-1) ... Setting up libtbbbind-2-5:arm64 (2021.11.0-2ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up pandoc (3.1.3+ds-2) ... Setting up libjs-jquery-metadata (12-4) ... Setting up libraqm0:arm64 (0.10.1-1) ... Setting up libjs-jquery-isonscreen (1.2.0-1.1) ... Setting up libjs-sphinxdoc (7.2.6-3) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libllvm14:arm64 (1:14.0.6-16build2) ... Setting up dwz (0.15-1) ... Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-3) ... Setting up groff-base (1.23.0-3) ... Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:arm64 (1.1.35-1) ... Setting up debugedit (1:5.0-5) ... Setting up libcurl4:arm64 (8.5.0-2ubuntu1) ... Setting up libx11-6:arm64 (2:1.8.7-1) ... Setting up libfontconfig1:arm64 (2.14.2-6ubuntu1) ... Setting up llvm-14-linker-tools (1:14.0.6-16build2) ... Setting up libpython3.12:arm64 (3.12.1-2) ... Setting up libpython3-stdlib:arm64 (3.12.1-0ubuntu1) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ... Setting up python3.11 (3.11.7-2) ... Setting up libpython3.11:arm64 (3.11.7-2) ... Setting up libxrender1:arm64 (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:arm64 (2:1.3.4-1build1) ... Setting up python3 (3.12.1-0ubuntu1) ... Setting up libpython3.12-dev:arm64 (3.12.1-2) ... Setting up libtbb12:arm64 (2021.11.0-2ubuntu2) ... Setting up python3-pandocfilters (1.5.0-1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer. Setting up python3-markupsafe (2.1.3-1build1) ... Setting up python3-webencodings (0.5.1-5) ... Setting up python3-platformdirs (4.1.0-1) ... Setting up python3-tz (2023.3.post1-2) ... Setting up python3-six (1.16.0-4) ... Setting up python3-pil:arm64 (10.2.0-1) ... Setting up python3-roman (3.3-3) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-jinja2 (3.1.2-1ubuntu1) ... Setting up python3-packaging (23.2-1) ... Setting up python3-pyproject-hooks (1.0.0-2) ... Setting up python3-pyparsing (3.1.1-1) ... Setting up llvm-14-runtime (1:14.0.6-16build2) ... Setting up python3-certifi (2023.11.17-1) ... Setting up python3-sphinx-bootstrap-theme (0.8.1-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up libpython3.11-dev:arm64 (3.11.7-2) ... Setting up python3-brotli (1.1.0-2) ... Setting up sphinx-common (7.2.6-3) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-kiwisolver (1.4.4-1build2) ... Setting up python3-idna (3.3-2) ... Setting up python3.12-dev (3.12.1-2) ... Setting up cython3 (3.0.8-1ubuntu1) ... Setting up jupyter-sphinx-theme-common (0.0.6+ds1-11) ... Setting up python3-typing-extensions (4.7.1-2) ... Setting up python3-html5lib (1.1-3ubuntu1) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-installer (0.7.0+dfsg1-2) ... Setting up python3-isort (5.6.4-1) ... Setting up python3-urllib3 (2.0.7-1) ... Setting up python3-pluggy (1.3.0-1) ... Setting up python3-fastjsonschema (2.19.0-1) ... Setting up python3-pyrsistent:arm64 (0.18.1-1build5) ... Setting up python3-lxml:arm64 (5.1.0-1) ... Setting up python3-traitlets (5.5.0-2) ... Setting up python3-scitrack (2021.5.3-3) ... Setting up python3-dateutil (2.8.2-3) ... Setting up libxss1:arm64 (1:1.2.3-1build2) ... Setting up python3-mpmath (1.2.1-2) ... Setting up python3-execnet (2.0.0-2) ... Setting up python3-lib2to3 (3.11.5-1) ... Setting up python3-tomli-w (1.0.0-2) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-soupsieve (2.5-1) ... Setting up python3-websocket (1.2.3-1) ... Setting up python3-cffi-backend:arm64 (1.16.0-2) ... 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 llvm-14 (1:14.0.6-16build2) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-entrypoints (0.4-2) ... Setting up python3-distutils (3.11.5-1) ... python3.12: can't get files for byte-compilation Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sniffio (1.3.0-2) ... Setting up python3-sympy (1.12-7) ... Setting up python3-attr (23.2.0-1) ... Setting up python3-tornado (6.4.0-0ubuntu1) ... /usr/lib/python3/dist-packages/tornado/test/runtests.py:166: SyntaxWarning: invalid escape sequence '\.' message="ssl\.PROTOCOL_TLS is deprecated") /usr/lib/python3/dist-packages/tornado/test/runtests.py:169: SyntaxWarning: invalid escape sequence '\.' message="ssl\.wrap_socket\(\) is deprecated, .*") /usr/lib/python3/dist-packages/tornado/test/runtests.py:172: SyntaxWarning: invalid escape sequence '\.' message="ssl\.OP_NO_SSL\*/ssl\.OP_NO_TLS\* options are deprecated") Setting up python3-send2trash (1.8.2-1) ... Setting up libxft2:arm64 (2.3.6-1) ... Setting up python3-tinycss2 (1.2.1-2) ... Setting up libpython3-dev:arm64 (3.12.1-0ubuntu1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-py (1.11.0-2) ... Setting up python3-anyio (4.2.0-1) ... Setting up python3-babel (2.10.3-3build1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-lz4 (4.0.2+dfsg-1build2) ... Setting up python3-defusedxml (0.7.1-2) ... Setting up python3-json5 (0.9.14-1) ... Setting up python3.11-dev (3.11.7-2) ... Setting up python3-pytest (7.4.4-1) ... Setting up python3-alabaster (0.7.12-1) ... Setting up python3-tenacity (8.2.3-2) ... Setting up libtk8.6:arm64 (8.6.13-2) ... Setting up python3-tqdm (4.64.1-1) ... Setting up python3-tinydb (3.15.2-4) ... Setting up python3-tabulate (0.8.10-1) ... Setting up python3-latexcodec (2.0.1-2) ... Setting up python3-all (3.12.1-0ubuntu1) ... Setting up python3-coverage (7.3.2-0ubuntu1) ... Setting up python3-yaml (6.0.1-2) ... Setting up debhelper (13.11.10ubuntu1) ... Setting up python3-pytest-cov (4.1.0-1) ... Setting up python3-wheel (0.42.0-1) ... Setting up python3-bs4 (4.12.3-1) ... Setting up python3-bleach (6.1.0-2) ... Setting up python3-fs (2.4.16-3) ... Setting up python3-prometheus-client (0.19.0+ds1-1) ... Setting up python3-llvmlite (0.41.1-1) ... Setting up python3-pygments (2.15.1+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-jsonschema (4.10.3-2ubuntu1) ... Setting up libpython3-all-dev:arm64 (3.12.1-0ubuntu1) ... Setting up python3-zmq (24.0.1-5) ... Setting up python3-dev (3.12.1-0ubuntu1) ... Setting up python3-requests (2.31.0+dfsg-1ubuntu1) ... Setting up python3-numpy (1:1.24.2-2) ... Setting up python3-pybtex (0.24.0-4) ... Setting up python3-terminado (0.18.0-1) ... Setting up python3-argon2 (21.1.0-2) ... Setting up python3-contourpy (1.0.7-1build2) ... Setting up python3-build (0.10.0-1) ... Setting up python3-jupyter-core (5.3.2-1) ... Setting up dh-python (6.20231223) ... Setting up python3-all-dev (3.12.1-0ubuntu1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up python3-scipy (1.10.1-7) ... Setting up python3-pytest-xdist (3.4.0-1) ... Setting up pybuild-plugin-pyproject (6.20231223) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3-pandas-lib:arm64 (1.5.3+dfsg-12) ... Setting up python3-tk:arm64 (3.11.5-1) ... Setting up python3-nbformat (5.9.1-1) ... Setting up python3-numba (0.58.1+dfsg-1) ... update-alternatives: using /usr/share/python3-numba/numba to provide /usr/bin/numba (numba) in auto mode /usr/lib/python3/dist-packages/numba/tests/test_dictobject.py:1306: SyntaxWarning: invalid escape sequence '\(' msg = '.*dict\(mapping\) is not supported.*' # noqa: W605 /usr/lib/python3/dist-packages/numba/tests/test_parfors.py:4068: SyntaxWarning: invalid escape sequence '\s' recipr_str = '\s+%s = fmul fast double %s, 5.000000e-01' /usr/lib/python3/dist-packages/numba/tests/test_parfors.py:4070: SyntaxWarning: invalid escape sequence '\s' fadd_inst = re.compile('\s+%s = fadd fast double %s, %s' /usr/lib/python3/dist-packages/numba/tests/test_parfors.py:4519: SyntaxWarning: invalid escape sequence '\s' schedty = re.compile('call\s+\w+\*\s+@do_scheduling_(\w+)\(') /usr/lib/python3/dist-packages/numba/tests/test_svml.py:174: SyntaxWarning: invalid escape sequence '\$' asm_filter = re.compile('|'.join(['\$[a-z_]\w+,']+list(svml_funcs))) /usr/lib/python3/dist-packages/numba/tests/test_typingerror.py:210: SyntaxWarning: invalid escape sequence '\(' "argument\(s\):\\n- argument 1:.*Cannot determine " /usr/lib/python3/dist-packages/numba/tests/test_withlifting.py:554: SyntaxWarning: invalid escape sequence '\(' "type\(ObjModeLiftedWith\(<.*>\)\)") /usr/lib/python3/dist-packages/numba/tests/test_withlifting.py:836: SyntaxWarning: invalid escape sequence '\.' "Global 'gv_type2' is not defined\.") Setting up python3-jupyterlab-pygments (0.2.2-3) ... Setting up python3-pandas (1.5.3+dfsg-12) ... Setting up python3-pil.imagetk:arm64 (10.2.0-1) ... Setting up python3-plotly (5.15.0+dfsg1-1) ... Setting up python3-jupyter-client (8.6.0-0ubuntu1) ... Setting up python3-nbclient (0.8.0-1) ... Setting up python3-nbconvert (6.5.3-4) ... Setting up python3-jupyter-server (1.23.3-2) ... Setting up python3-jupyterlab-server (2.25.2-1) ... Setting up python3-fonttools (4.46.0-1) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Setting up python3-matplotlib (3.6.3-1ubuntu3) ... Processing triggers for libc-bin (2.38-3ubuntu1) ... Processing triggers for systemd (255.2-3ubuntu2) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.20.1+dfsg-3) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.20.1+dfsg-3) ... Setting up flit (3.9.0-2) ... Setting up python3-pybtex-docutils (1.0.2-1) ... Setting up python3-sphinx (7.2.6-3) ... Setting up python3-sphinx-gallery (0.10.1-4) ... Setting up python3-sphinxcontrib.bibtex (2.6.2-1) ... Setting up python3-sphinx-design (0.5.0-2) ... Setting up python3-nbsphinx (0.8.11+ds-1) ... Setting up python3-recommonmark (0.7.1+ds-5) ... /usr/lib/python3/dist-packages/recommonmark/transform.py:254: SyntaxWarning: invalid escape sequence '\w' match = re.search('[ ]?[\w_-]+::.*', language) Setting up python3-numpydoc (1.6.0-1) ... Setting up python3-pydata-sphinx-theme (0.7.2-3) ... 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 (arm64 included in any-amd64 arm64 loong64 mips64el ppc64el s390x ia64 ppc64 riscv64 sparc64 alpha all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:53:38 UTC 2023 arm64 (aarch64) Toolchain package versions: binutils_2.41.90.20240122-1ubuntu1 dpkg-dev_1.22.2ubuntu2 g++-13_13.2.0-11ubuntu1 gcc-13_13.2.0-11ubuntu1 libc6-dev_2.38-3ubuntu1 libstdc++-13-dev_13.2.0-11ubuntu1 libstdc++6_14-20240126-2ubuntu1 linux-libc-dev_6.6.0-14.14 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.10 apt-utils_2.7.10 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14ubuntu1 autotools-dev_20220109.1 base-files_13ubuntu6 base-passwd_3.6.3 bash_5.2.21-2ubuntu1 bash-completion_1:2.11-8 binutils_2.41.90.20240122-1ubuntu1 binutils-aarch64-linux-gnu_2.41.90.20240122-1ubuntu1 binutils-common_2.41.90.20240122-1ubuntu1 blt_2.5.3+dfsg-7 bsdextrautils_2.39.2-6ubuntu1 bsdutils_1:2.39.2-6ubuntu1 build-essential_12.10ubuntu1 bzip2_1.0.8-5build1 ca-certificates_20230311ubuntu1 coreutils_9.4-2ubuntu2 cpp_4:13.2.0-3ubuntu1 cpp-13_13.2.0-11ubuntu1 cpp-13-aarch64-linux-gnu_13.2.0-11ubuntu1 cpp-aarch64-linux-gnu_4:13.2.0-3ubuntu1 cython3_3.0.8-1ubuntu1 dash_0.5.12-6ubuntu1 debconf_1.5.85 debconf-i18n_1.5.85 debhelper_13.11.10ubuntu1 debianutils_5.16 debugedit_1:5.0-5 dh-autoreconf_20 dh-python_6.20231223 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 docutils-common_0.20.1+dfsg-3 dpkg_1.22.2ubuntu2 dpkg-dev_1.22.2ubuntu2 dwz_0.15-1 e2fsprogs_1.47.0-2ubuntu1 fakeroot_1.33-1 file_1:5.45-2 findutils_4.9.0-5 flit_3.9.0-2 fontconfig-config_2.14.2-6ubuntu1 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3 fonts-lyx_2.4.0~RC1-2 g++_4:13.2.0-3ubuntu1 g++-13_13.2.0-11ubuntu1 g++-13-aarch64-linux-gnu_13.2.0-11ubuntu1 g++-aarch64-linux-gnu_4:13.2.0-3ubuntu1 gcc_4:13.2.0-3ubuntu1 gcc-13_13.2.0-11ubuntu1 gcc-13-aarch64-linux-gnu_13.2.0-11ubuntu1 gcc-13-base_13.2.0-11ubuntu1 gcc-14-base_14-20240126-2ubuntu1 gcc-aarch64-linux-gnu_4:13.2.0-3ubuntu1 gettext_0.21-14ubuntu1 gettext-base_0.21-14ubuntu1 gpg_2.2.40-1.1ubuntu1 gpg-agent_2.2.40-1.1ubuntu1 gpgconf_2.2.40-1.1ubuntu1 gpgv_2.2.40-1.1ubuntu1 grep_3.11-4 groff-base_1.23.0-3 gzip_1.12-1ubuntu1 hostname_3.23+nmu1ubuntu1 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 jupyter-sphinx-theme-common_0.0.6+ds1-11 krb5-locales_1.20.1-5build1 libacl1_2.3.1-4ubuntu1 libapparmor1_4.0.0~alpha2-0ubuntu8 libapt-pkg6.0_2.7.10 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-4 libasan8_14-20240126-2ubuntu1 libassuan0_2.5.6-1 libatomic1_14-20240126-2ubuntu1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2 libaudit1_1:3.1.2-2 libbinutils_2.41.90.20240122-1ubuntu1 libblas3_3.11.0-2build1 libblkid1_2.39.2-6ubuntu1 libbrotli1_1.1.0-2 libbsd0_0.11.8-1 libbz2-1.0_1.0.8-5build1 libc-bin_2.38-3ubuntu1 libc-dev-bin_2.38-3ubuntu1 libc6_2.38-3ubuntu1 libc6-dev_2.38-3ubuntu1 libcap-ng0_0.8.4-1 libcap2_1:2.66-4ubuntu1 libcc1-0_14-20240126-2ubuntu1 libcom-err2_1.47.0-2ubuntu1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libcryptsetup12_2:2.6.1-6ubuntu1 libctf-nobfd0_2.41.90.20240122-1ubuntu1 libctf0_2.41.90.20240122-1ubuntu1 libcurl4_8.5.0-2ubuntu1 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271ubuntu1 libdebhelper-perl_13.11.10ubuntu1 libdeflate0_1.18-1 libdevmapper1.02.1_2:1.02.185-2ubuntu1 libdpkg-perl_1.22.2ubuntu2 libdw1_0.190-1 libedit2_3.1-20230828-1 libelf1_0.190-1 libexpat1_2.5.0-2 libexpat1-dev_2.5.0-2 libext2fs2_1.47.0-2ubuntu1 libfakeroot_1.33-1 libfdisk1_2.39.2-6ubuntu1 libffi8_3.4.4-2 libfile-stripnondeterminism-perl_1.13.1-1 libfontconfig1_2.14.2-6ubuntu1 libfreetype6_2.13.2+dfsg-1 libfribidi0_1.0.13-3 libgcc-13-dev_13.2.0-11ubuntu1 libgcc-s1_14-20240126-2ubuntu1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgfortran5_14-20240126-2ubuntu1 libglib2.0-0_2.78.3-2 libgmp10_2:6.3.0+dfsg-2ubuntu4 libgnutls30_3.8.3-1ubuntu1 libgomp1_14-20240126-2ubuntu1 libgpg-error-l10n_1.47-3build1 libgpg-error0_1.47-3build1 libgpm2_1.20.7-10build1 libgprofng0_2.41.90.20240122-1ubuntu1 libgraphite2-3_1.3.14-2 libgssapi-krb5-2_1.20.1-5build1 libharfbuzz0b_8.3.0-2 libhogweed6_3.9.1-2 libhwasan0_14-20240126-2ubuntu1 libhwloc15_2.10.0-1 libicu74_74.2-1ubuntu1 libidn2-0_2.3.4-1build1 libimagequant0_2.18.0-1 libip4tc2_1.8.9-2ubuntu2 libisl23_0.26-3 libitm1_14-20240126-2ubuntu1 libjansson4_2.14-2 libjbig0_2.1-6.1ubuntu1 libjpeg-turbo8_2.1.5-2ubuntu1 libjpeg8_8c-2ubuntu11 libjs-bootstrap_3.4.1+dfsg-3 libjs-bootswatch_3.3.7+dfsg2-1.1 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python-cogent-doc Architecture: any-amd64 arm64 loong64 mips64el ppc64el s390x ia64 ppc64 riscv64 sparc64 alpha all Version: 2023.12.15a1+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-sequence-python3, 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, 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check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-cogent_2023.12.15a1+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting python-cogent in /<> dpkg-source: info: unpacking python-cogent_2023.12.15a1+dfsg.orig.tar.xz dpkg-source: info: unpacking python-cogent_2023.12.15a1+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 skip-parallel-tests-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-27687842 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27687842 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27687842 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 2023.12.15a1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --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 --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:129: Building wheel for python3.11 with "build" module I: pybuild base:305: python3.11 -m build --skip-dependency-check --no-isolation --wheel --outdir /<>/.pybuild/cpython3_3.11_cogent3 * Building wheel... Successfully built cogent3-2023.12.15a1-py3-none-any.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.11 with "installer" module I: pybuild plugin_pyproject:129: Building wheel for python3.12 with "build" module I: pybuild base:305: python3.12 -m build --skip-dependency-check --no-isolation --wheel --outdir /<>/.pybuild/cpython3_3.12_cogent3 * Building wheel... Successfully built cogent3-2023.12.15a1-py3-none-any.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.12 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 v7.2.6 making output directory... done WARNING: html_static_path entry '_static' does not exist WARNING: The config value `today' has type `date', defaults to `str'. checking bibtex cache... out of date parsing bibtex file /<>/doc/cogent3.bib... parsed 21 entries building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 152 source files that are out of date updating environment: [new config] 152 added, 0 changed, 0 removed reading sources... [ 1%] COGENT3_LICENSE reading sources... [ 1%] api/__init__/cogent3.__init__.available_apps reading sources... [ 2%] api/__init__/cogent3.__init__.available_codes reading sources... [ 3%] 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... [ 5%] 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_annotations reading sources... [ 7%] api/__init__/cogent3.__init__.load_delimited reading sources... [ 8%] api/__init__/cogent3.__init__.load_seq reading sources... [ 9%] 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... 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[100%] templates/class WARNING: autodoc: failed to import function '__init__.available_apps' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.available_codes' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.available_models' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.available_moltypes' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.get_code' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.get_model' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.get_moltype' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.load_aligned_seqs' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.load_annotations' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.load_delimited' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.load_seq' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.load_table' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.load_tree' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.load_unaligned_seqs' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.make_aligned_seqs' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.make_seq' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.make_table' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.make_tree' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.make_unaligned_seqs' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.open_' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.open_data_store' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /<>/doc/api/alignment/alignment.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst SequenceCollection Alignment ArrayAlignment WARNING: autodoc: failed to import class 'core.alignment.Alignment' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'core.alignment.ArrayAlignment' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'core.alignment.SequenceCollection' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /<>/doc/api/alphabet/alphabet.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst Alphabet WARNING: autodoc: failed to import class 'core.alphabet.Alphabet' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /<>/doc/api/annotation/annotation.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst Feature WARNING: autodoc: failed to import class 'core.annotation.Feature' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /<>/doc/api/annotation_db/annotation_db.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst BasicAnnotationDb GffAnnotationDb GenbankAnnotationDb WARNING: autodoc: failed to import class 'core.annotation_db.BasicAnnotationDb' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'core.annotation_db.GenbankAnnotationDb' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'core.annotation_db.GffAnnotationDb' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function 'app.composable.define_app' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'app.data_store.DataMember' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'app.data_store.DataStoreDirectory' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'app.data_store.ReadOnlyDataStoreZipped' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function 'app.io.register_datastore_reader' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'app.sqlite_data_store.DataStoreSqlite' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'core.genetic_code.GeneticCode' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /<>/doc/api/genetic_code/genetic_code.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst GeneticCode WARNING: autodoc: failed to import class 'core.moltype.MolType' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /<>/doc/api/moltype/moltype.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst MolType WARNING: autodoc: failed to import class 'core.sequence.DnaSequence' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'core.sequence.ProteinSequence' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'core.sequence.RnaSequence' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /<>/doc/api/sequence/sequence.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst DnaSequence RnaSequence ProteinSequence WARNING: autodoc: failed to import class 'parse.table.FilteringParser' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'util.table.Columns' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'util.table.Table' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /<>/doc/api/table/table.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst Table Columns /<>/doc/api/table/table.rst:15: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst FilteringParser WARNING: autodoc: failed to import class 'core.tree.PhyloNode' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /<>/doc/api/tree/tree.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst PhyloNode WARNING: autodoc: failed to import class 'util.deserialise.register_deserialiser' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function 'util.deserialise.deserialise_object' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /<>/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:77: 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:88: 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:101: 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:118: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: process = loader + cpos3 + writer m = process("data/primate_brca1.fasta") /<>/doc/app/app-overview.rst:128: 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:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.summary_logs /<>/doc/app/app-overview.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.describe /<>/doc/app/app-overview.rst:158: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.summary_not_completed /<>/doc/app/app-overview.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result = process.apply_to(dstore, show_progress=True) /<>/doc/app/app-overview.rst:185: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import shutil shutil.rmtree(path_to_dir, ignore_errors=True) /<>/doc/app/available-apps.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_apps available_apps() /<>/doc/app/available-apps.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: available_apps(name_filter="load") /<>/doc/app/dstore.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/dstore.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import open_data_store dstore = open_data_store("data/raw.zip", suffix="fa", mode="r") print(dstore) /<>/doc/app/dstore.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.describe /<>/doc/app/dstore.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: m = dstore[0] m /<>/doc/app/dstore.rst:102: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for m in dstore[:5]: print(m) /<>/doc/app/dstore.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: m.read()[:20] # truncating /<>/doc/app/dstore.rst:130: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore = open_data_store("data/demo-locked.sqlitedb") dstore.describe /<>/doc/app/dstore.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.unlock(force=True) /<>/doc/app/dstore.rst:146: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.summary_logs /<>/doc/app/dstore.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.logs /<>/doc/app/dstore.rst:158: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(dstore.logs[0].read()[:225]) # truncated for clarity /<>/doc/app/dstore.rst:172: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import open_data_store in_dstore = open_data_store("data/raw.zip", suffix="fa") /<>/doc/app/dstore.rst:180: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore = open_data_store("translated.sqlitedb", mode="w") /<>/doc/app/dstore.rst:189: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app load = get_app("load_unaligned", moltype="dna") translate = get_app("translate_seqs") write = get_app("write_db", data_store=out_dstore) app = load + translate + write app /<>/doc/app/dstore.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore = app.apply_to(in_dstore) /<>/doc/app/dstore.rst:210: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.describe /<>/doc/app/dstore.rst:216: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.validate() /<>/doc/app/dstore.rst:222: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.summary_not_completed /<>/doc/app/dstore.rst:232: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: len(out_dstore.not_completed) /<>/doc/app/dstore.rst:238: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.not_completed[:2] /<>/doc/app/dstore.rst:242: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pathlib fn = pathlib.Path("translated.sqlitedb") fn.unlink() /<>/doc/app/dstore.rst:11: WARNING: download file not readable: /<>/doc/app/data/raw.zip /<>/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:23: 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) assert result == False result /<>/doc/app/not-completed.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.source /<>/doc/app/not-completed.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.origin /<>/doc/app/not-completed.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.message /<>/doc/app/not-completed.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = reader("primate_brca1.fasta") result /<>/doc/app/not-completed.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: app = reader + select_seqs result = app("data/primate_brca1.fasta") result /<>/doc/app/not-completed.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = app("primate_brca1.fasta") result /<>/doc/app/user_function.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app.typing import defined_types defined_types() /<>/doc/app/user_function.rst:31: 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:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: first4 = up_to(index=4) first4 /<>/doc/app/user_function.rst:51: 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:68: 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:91: 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="pdist") result = percent_dist(aln) result /<>/doc/cookbook/DNA_and_RNA_sequences.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT") my_seq.moltype.label /<>/doc/cookbook/DNA_and_RNA_sequences.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq /<>/doc/cookbook/DNA_and_RNA_sequences.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq = make_seq("AGTACACTGGT", moltype="bytes") my_seq.moltype.label /<>/doc/cookbook/DNA_and_RNA_sequences.rst:31: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq /<>/doc/cookbook/DNA_and_RNA_sequences.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") my_seq /<>/doc/cookbook/DNA_and_RNA_sequences.rst:57: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq rnaseq = make_seq("ACGUACGUACGUACGU", moltype="rna") /<>/doc/cookbook/DNA_and_RNA_sequences.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") my_seq /<>/doc/cookbook/DNA_and_RNA_sequences.rst:76: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq rnaseq = make_seq("ACGUACGUACGUACGU", moltype="rna") rnaseq /<>/doc/cookbook/DNA_and_RNA_sequences.rst:88: 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:99: 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" my_seq /<>/doc/cookbook/DNA_and_RNA_sequences.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") my_seq.complement() /<>/doc/cookbook/DNA_and_RNA_sequences.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq.rc() /<>/doc/cookbook/DNA_and_RNA_sequences.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("GCTTGGGAAAGTCAAATGGAA", name="s1", moltype="dna") pep = my_seq.get_translation() type(pep) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pep /<>/doc/cookbook/DNA_and_RNA_sequences.rst:144: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("ACGTACGTACGTACGT", moltype="dna") rnaseq = my_seq.to_rna() rnaseq /<>/doc/cookbook/DNA_and_RNA_sequences.rst:155: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq rnaseq = make_seq("ACGUACGUACGUACGU", moltype="rna") dnaseq = rnaseq.to_dna() dnaseq /<>/doc/cookbook/DNA_and_RNA_sequences.rst:166: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq a = make_seq("AGTACACTGGT", moltype="dna") a.can_pair(a.complement()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:173: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: a.can_pair(a.rc()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:180: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") extra_seq = make_seq("CTGAC", moltype="dna") long_seq = my_seq + extra_seq long_seq /<>/doc/cookbook/DNA_and_RNA_sequences.rst:192: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq[1:6] /<>/doc/cookbook/DNA_and_RNA_sequences.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq seq = make_seq("ATGATGATGATG", moltype="dna") pos3 = seq[2::3] assert str(pos3) == "GGGG" /<>/doc/cookbook/DNA_and_RNA_sequences.rst:214: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq seq = make_seq("ATGATGATGATG", moltype="dna") indices = [(i, i + 2) for i in range(len(seq))[::3]] pos12 = seq.add_feature(biotype="pos12", name="pos12", spans=indices) pos12 = pos12.get_slice() assert str(pos12) == "ATATATAT" /<>/doc/cookbook/DNA_and_RNA_sequences.rst:227: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rnaseq.shuffle() /<>/doc/cookbook/DNA_and_RNA_sequences.rst:234: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq s = make_seq("--AUUAUGCUAU-UAu--", moltype="rna") 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") type(seqs) /<>/doc/cookbook/alignments.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = make_unaligned_seqs(dna, moltype="dna") type(seqs) /<>/doc/cookbook/alignments.rst:44: 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)) seqs /<>/doc/cookbook/alignments.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs seqs = load_unaligned_seqs("data/test.paml") seqs /<>/doc/cookbook/alignments.rst:73: 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", ) aln /<>/doc/cookbook/alignments.rst:83: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new_seqs = make_aligned_seqs( [("seq0", "ATG-AGT-AGG"), ("seq4", "ATGCC------")], moltype="dna" ) new_aln = aln.add_seqs(new_seqs) new_aln /<>/doc/cookbook/alignments.rst:98: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new_aln = aln.add_seqs(new_seqs, before_name="seq2") new_aln /<>/doc/cookbook/alignments.rst:103: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new_aln = aln.add_seqs(new_seqs, after_name="seq2") new_aln /<>/doc/cookbook/alignments.rst:113: 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) new_aln /<>/doc/cookbook/alignments.rst:135: 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") new_aln /<>/doc/cookbook/alignments.rst:154: 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:170: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = aln.get_gapped_seq("seq1") seq.is_gapped() seq /<>/doc/cookbook/alignments.rst:178: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.names /<>/doc/cookbook/alignments.rst:187: 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] /<>/doc/cookbook/alignments.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(my_seq) /<>/doc/cookbook/alignments.rst:200: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs(fn, moltype="dna") aln.seqs[0][:24] /<>/doc/cookbook/alignments.rst:209: 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 /<>/doc/cookbook/alignments.rst:216: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new = aln.take_seqs(["Human", "HowlerMon"]) new.names /<>/doc/cookbook/alignments.rst:229: 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", moltype="dna") seq /<>/doc/cookbook/alignments.rst:237: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = Alignment(seq) aln /<>/doc/cookbook/alignments.rst:247: 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:258: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.to_moltype("dna") /<>/doc/cookbook/alignments.rst:264: 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:275: 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:292: 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:307: 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:317: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.write("sample", format="fasta") /<>/doc/cookbook/alignments.rst:323: 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:332: 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:344: 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:357: 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:374: 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") aln[:24] /<>/doc/cookbook/alignments.rst:384: 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) seqs[:24] /<>/doc/cookbook/alignments.rst:396: 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:406: 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:416: 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:430: 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 /<>/doc/cookbook/alignments.rst:441: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pos3 = aln.add_feature(biotype="pos3", name="pos3", spans=indices) pos3 = pos3.get_slice() pos3 /<>/doc/cookbook/alignments.rst:452: 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] pos3 /<>/doc/cookbook/alignments.rst:472: 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() new /<>/doc/cookbook/alignments.rst:485: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln = make_aligned_seqs( data={ "seq1": "ACGTAA---", "seq2": "ACGAC----", # terminal codon incomplete "seq3": "ACGCAATGA", }, moltype="dna", ) new = aln.trim_stop_codons(strict=True) /<>/doc/cookbook/alignments.rst:504: 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:519: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nucs = aln.no_degenerates() nucs /<>/doc/cookbook/alignments.rst:526: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: trinucs = aln.no_degenerates(motif_length=3) trinucs /<>/doc/cookbook/alignments.rst:534: 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) just_variable_aln[:10] /<>/doc/cookbook/alignments.rst:546: 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) just_constant_aln[:10] /<>/doc/cookbook/alignments.rst:560: 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 ) just_variable_aln[:9] /<>/doc/cookbook/alignments.rst:572: 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) just_variable_aln[:9] /<>/doc/cookbook/alignments.rst:586: 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:595: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.take_seqs(["Human", "Mouse"], negate=True) /<>/doc/cookbook/alignments.rst:604: 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:624: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.take_seqs_if(no_N_chars, negate=True) /<>/doc/cookbook/alignments.rst:636: 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() counts /<>/doc/cookbook/alignments.rst:651: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.counts(motif_length=3) counts /<>/doc/cookbook/alignments.rst:656: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.counts(include_ambiguity=True) counts /<>/doc/cookbook/alignments.rst:670: 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() motif_probs /<>/doc/cookbook/alignments.rst:680: 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:694: 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:706: 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:716: 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:727: 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:742: 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:756: 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:771: 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:787: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq_to_aln_map[3] seq_to_aln_map[8] /<>/doc/cookbook/alignments.rst:796: 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:804: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: KeyError seq_pos = aln_to_seq_map[7] /<>/doc/cookbook/alignments.rst:818: 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", ) aln.omit_gap_runs(2) /<>/doc/cookbook/alignments.rst:832: 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", ) aln.omit_gap_pos(0.40) /<>/doc/cookbook/alignments.rst:846: 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) filtered_aln /<>/doc/cookbook/alignments.rst:861: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: 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/annotation_db.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/annotation_db.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3.core.annotation_db import BasicAnnotationDb anno_db = BasicAnnotationDb() anno_db /<>/doc/cookbook/annotation_db.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_annotations gff_db = load_annotations(path="data/mycoplasma-genitalium.gff") gff_db /<>/doc/cookbook/annotation_db.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_annotations gb_db = load_annotations(path="data/mycoplasma-genitalium.gb") gb_db /<>/doc/cookbook/annotation_db.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: summary = gff_db.describe summary /<>/doc/cookbook/annotation_db.rst:82: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: anno_db.add_feature( seqid="NC_000908", biotype="gene", name="interesting_gene", spans=[(1, 4)], strand="+", ) anno_db.describe /<>/doc/cookbook/annotation_db.rst:96: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_db.add_feature( seqid="seq1", biotype="gene", name="interesting_gene", spans=[(1, 4)], strand="+", ) gff_db.describe[-2:, :] # showing just last two rows /<>/doc/cookbook/annotation_db.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: mg_16s = list( gb_db.get_features_matching( name="MG_RS00775", biotype="gene", seqid="NC_000908" ) ) mg_16s /<>/doc/cookbook/annotation_db.rst:160: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: pseudogenes = list(gff_db.get_features_matching(biotype="pseudogene")) pseudogenes[:2] # showing just the first two /<>/doc/cookbook/annotation_db.rst:173: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: operon_cds = list( gff_db.get_features_matching(start=220600, end=229067, biotype="CDS") ) operon_cds /<>/doc/cookbook/annotation_db.rst:188: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: replication_records = list( gff_db.get_records_matching(attributes="replication", biotype="CDS") ) replication_records[0] # showing just the first match /<>/doc/cookbook/annotation_db.rst:208: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gb_db.num_matches(biotype="gene") /<>/doc/cookbook/annotation_db.rst:215: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: total_genes = gb_db.count_distinct(biotype="gene", name=True) single_copy = total_genes[total_genes.columns["count"] == 1, :] len(single_copy) /<>/doc/cookbook/annotation_db.rst:226: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: total_genes = gff_db.num_matches(biotype="gene") print("total genes: ", total_genes) genes = gff_db.count_distinct(biotype="gene", name=True) single_copy = genes[genes.columns["count"] == 1, :] print("single copy genes: ", len(single_copy)) /<>/doc/cookbook/annotation_db.rst:246: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: children = list(gff_db.get_feature_children(name="gene-MG_RS00035")) children /<>/doc/cookbook/annotation_db.rst:259: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: parents = list(gff_db.get_feature_parent(name="cds-WP_009885556.1")) parents /<>/doc/cookbook/annotation_db.rst:273: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_db.compatible(anno_db) /<>/doc/cookbook/annotation_db.rst:282: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_db.compatible(gb_db) /<>/doc/cookbook/annotation_db.rst:294: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: union_db = gb_db.union(anno_db) union_db.describe[-2:, :] /<>/doc/cookbook/annotation_db.rst:307: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_db.update(anno_db) gff_db.describe[-2:, :] /<>/doc/cookbook/annotation_db.rst:318: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3.core.annotation_db import GenbankAnnotationDb new_gb_db = GenbankAnnotationDb(source="m-genitalium-database.gbdb", db=anno_db) new_gb_db /<>/doc/cookbook/annotation_db.rst:331: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_annotations gff_db = load_annotations(path="data/mycoplasma-genitalium.gff") just_cds = gff_db.subset(biotype="CDS") just_cds.describe /<>/doc/cookbook/annotation_db.rst:354: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_seq seq1 = make_seq( "AAGAAGAAGACCCCCAAAAAAAAAATTTTTTTTTTAAAAAGGGAACCCT", name="NC_000908", moltype="dna", ) seq1.annotation_db = anno_db seq1.annotation_db /<>/doc/cookbook/annotation_db.rst:376: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq gb_seq = load_seq("data/mycoplasma-genitalium.gb") gb_seq.annotation_db /<>/doc/cookbook/annotation_db.rst:389: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_seq = load_seq( "data/mycoplasma-genitalium.fa", annotation_path="data/mycoplasma-genitalium.gff", ) gff_seq.annotation_db /<>/doc/cookbook/annotation_db.rst:402: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: seq = load_seq( "data/mycoplasma-genitalium.fa", annotation_path="data/mycoplasma-genitalium.gff", label_to_name=lambda x: x.split()[0], ) seq.annotation_db /<>/doc/cookbook/annotation_db.rst:412: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pathlib # clean up files path = pathlib.Path("m-genitalium-database.gbdb") path.unlink() /<>/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 tree_align /<>/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 = tree_align("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 = tree_align( "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 tree_align 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 = tree_align( "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 tree_align from cogent3.evolve.models import get_model seqs = [ ( "hum", "AAGCAGATCCAGGAAAGCAGCGAGAATGGCAGCCTGGCCGCGCGCCAGGAGAGGCAGGCCCAGGTCAACCTCACT", ), ( "mus", "AAGCAGATCCAGGAGAGCGGCGAGAGCGGCAGCCTGGCCGCGCGGCAGGAGAGGCAGGCCCAAGTCAACCTCACG", ), ("rat", "CTGAACAAGCAGCCACTTTCAAACAAGAAA"), ] unaligned_DNA = make_unaligned_seqs(seqs, moltype="dna") unaligned_DNA /<>/doc/cookbook/building_alignments.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: 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/calc_genetic_distance.rst:82: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: 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.max_pair() /<>/doc/cookbook/calc_genetic_distance.rst:93: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: dists[dists.max_pair()] /<>/doc/cookbook/calc_genetic_distance.rst:106: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: 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.min_pair() /<>/doc/cookbook/calc_genetic_distance.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: dists[dists.min_pair()] /<>/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/features.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/features.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_seq # create an example sequence seq = make_seq( "GCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAATACTAAGCCTAAGCCTAAGACTAA", name="seq1", moltype="dna", ) # Add a feature seq.add_feature(biotype="gene", name="a_gene", spans=[(12, 48)], seqid="seq1") /<>/doc/cookbook/features.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: # Add a feature as a series seq.add_feature( biotype="cpgsite", name="a_cpgsite", spans=[(12, 18), (21, 29), (35, 48)], seqid="seq1", ) /<>/doc/cookbook/features.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs # make demo alignment aln1 = make_aligned_seqs( data=[["seq1", "-AAACCCCCA"], ["seq2", "TTTT--TTTT"]], array_align=False ) # add feature to seq1 aln1.add_feature( seqid="seq1", biotype="exon", name="A", spans=[(3, 8)], on_alignment=False ) /<>/doc/cookbook/features.rst:84: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs # make demo alignment aln1 = make_aligned_seqs( data=[["seq1", "-AAACCCCCA"], ["seq2", "TTTT--TTTT"]], array_align=False ) aln1.add_feature( biotype="exon", name="aligned_exon", spans=[(0, 8)], on_alignment=True, ) /<>/doc/cookbook/features.rst:108: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq from cogent3.core.annotation_db import BasicAnnotationDb # init empty db and add feature db = BasicAnnotationDb() db.add_feature(seqid="seq1", biotype="exon", name="C", spans=[(45, 48)]) # make demo seq s1 = make_seq( "AAGAAGAAGACCCCCAAAAAAAAAATTTTTTTTTTAAAAAGGGAACCCT", name="seq1", moltype="dna" ) # assign db to sequence s1.annotation_db = db s1.annotation_db /<>/doc/cookbook/features.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq %timeit load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") /<>/doc/cookbook/features.rst:150: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: :hide-code: seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") /<>/doc/cookbook/features.rst:158: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: seq.annotation_db /<>/doc/cookbook/features.rst:173: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq( filename="data/C-elegans-chromosome-I.fa", annotation_path="data/C-elegans-chromosome-I.gff", moltype="dna", ) seq.annotation_db /<>/doc/cookbook/features.rst:189: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq( "data/C-elegans-chromosome-I.fa", annotation_path="data/C-elegans-chromosome-I.gff", label_to_name=lambda x: x.split()[0], moltype="dna", ) seq.annotation_db /<>/doc/cookbook/features.rst:209: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3 import load_seq loaded_seq = load_seq( "data/C-elegans-chromosome-I.fa", label_to_name=lambda x: x.split()[0], moltype="dna", ) /<>/doc/cookbook/features.rst:220: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: # loaded_seq = < loaded / created the seq> loaded_seq.annotate_from_gff("data/C-elegans-chromosome-I.gff") loaded_seq.annotation_db /<>/doc/cookbook/features.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3 import make_seq sub_seq = make_seq( "GCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAAGACTAAGCCTAAGA", name="I", moltype="dna", ) /<>/doc/cookbook/features.rst:240: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: # sub_seq = sub_seq.annotate_from_gff("data/C-elegans-chromosome-I.gff", offset=600) sub_seq.annotation_db /<>/doc/cookbook/features.rst:254: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs brca1_aln = load_aligned_seqs( "data/primate_brca1.fasta", array_align=False, moltype="dna" ) brca1_aln /<>/doc/cookbook/features.rst:266: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: brca1_aln.annotate_from_gff("data/brca1_hsa_shortened.gff", seq_ids=["Human"]) brca1_aln.annotation_db /<>/doc/cookbook/features.rst:274: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: brca1_aln.get_seq("Human").annotation_db /<>/doc/cookbook/features.rst:296: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") # note we wrap `get_features` in `list` as generator is returned gene = list(seq.get_features(name="WBGene00021661", biotype="gene")) gene /<>/doc/cookbook/features.rst:312: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") cds = list(seq.get_features(biotype="CDS")) cds[:3] /<>/doc/cookbook/features.rst:323: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: cds = list(seq.get_features(biotype="CDS", name="WBGene00021661")) cds /<>/doc/cookbook/features.rst:334: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") region_features = list(seq.get_features(start=10148, stop=26732)) region_features[:3] /<>/doc/cookbook/features.rst:345: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: mRNA = list(seq.get_features(start=10148, stop=29322, biotype="mRNA"))[0] mRNA /<>/doc/cookbook/features.rst:358: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs # first load alignment and annotate the human seq aln = load_aligned_seqs( "data/primate_brca1.fasta", array_align=False, moltype="dna" ) aln.annotate_from_gff("data/brca1_hsa_shortened.gff", seq_ids=["Human"]) # query alignment providing seqid of interest human_exons = list(aln.get_features(biotype="exon", seqid="Human")) human_exons /<>/doc/cookbook/features.rst:383: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs # add a feature to the alignment we created above on difference sequence aln.add_feature(biotype="gene", name="gene:101", spans=[(40, 387)], seqid="Rhesus") any_feature = list(aln.get_features(on_alignment=False)) any_feature /<>/doc/cookbook/features.rst:405: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs # first we add the feature to the alignment aln.add_feature( biotype="pseudogene", name="pseudogene1", spans=[(420, 666)], on_alignment=True ) # query for features on the alignment aln_features = list(aln.get_features(on_alignment=True)) aln_features /<>/doc/cookbook/features.rst:426: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln3 = make_aligned_seqs( data=[["x", "C-CCCAAAAA"], ["y", "-T----TTTT"]], array_align=False, moltype="dna", ) exon = aln3.add_feature( seqid="x", biotype="exon", name="ex1", spans=[(0, 4)], on_alignment=False ) exon.get_slice() /<>/doc/cookbook/features.rst:441: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln_exons = list(aln3.get_features(seqid="x", biotype="exon"))[0] aln_exons /<>/doc/cookbook/features.rst:451: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: exon.get_slice(allow_gaps=True) /<>/doc/cookbook/features.rst:466: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq( "data/C-elegans-chromosome-I.fa", annotation_path="data/C-elegans-chromosome-I.gff", label_to_name=lambda x: x.split()[0], moltype="dna", ) pseudogene = list(seq.get_features(start=10148, stop=26732, biotype="pseudogene"))[0] seq[pseudogene] /<>/doc/cookbook/features.rst:484: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: pseudogene.get_slice() /<>/doc/cookbook/features.rst:494: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") subseq = seq[25000:35000] fig = subseq.get_drawable(biotype=("gene", "mRNA", "CDS", "misc_RNA")) fig.show() /<>/doc/cookbook/features.rst:508: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: pseudogene.get_coordinates() /<>/doc/cookbook/features.rst:515: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") cds = list(seq.get_features(biotype="CDS"))[0] exon_coords = cds.get_coordinates() exon_coords /<>/doc/cookbook/features.rst:528: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: intron_coords = [] for i in range(len(exon_coords) - 1): intron_coords.append((exon_coords[i][1], exon_coords[i + 1][0])) intron_coords /<>/doc/cookbook/features.rst:540: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: intron = seq.add_feature( biotype="intron", name="intron:Y74C9A.3.1", seqid="I", spans=intron_coords ) intron /<>/doc/cookbook/features.rst:553: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") cds = list(seq.get_features(biotype="CDS")) union_cds = cds[0].union(cds[1:]) /<>/doc/cookbook/features.rst:572: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") genes = list(seq.get_features(biotype="gene")) genes = genes[0].union(genes[1:]) genes /<>/doc/cookbook/features.rst:584: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: intergenic = genes.shadow() intergenic /<>/doc/cookbook/features.rst:592: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: intergenic.get_slice() /<>/doc/cookbook/features.rst:605: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") no_cds = seq.with_masked_annotations("CDS") no_cds[2575800:2575900] /<>/doc/cookbook/features.rst:621: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: 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.add_feature( seqid="x", biotype="exon", name="exon-be-gone", spans=[(0, 4)], on_alignment=False, ) aln.with_masked_annotations("exon", mask_char="?") /<>/doc/cookbook/features.rst:642: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: rc = aln.rc() rc /<>/doc/cookbook/features.rst:650: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: rc.with_masked_annotations("exon", mask_char="?") /<>/doc/cookbook/features.rst:664: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq( "data/C-elegans-chromosome-I.fa", annotation_path="data/C-elegans-chromosome-I.gff", label_to_name=lambda x: x.split()[0], moltype="dna", ) gene = list(seq.get_features(name="gene:WBGene00022276", biotype="gene"))[0] children = list(gene.get_children()) children /<>/doc/cookbook/features.rst:686: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: child = list(seq.get_features(name="transcript:Y74C9A.2a.3", biotype="mRNA"))[0] parent = list(child.get_parent()) parent /<>/doc/cookbook/features.rst:698: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln2 = make_aligned_seqs( data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False, moltype="dna", ) x, y = aln2.get_seq("x"), aln2.get_seq("y") x.annotation_db is y.annotation_db is aln2.annotation_db /<>/doc/cookbook/features.rst:711: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: seq = make_seq("CCCCCCCCCCCCCCCCCCCC", name="x", moltype="dna") match_exon = seq.add_feature(biotype="exon", name="A", spans=[(3, 8)]) aln2.copy_annotations(seq.annotation_db) aln2.annotation_db /<>/doc/cookbook/features.rst:721: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: copied = list(aln2.get_features(seqid="x", biotype="exon")) copied /<>/doc/cookbook/features.rst:732: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: unified = aln_exons.as_one_span() aln3[unified] /<>/doc/cookbook/features.rst:743: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: plus = make_seq("CCCCCAAAAAAAAAATTTTTTTTTTAAAGG", moltype="dna") plus_rpt = plus.add_feature(biotype="blah", name="a", spans=[(5, 15), (25, 28)]) plus[plus_rpt] /<>/doc/cookbook/features.rst:750: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: minus = plus.rc() minus /<>/doc/cookbook/features.rst:756: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: minus_rpt = list(minus.get_features(biotype="blah"))[0] minus[minus_rpt] /<>/doc/cookbook/genetic_code.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = { "s1": "GCTCATGCCAGCTCTTTACAGCATGAGAACA--AGT", "s2": "ACTCATGCCAACTCATTACAGCATGAGAACAGCAGT", "s3": "ACTCATGCCAGCTCATTACAGCATGAGAACAGCAGT", "s4": "ACTCATGCCAGCTCATTACAGCATGAGAACAGCAGT", "s5": "ACTCATGCCAGCTCAGTACAGCATGAGAACAGCAGT", } nt_seqs = make_aligned_seqs(data=data, moltype="dna") nt_seqs /<>/doc/cookbook/genetic_code.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nt_seqs.get_translation(gc=1, incomplete_ok=True) /<>/doc/cookbook/genetic_code.rst:36: 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:48: 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:60: 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 /<>/doc/cookbook/genetic_code.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: stop_index = stops_frame1[0] seq[stop_index : stop_index + 3] /<>/doc/cookbook/genetic_code.rst:77: 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:86: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: standard_code["A"] /<>/doc/cookbook/genetic_code.rst:93: 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:103: 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:113: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: targets = ["A", "C"] codons = [standard_code[aa] for aa in targets] codons /<>/doc/cookbook/genetic_code.rst:119: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: flat_list = sum(codons, []) flat_list /<>/doc/cookbook/genetic_code.rst:127: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code gc = get_code(1) alphabet = gc.get_alphabet() print(alphabet) /<>/doc/cookbook/genetic_code.rst:140: 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) codons /<>/doc/cookbook/genetic_code.rst:153: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pep = my_seq.get_translation() pep /<>/doc/cookbook/genetic_code.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.core.alphabet import AlphabetError /<>/doc/cookbook/genetic_code.rst:168: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_seq seq = make_seq("ATGTGATGGTAA", name="s1", moltype="dna") /<>/doc/cookbook/genetic_code.rst:177: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AlphabetError pep = seq.get_translation() /<>/doc/cookbook/genetic_code.rst:184: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pep = seq.get_translation(include_stop=True) pep /<>/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:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_seq seq = load_seq("data/mycoplasma-genitalium.fa", moltype="dna") seq /<>/doc/cookbook/loading_sequences.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = load_seq("data/brca1-bats.fasta", moltype="dna") seq /<>/doc/cookbook/loading_sequences.rst:39: 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:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.info.source /<>/doc/cookbook/loading_sequences.rst:61: 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:75: 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:89: 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:101: 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 proteins_loaded /<>/doc/cookbook/loading_sequences.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: proteins_loaded = make_aligned_seqs(protein_seqs, moltype="protein") proteins_loaded /<>/doc/cookbook/loading_sequences.rst:123: 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:133: 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) seqs_loaded /<>/doc/cookbook/loading_sequences.rst:146: 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:164: 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:184: 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:197: 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:213: 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_sequences.rst:54: WARNING: TODO entry found: add cross ref for description of Info class /<>/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 make_seq p = make_seq("THISISAPRQTEIN", "myProtein", moltype="protein") type(p) /<>/doc/cookbook/protein_sequences.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: p /<>/doc/cookbook/protein_sequences.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code.translate("TTTGCAAAC") /<>/doc/cookbook/protein_sequences.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq nuc = make_seq("TTTGCAAAC", moltype="dna") pep = nuc.get_translation() pep /<>/doc/cookbook/protein_sequences.rst:51: 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 make_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 make_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:467: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: # Distance metrics for rooted trees from cogent3 import make_tree tr1 = make_tree(treestring="(a,(b,(c,(d,e))));") tr2 = make_tree(treestring="(e,(d,(c,(b,a))));") mc_distance = tr1.tree_distance(tr2, method="matching_cluster") # or method="mc" or method="matching" rooted_rf_distance = tr1.tree_distance(tr2, method="rooted_robinson_foulds") # or method="rrf" or method="rf" print("Matching Cluster Distance:", mc_distance) print("Rooted Robinson Foulds Distance:", rooted_rf_distance) /<>/doc/cookbook/simple_trees.rst:481: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: # Distance metrics for unrooted trees from cogent3 import make_tree tr1 = make_tree(treestring="(a,b,(c,(d,e)));") tr2 = make_tree(treestring="((a,c),(b,d),e);") lrm_distance = tr1.tree_distance(tr2, method="lin_rajan_moret") # or method="lrm" or method="matching" unrooted_rf_distance = tr1.tree_distance(tr2, method="unrooted_robinson_foulds") # or method="urf" or method="rf" print("Lin-Rajan-Moret Distance:", lrm_distance) print("Unrooted Robinson Foulds Distance:", unrooted_rf_distance) /<>/doc/cookbook/simple_trees.rst:501: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_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:508: 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:517: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tr = make_tree("(B:0.2,(C:0.3,D:0.4)F:0.5)G;") print(tr) /<>/doc/cookbook/simple_trees.rst:524: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.scale_branch_lengths() print(tr) /<>/doc/cookbook/simple_trees.rst:534: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_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:554: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_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.to_list("Locus") locus /<>/doc/cookbook/tables.rst:300: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Locus"].tolist() /<>/doc/cookbook/tables.rst:311: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") rows = table.to_list(["Region", "Locus"]) rows /<>/doc/cookbook/tables.rst:324: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.to_dict() /<>/doc/cookbook/tables.rst:334: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.columns.to_dict() /<>/doc/cookbook/tables.rst:342: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") df = table.to_pandas() df /<>/doc/cookbook/tables.rst:350: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: df = table.to_pandas(categories="Region") /<>/doc/cookbook/tables.rst:359: 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:364: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: contingency = table.to_categorical(["Ts", "Tv"]) contingency /<>/doc/cookbook/tables.rst:369: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: g_test = contingency.G_independence() g_test /<>/doc/cookbook/tables.rst:376: 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:388: 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:397: 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:409: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.summed("Ratio") /<>/doc/cookbook/tables.rst:416: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Ratio"].sum() /<>/doc/cookbook/tables.rst:425: 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:436: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_numeric.summed() /<>/doc/cookbook/tables.rst:442: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_numeric.summed(col_sum=False) /<>/doc/cookbook/tables.rst:451: 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:460: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed.summed(strict=False) /<>/doc/cookbook/tables.rst:466: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed.summed(col_sum=False, strict=False) /<>/doc/cookbook/tables.rst:475: 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:483: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sub_table = table.filtered("Ratio < 10.0") sub_table /<>/doc/cookbook/tables.rst:490: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sub_table = table.filtered("Ratio < 10.0 and Region == 'NonCon'") sub_table /<>/doc/cookbook/tables.rst:500: 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:508: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.sorted(columns="Ratio") /<>/doc/cookbook/tables.rst:516: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.sorted(columns="Ratio", reverse="Ratio") /<>/doc/cookbook/tables.rst:523: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.sorted(columns=["Region", "Ratio"], reverse="Ratio") /<>/doc/cookbook/tables.rst:530: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") raw = table.to_list("Region") raw /<>/doc/cookbook/tables.rst:539: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") raw = table.to_list(["Locus", "Region"]) raw /<>/doc/cookbook/tables.rst:548: 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:556: 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:566: 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:576: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unique /<>/doc/cookbook/tables.rst:582: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unique = table.count_unique(["A", "B"]) unique /<>/doc/cookbook/tables.rst:587: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: r = unique.to_table() r /<>/doc/cookbook/tables.rst:597: 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:617: 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:633: 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:643: 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:655: 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:667: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.to_markdown(justify="ccr")) /<>/doc/cookbook/tables.rst:675: 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:685: 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:695: 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:707: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.to_string(format="latex")) /<>/doc/cookbook/tables.rst:717: 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:756: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bgraph.head() /<>/doc/cookbook/tables.rst:762: 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:777: 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:789: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.format.table import known_formats known_formats /<>/doc/cookbook/tables.rst:798: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.write("stats_tab.tex", justify="ccr", label="tab:table1") /<>/doc/cookbook/tables.rst:807: 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:814: 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() /<>/doc/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 /<>/doc/cookbook/union_dict.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data["a"] /<>/doc/cookbook/union_dict.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.d /<>/doc/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 /<>/doc/cookbook/union_dict.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.union({"d": [25]}) /<>/doc/cookbook/union_dict.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b {"c": 24, "d": [25]} /<>/doc/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"] /<>/doc/cookbook/union_dict.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AttributeError data.k 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/union_dict.rst:4: WARNING: duplicate label union_dict, other instance in /<>/doc/cookbook/union_dict.rst /<>/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:23: 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-coevolution.rst:11: WARNING: TODO entry found: add citation for NMI /<>/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:: 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:23: 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:37: 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:45: 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:57: 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-1.rst:11: WARNING: TODO entry found: Change dotplot ref to a citation /<>/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 import get_app loader = get_app("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-dotplot-3.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/draw/aln/plot_aln-dotplot-3.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs, get_app seqs = load_aligned_seqs("data/brca1.fasta", moltype="dna").degap() seqs = seqs.take_seqs( ["LeafNose", "FalseVamp", "RoundEare", "Sloth", "Anteater", "HairyArma"] ) /<>/doc/draw/aln/plot_aln-dotplot-3.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligner = get_app("progressive_align", "nucleotide", indel_rate=1e-2, indel_length=1e-9) aln = aligner(seqs) dp = aln[2200:2500].dotplot("HairyArma", "RoundEare") dp.show() /<>/doc/draw/aln/plot_aln-dotplot-3.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-dotplot-3.png" dp.write(outpath) /<>/doc/draw/aln/plot_aln-dotplot-3.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln[2300:2500] /<>/doc/draw/aln/plot_aln-dotplot-3.rst:61: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligner = get_app("progressive_align", "nucleotide") aln = aligner(seqs) aln[2200:2500].dotplot("HairyArma", "RoundEare").show() /<>/doc/draw/aln/plot_aln-dotplot-3.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln[2300:2500] /<>/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/aln/plot_seq-features.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/draw/aln/plot_seq-features.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") seq /<>/doc/draw/aln/plot_seq-features.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = seq[25000:35000] /<>/doc/draw/aln/plot_seq-features.rst:31: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig = seq.get_drawable() fig.show(height=400, width=700) /<>/doc/draw/aln/plot_seq-features.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig = seq.get_drawable(biotype=("gene", "CDS", "mRNA")) fig.show(height=300, width=650) /<>/doc/draw/aln/plot_seq-features.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_seq-features.png" fig.write(outpath) /<>/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") unaligned_DNA /<>/doc/examples/align_codons_to_protein.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unaligned_aa = unaligned_DNA.get_translation() unaligned_aa /<>/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/calculate_pairwise_distances.rst:48: WARNING: TODO entry found: write out in json format /<>/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:241: 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:255: 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.to_list()[0])) bin_params = [t for t in tables if "bin" in t.title][0] rate_class_omegas = dict(bin_params.to_list(["bin", "omega"])) rate_class_probs = dict(bin_params.to_list(["bin", "bprobs"])) lengths = [t for t in tables if "edge" in t.title][0] lengths = dict(lengths.to_list(["edge", "length"])) /<>/doc/examples/codon_models.rst:267: 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:275: 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:282: 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:289: 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:309: 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:323: 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/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:: 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/hmm_par_heterogeneity.rst:139: WARNING: TODO entry found: FOR RELEASE did we fix this silliness of requiring a formattedy.array? /<>/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/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/templates/class.rst:3: ERROR: Error in "currentmodule" directive: maximum 1 argument(s) allowed, 3 supplied. .. currentmodule:: {{ module }} WARNING: invalid signature for autoclass ('{{ name }}') WARNING: don't know which module to import for autodocumenting '{{ name }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name) looking for now-outdated files... none found pickling environment... done checking consistency... /<>/doc/api/alignment/classes/cogent3.core.alignment.Alignment.rst: WARNING: document isn't included in any toctree /<>/doc/api/alignment/classes/cogent3.core.alignment.ArrayAlignment.rst: WARNING: document isn't included in any toctree /<>/doc/api/alignment/classes/cogent3.core.alignment.SequenceCollection.rst: WARNING: document isn't included in any toctree /<>/doc/api/alphabet/classes/cogent3.core.alphabet.Alphabet.rst: WARNING: document isn't included in any toctree /<>/doc/api/annotation/classes/cogent3.core.annotation.Feature.rst: WARNING: document isn't included in any toctree /<>/doc/api/annotation_db/classes/cogent3.core.annotation_db.BasicAnnotationDb.rst: WARNING: document isn't included in any toctree /<>/doc/api/annotation_db/classes/cogent3.core.annotation_db.GenbankAnnotationDb.rst: WARNING: document isn't included in any toctree /<>/doc/api/annotation_db/classes/cogent3.core.annotation_db.GffAnnotationDb.rst: WARNING: document isn't included in any toctree /<>/doc/api/genetic_code/classes/cogent3.core.genetic_code.GeneticCode.rst: WARNING: document isn't included in any toctree /<>/doc/api/moltype/classes/cogent3.core.moltype.MolType.rst: WARNING: document isn't included in any toctree 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WARNING: unsupported theme option 'show_nav_level' given WARNING: unsupported theme option 'logo' given done copying assets... copying downloadable files... [ 3%] data/abglobin_aa.phylip copying downloadable files... [ 6%] data/dists_for_phylo.json copying downloadable files... [ 9%] data/long_testseqs.fasta copying downloadable files... [ 12%] data/mycoplasma-genitalium.fa copying downloadable files... [ 15%] data/mycoplasma-genitalium.gb copying downloadable files... [ 18%] data/mycoplasma-genitalium.gff copying downloadable files... [ 21%] data/C-elegans-chromosome-I.fa copying downloadable files... [ 24%] data/C-elegans-chromosome-I.gb copying downloadable files... [ 27%] data/C-elegans-chromosome-I.gff copying downloadable files... [ 30%] data/primate_brca1.fasta copying downloadable files... [ 33%] data/primate_brca1.tree copying downloadable files... [ 36%] data/brca1_hsa_shortened.gff copying downloadable files... 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[ 97%] index writing output... [ 98%] install writing output... [ 99%] licenses writing output... [ 99%] pycogent writing output... [100%] templates/class generating indices... genindex done /usr/lib/python3/dist-packages/nbsphinx.py:2094: RemovedInSphinx80Warning: The alias 'sphinx.util.status_iterator' is deprecated, use 'sphinx.util.display.status_iterator' instead. Check CHANGES for Sphinx API modifications. status_iterator = sphinx.util.status_iterator copying linked files... copying notebooks ... writing additional pages... search done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 1069 warnings. The HTML pages are in _build/html. Build finished. 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[ 89%] tests/test_evolve/test_substitution_model.py ...................... [ 89%] tests/test_format/test_bedgraph.py ........ [ 89%] tests/test_format/test_clustal.py ... [ 89%] tests/test_format/test_fasta.py . [ 89%] tests/test_maths/test_distance_transform.py ............................ [ 89%] ....... [ 90%] tests/test_maths/test_geometry.py .......... [ 90%] tests/test_maths/test_matrix_exponential_integration.py .... [ 90%] tests/test_maths/test_matrix_logarithm.py ... [ 90%] tests/test_maths/test_measure.py ........ [ 90%] tests/test_maths/test_optimisers.py ........... [ 90%] tests/test_maths/test_period.py ....... [ 90%] tests/test_maths/test_util.py ....... [ 90%] tests/test_maths/test_stats/test_contingency.py .................... [ 90%] tests/test_maths/test_stats/test_distribution.py ....................... [ 90%] . [ 91%] tests/test_maths/test_stats/test_information_criteria.py ... [ 91%] tests/test_maths/test_stats/test_jackknife.py .... 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[100%] =============================== warnings summary =============================== cogent3/parse/newick.py:69 /<>/.pybuild/cpython3_3.11_cogent3/build/cogent3/parse/newick.py:69: DeprecationWarning: invalid escape sequence '\[' splits = re.split("""([\\t ]+|\\n|''|""|[]['"(),:;\[\]])""", self.text) ../../../../../../usr/lib/python3/dist-packages/_pytest/config/__init__.py:1433 /usr/lib/python3/dist-packages/_pytest/config/__init__.py:1433: PytestConfigWarning: No files were found in testpaths; consider removing or adjusting your testpaths configuration. Searching recursively from the current directory instead. self.args, self.args_source = self._decide_args( tests/test_app/test_evo.py::TestHypothesisResult::test_alt_hyp_fail_error /<>/.pybuild/cpython3_3.11_cogent3/build/cogent3/core/sequence.py:1448: UserWarning: Dropped remainder "GA" from end of sequence warnings.warn( tests/test_evolve/test_likelihood_function.py::LikelihoodFunctionTests::test_get_param_rules_multilocus tests/test_util/test_deserialise.py::TestDeserialising::test_deserialise_likelihood_function_multilocus /<>/.pybuild/cpython3_3.11_cogent3/build/cogent3/evolve/parameter_controller.py:411: UserWarning: Used mean of 12 mprobs values 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:411: UserWarning: Used mean of 7 beta values tests/test_evolve/test_newq.py::NewQ::test_cond_pos_differ tests/test_evolve/test_newq.py::NewQ::test_get_motif_probs tests/test_evolve/test_newq.py::NewQ::test_get_statistics tests/test_evolve/test_newq.py::NewQ::test_newQ_is_nuc_process tests/test_evolve/test_newq.py::NewQ::test_results_different tests/test_evolve/test_newq.py::NewQ::test_sim_alignment /<>/.pybuild/cpython3_3.11_cogent3/build/cogent3/evolve/substitution_model.py:742: UserWarning: Motif probs over specified tests/test_evolve/test_ns_substitution_model.py::NonStatMarkov::test_general_vs_constructed_general /<>/.pybuild/cpython3_3.11_cogent3/build/cogent3/maths/optimisers.py:205: UserWarning: Unused arg for local alignment: results 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 -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html = 9541 passed, 9 skipped, 4 deselected, 1 xfailed, 2 xpassed, 14 warnings in 6155.86s (1:42:35) = I: pybuild pybuild:310: cp -r /<>/tests/data /<>/.pybuild/cpython3_3.12_cogent3/build I: pybuild base:305: cd /<>/.pybuild/cpython3_3.12_cogent3/build; python3.12 -m pytest -k 'not test_pickleable_member_roundtrip and not test_pickleable_roundtrip' ============================= test session starts ============================== platform linux -- Python 3.12.1, pytest-7.4.4, pluggy-1.3.0 rootdir: /<>/.pybuild/cpython3_3.12_cogent3/build configfile: pyproject.toml plugins: xdist-3.4.0, cov-4.1.0, anyio-4.2.0 collected 9557 items / 4 deselected / 9553 selected tests/test_phylo.py .................. 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[100%] =============================== warnings summary =============================== cogent3/parse/newick.py:69 /<>/.pybuild/cpython3_3.12_cogent3/build/cogent3/parse/newick.py:69: SyntaxWarning: invalid escape sequence '\[' splits = re.split("""([\\t ]+|\\n|''|""|[]['"(),:;\[\]])""", self.text) ../../../../../../usr/lib/python3/dist-packages/_pytest/config/__init__.py:1433 /usr/lib/python3/dist-packages/_pytest/config/__init__.py:1433: PytestConfigWarning: No files were found in testpaths; consider removing or adjusting your testpaths configuration. Searching recursively from the current directory instead. self.args, self.args_source = self._decide_args( ../../../../../../usr/lib/python3/dist-packages/dateutil/tz/tz.py:37 /usr/lib/python3/dist-packages/dateutil/tz/tz.py:37: DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.fromtimestamp(timestamp, datetime.UTC). EPOCH = datetime.datetime.utcfromtimestamp(0) tests/test_app/test_composable.py: 8 warnings tests/test_app/test_data_store.py: 14 warnings tests/test_app/test_io.py: 5 warnings tests/test_app/test_sqlite_data_store.py: 46 warnings /<>/.pybuild/cpython3_3.12_cogent3/build/cogent3/app/sqlite_data_store.py:159: DeprecationWarning: The default datetime adapter is deprecated as of Python 3.12; see the sqlite3 documentation for suggested replacement recipes self.db.execute(f"INSERT INTO {_LOG_TABLE}(date) VALUES (?)", (timestamp,)) tests/test_app/test_composable.py: 8 warnings tests/test_app/test_data_store.py: 14 warnings tests/test_app/test_io.py: 5 warnings tests/test_app/test_sqlite_data_store.py: 46 warnings /<>/.pybuild/cpython3_3.12_cogent3/build/cogent3/app/sqlite_data_store.py:160: DeprecationWarning: The default datetime adapter is deprecated as of Python 3.12; see the sqlite3 documentation for suggested replacement recipes self._log_id = self._db.execute( tests/test_app/test_data_store.py::test_convert_tinydbs_to_sqlite[sample_locked_w_log.tinydb-2] /<>/.pybuild/cpython3_3.12_cogent3/build/cogent3/app/data_store.py:848: DeprecationWarning: The default datetime adapter is deprecated as of Python 3.12; see the sqlite3 documentation for suggested replacement recipes dstore.db.execute(cmnd, values) tests/test_app/test_evo.py::TestHypothesisResult::test_alt_hyp_fail_error /<>/.pybuild/cpython3_3.12_cogent3/build/cogent3/core/sequence.py:1448: UserWarning: Dropped remainder "GA" from end of sequence warnings.warn( tests/test_app/test_sqlite_data_store.py::test_open_existing tests/test_app/test_sqlite_data_store.py::test_read tests/test_app/test_sqlite_data_store.py::test_read_log tests/test_app/test_sqlite_data_store.py::test_summary_logs tests/test_app/test_sqlite_data_store.py::test_append_makes_logs[appended.sqlitedb-None] tests/test_app/test_sqlite_data_store.py::test_append_makes_logs[appended.sqlitedb-None] /<>/.pybuild/cpython3_3.12_cogent3/build/cogent3/app/sqlite_data_store.py:187: DeprecationWarning: The default timestamp converter is deprecated as of Python 3.12; see the sqlite3 documentation for suggested replacement recipes result = self.db.execute(cmnd, (identifier.name,)).fetchone() tests/test_app/test_sqlite_data_store.py::test_db_init_log /<>/.pybuild/cpython3_3.12_cogent3/build/tests/test_app/test_sqlite_data_store.py:152: DeprecationWarning: The default timestamp converter is deprecated as of Python 3.12; see the sqlite3 documentation for suggested replacement recipes rows = dstore.db.execute(f"Select * from {_LOG_TABLE}").fetchall() tests/test_evolve/test_likelihood_function.py::LikelihoodFunctionTests::test_get_param_rules_multilocus tests/test_util/test_deserialise.py::TestDeserialising::test_deserialise_likelihood_function_multilocus /<>/.pybuild/cpython3_3.12_cogent3/build/cogent3/evolve/parameter_controller.py:411: UserWarning: Used mean of 12 mprobs values tests/test_evolve/test_likelihood_function.py::LikelihoodFunctionTests::test_set_param_rule_adjust_bounds /<>/.pybuild/cpython3_3.12_cogent3/build/cogent3/evolve/parameter_controller.py:411: UserWarning: Used mean of 7 beta values tests/test_evolve/test_newq.py::NewQ::test_cond_pos_differ tests/test_evolve/test_newq.py::NewQ::test_get_motif_probs tests/test_evolve/test_newq.py::NewQ::test_get_statistics tests/test_evolve/test_newq.py::NewQ::test_newQ_is_nuc_process tests/test_evolve/test_newq.py::NewQ::test_results_different tests/test_evolve/test_newq.py::NewQ::test_sim_alignment /<>/.pybuild/cpython3_3.12_cogent3/build/cogent3/evolve/substitution_model.py:742: UserWarning: Motif probs over specified tests/test_evolve/test_ns_substitution_model.py::NonStatMarkov::test_general_vs_constructed_general /<>/.pybuild/cpython3_3.12_cogent3/build/cogent3/maths/optimisers.py:205: UserWarning: Unused arg for local alignment: results 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 -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html = 9541 passed, 9 skipped, 4 deselected, 1 xfailed, 2 xpassed, 169 warnings in 6109.50s (1:41:49) = 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:178: Copying package built for python3.11 to destdir I: pybuild plugin_pyproject:178: Copying package built for python3.12 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 dh_installchangelogs: warning: Could not parse timestamp 'Sat Oct 28 22:30:00 2023 +0200'. debian/changelog will not be trimmed. dh_installchangelogs: warning: debian/changelog could not be trimmed. The full changelog will be installed. debian/rules override_dh_python3 make[1]: Entering directory '/<>' dh_python3 --shebang=/usr/bin/python3 W: dh_python3 fs:134: Paths differ: debian/python3-cogent3/usr/lib/python3.12/dist-packages/.pytest_cache/v/cache/nodeids and debian/python3-cogent3/usr/lib/python3/dist-packages/.pytest_cache/v/cache/nodeids 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 dh_strip_nondeterminism: warning: debian/changelog(l22): badly formatted trailer line LINE: -- Santiago Vila Sat Oct 28 22:30:00 2023 +0200 dh_strip_nondeterminism: warning: debian/changelog(l24): found start of entry where expected more change data or trailer LINE: python-cogent (2023.2.12a1+dfsg-3) unstable; urgency=medium dh_strip_nondeterminism: warning: debian/changelog(l24): found end of file where expected more change data or trailer 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 154 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: Truncating usr/share/doc/python3-cogent3/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-cogent3 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-cogent3' in '../python3-cogent3_2023.12.15a1+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=any -O../python-cogent_2023.12.15a1+dfsg-1_arm64.buildinfo dpkg-genbuildinfo: warning: debian/changelog(l22): badly formatted trailer line LINE: -- Santiago Vila Sat Oct 28 22:30:00 2023 +0200 dpkg-genbuildinfo: warning: debian/changelog(l24): found start of entry where expected more change data or trailer LINE: python-cogent (2023.2.12a1+dfsg-3) unstable; urgency=medium dpkg-genbuildinfo: warning: debian/changelog(l24): found end of file where expected more change data or trailer dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../python-cogent_2023.12.15a1+dfsg-1_arm64.changes dpkg-genchanges: warning: debian/changelog(l22): badly formatted trailer line LINE: -- Santiago Vila Sat Oct 28 22:30:00 2023 +0200 dpkg-genchanges: warning: debian/changelog(l24): found start of entry where expected more change data or trailer LINE: python-cogent (2023.2.12a1+dfsg-3) unstable; urgency=medium dpkg-genchanges: warning: debian/changelog(l24): found end of file where expected more change data or trailer 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 2024-01-27T03:44:26Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ python-cogent_2023.12.15a1+dfsg-1_arm64.changes: ------------------------------------------------ Format: 1.8 Date: Fri, 26 Jan 2024 15:36:11 +0100 Source: python-cogent Binary: python3-cogent3 Built-For-Profiles: noudeb Architecture: arm64 Version: 2023.12.15a1+dfsg-1 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: python3-cogent3 - framework for genomic biology Closes: 1058370 1059557 Changes: python-cogent (2023.12.15a1+dfsg-1) unstable; urgency=medium . * New upstream version Closes: #1058370 * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update) * Build-Depends: python3-sphinxcontrib.bibtex, python3-sphinx-design, python3-pydata-sphinx-theme * Add build support for loongarch64 Closes: #1059557 * Fix patch to skip some tests which was lacking `import multiprocessing` Checksums-Sha1: 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+------------------------------------------------------------------------------+ Format: 1.0 Source: python-cogent Binary: python3-cogent3 Architecture: arm64 Version: 2023.12.15a1+dfsg-1 Checksums-Md5: 7b565e2c24d1302c141f970625f18e55 2030252 python3-cogent3_2023.12.15a1+dfsg-1_arm64.deb Checksums-Sha1: cc472ba528f163ff20d898ceb97f983c84797022 2030252 python3-cogent3_2023.12.15a1+dfsg-1_arm64.deb Checksums-Sha256: 05f10fafc27fd25e3d690cb8cf2cd6178acbbcedac9956dd9cda3c5345c9fa7b 2030252 python3-cogent3_2023.12.15a1+dfsg-1_arm64.deb Build-Origin: Ubuntu Build-Architecture: arm64 Build-Date: Sat, 27 Jan 2024 03:44:17 +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 (= 0.21-14ubuntu1), autotools-dev (= 20220109.1), base-files (= 13ubuntu6), base-passwd (= 3.6.3), bash (= 5.2.21-2ubuntu1), binutils (= 2.41.90.20240122-1ubuntu1), binutils-aarch64-linux-gnu (= 2.41.90.20240122-1ubuntu1), binutils-common (= 2.41.90.20240122-1ubuntu1), blt (= 2.5.3+dfsg-7), bsdextrautils (= 2.39.2-6ubuntu1), bsdutils (= 1:2.39.2-6ubuntu1), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5build1), ca-certificates (= 20230311ubuntu1), coreutils (= 9.4-2ubuntu2), cpp (= 4:13.2.0-3ubuntu1), cpp-13 (= 13.2.0-11ubuntu1), cpp-13-aarch64-linux-gnu (= 13.2.0-11ubuntu1), cpp-aarch64-linux-gnu (= 4:13.2.0-3ubuntu1), cython3 (= 3.0.8-1ubuntu1), dash (= 0.5.12-6ubuntu1), debconf (= 1.5.85), debhelper (= 13.11.10ubuntu1), debianutils (= 5.16), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-python (= 6.20231223), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), docutils-common (= 0.20.1+dfsg-3), dpkg (= 1.22.2ubuntu2), dpkg-dev (= 1.22.2ubuntu2), dwz (= 0.15-1), file (= 1:5.45-2), findutils (= 4.9.0-5), flit (= 3.9.0-2), fontconfig-config (= 2.14.2-6ubuntu1), fonts-dejavu-core (= 2.37-8), fonts-dejavu-mono (= 2.37-8), fonts-glyphicons-halflings (= 1.009~3.4.1+dfsg-3), fonts-lyx (= 2.4.0~RC1-2), g++ (= 4:13.2.0-3ubuntu1), g++-13 (= 13.2.0-11ubuntu1), g++-13-aarch64-linux-gnu (= 13.2.0-11ubuntu1), g++-aarch64-linux-gnu (= 4:13.2.0-3ubuntu1), gcc (= 4:13.2.0-3ubuntu1), gcc-13 (= 13.2.0-11ubuntu1), gcc-13-aarch64-linux-gnu (= 13.2.0-11ubuntu1), gcc-13-base (= 13.2.0-11ubuntu1), gcc-14-base (= 14-20240126-2ubuntu1), gcc-aarch64-linux-gnu (= 4:13.2.0-3ubuntu1), gettext (= 0.21-14ubuntu1), gettext-base (= 0.21-14ubuntu1), grep (= 3.11-4), groff-base (= 1.23.0-3), gzip (= 1.12-1ubuntu1), hostname (= 3.23+nmu1ubuntu1), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), jupyter-sphinx-theme-common (= 0.0.6+ds1-11), libacl1 (= 2.3.1-4ubuntu1), libarchive-zip-perl (= 1.68-1), libargon2-1 (= 0~20190702+dfsg-4), libasan8 (= 14-20240126-2ubuntu1), libatomic1 (= 14-20240126-2ubuntu1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2), libaudit1 (= 1:3.1.2-2), libbinutils (= 2.41.90.20240122-1ubuntu1), libblas3 (= 3.11.0-2build1), libblkid1 (= 2.39.2-6ubuntu1), libbrotli1 (= 1.1.0-2), libbsd0 (= 0.11.8-1), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.38-3ubuntu1), libc-dev-bin (= 2.38-3ubuntu1), libc6 (= 2.38-3ubuntu1), libc6-dev (= 2.38-3ubuntu1), libcap-ng0 (= 0.8.4-1), libcap2 (= 1:2.66-4ubuntu1), libcc1-0 (= 14-20240126-2ubuntu1), libcom-err2 (= 1.47.0-2ubuntu1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.41.90.20240122-1ubuntu1), libctf0 (= 2.41.90.20240122-1ubuntu1), libcurl4 (= 8.5.0-2ubuntu1), libdb5.3 (= 5.3.28+dfsg2-4), libdebconfclient0 (= 0.271ubuntu1), libdebhelper-perl (= 13.11.10ubuntu1), libdeflate0 (= 1.18-1), libdpkg-perl (= 1.22.2ubuntu2), libdw1 (= 0.190-1), libedit2 (= 3.1-20230828-1), libelf1 (= 0.190-1), libexpat1 (= 2.5.0-2), libexpat1-dev (= 2.5.0-2), libffi8 (= 3.4.4-2), libfile-stripnondeterminism-perl (= 1.13.1-1), libfontconfig1 (= 2.14.2-6ubuntu1), libfreetype6 (= 2.13.2+dfsg-1), libfribidi0 (= 1.0.13-3), libgcc-13-dev (= 13.2.0-11ubuntu1), libgcc-s1 (= 14-20240126-2ubuntu1), libgcrypt20 (= 1.10.3-2), libgdbm-compat4 (= 1.23-5), libgdbm6 (= 1.23-5), libgfortran5 (= 14-20240126-2ubuntu1), libglib2.0-0 (= 2.78.3-2), libgmp10 (= 2:6.3.0+dfsg-2ubuntu4), libgnutls30 (= 3.8.3-1ubuntu1), libgomp1 (= 14-20240126-2ubuntu1), libgpg-error0 (= 1.47-3build1), libgprofng0 (= 2.41.90.20240122-1ubuntu1), libgraphite2-3 (= 1.3.14-2), libgssapi-krb5-2 (= 1.20.1-5build1), libharfbuzz0b (= 8.3.0-2), libhogweed6 (= 3.9.1-2), libhwasan0 (= 14-20240126-2ubuntu1), libhwloc15 (= 2.10.0-1), libicu74 (= 74.2-1ubuntu1), libidn2-0 (= 2.3.4-1build1), libimagequant0 (= 2.18.0-1), libisl23 (= 0.26-3), libitm1 (= 14-20240126-2ubuntu1), libjansson4 (= 2.14-2), libjbig0 (= 2.1-6.1ubuntu1), 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 (= 7.2.6-3), libjs-underscore (= 1.13.4~dfsg+~1.11.4-3), libjson-perl (= 4.10000-1), libk5crypto3 (= 1.20.1-5build1), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-5build1), libkrb5support0 (= 1.20.1-5build1), liblapack3 (= 3.11.0-2build1), liblbfgsb0 (= 3.0+dfsg.4-1), liblcms2-2 (= 2.14-2), libldap2 (= 2.6.6+dfsg-1~exp1ubuntu2), liblerc4 (= 4.0.0+ds-4ubuntu1), libllvm14 (= 1:14.0.6-16build2), liblsan0 (= 14-20240126-2ubuntu1), liblua5.4-0 (= 5.4.6-2), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.4.5-0.3), libmagic-mgc (= 1:5.45-2), libmagic1 (= 1:5.45-2), libmd0 (= 1.1.0-2), libmount1 (= 2.39.2-6ubuntu1), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libncursesw6 (= 6.4+20240113-1), libnettle8 (= 3.9.1-2), libnghttp2-14 (= 1.58.0-1), libnorm1 (= 1.5.9+dfsg-3), libnsl-dev (= 1.3.0-3), libnsl2 (= 1.3.0-3), libopenjp2-7 (= 2.5.0-2), libp11-kit0 (= 0.25.3-2ubuntu2), libpam-modules (= 1.5.2-9.1ubuntu2), libpam-modules-bin (= 1.5.2-9.1ubuntu2), libpam-runtime (= 1.5.2-9.1ubuntu2), libpam0g (= 1.5.2-9.1ubuntu2), libpcre2-8-0 (= 10.42-4ubuntu1), libperl5.38 (= 5.38.2-3), libpfm4 (= 4.13.0+git16-g535c204-1), libpgm-5.3-0 (= 5.3.128~dfsg-2), libpipeline1 (= 1.5.7-1), libpng16-16 (= 1.6.40-3), libpsl5 (= 0.21.2-1build1), libpython3-all-dev (= 3.12.1-0ubuntu1), libpython3-dev (= 3.12.1-0ubuntu1), libpython3-stdlib (= 3.12.1-0ubuntu1), libpython3.11 (= 3.11.7-2), libpython3.11-dev (= 3.11.7-2), libpython3.11-minimal (= 3.11.7-2), libpython3.11-stdlib (= 3.11.7-2), libpython3.12 (= 3.12.1-2), libpython3.12-dev (= 3.12.1-2), libpython3.12-minimal (= 3.12.1-2), libpython3.12-stdlib (= 3.12.1-2), libqhull-r8.0 (= 2020.2-6), libraqm0 (= 0.10.1-1), libreadline8 (= 8.2-3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg1-4), libsasl2-modules-db (= 2.1.28+dfsg1-4), libseccomp2 (= 2.5.4-2ubuntu1), libselinux1 (= 3.5-2), libsframe1 (= 2.41.90.20240122-1ubuntu1), libsharpyuv0 (= 1.3.2-0.3), libsmartcols1 (= 2.39.2-6ubuntu1), libsodium23 (= 1.0.18-1build2), libsqlite3-0 (= 3.45.0-1), libssh-4 (= 0.10.6-2), libssl3 (= 3.0.10-1ubuntu3), libstdc++-13-dev (= 13.2.0-11ubuntu1), libstdc++6 (= 14-20240126-2ubuntu1), libsub-override-perl (= 0.10-1), libsystemd0 (= 255.2-3ubuntu2), libtasn1-6 (= 4.19.0-3), libtbb12 (= 2021.11.0-2ubuntu2), libtbbbind-2-5 (= 2021.11.0-2ubuntu2), libtbbmalloc2 (= 2021.11.0-2ubuntu2), libtcl8.6 (= 8.6.13+dfsg-2), libtiff6 (= 4.5.1+git230720-3ubuntu1), libtinfo6 (= 6.4+20240113-1), libtirpc-common (= 1.3.4+ds-1build1), libtirpc-dev (= 1.3.4+ds-1build1), libtirpc3 (= 1.3.4+ds-1build1), libtk8.6 (= 8.6.13-2), libtool (= 2.4.7-7), libtsan2 (= 14-20240126-2ubuntu1), libubsan1 (= 14-20240126-2ubuntu1), libuchardet0 (= 0.0.8-1), libudev1 (= 255.2-3ubuntu2), libunistring5 (= 1.1-2), libuuid1 (= 2.39.2-6ubuntu1), libwebp7 (= 1.3.2-0.3), libwebpdemux2 (= 1.3.2-0.3), libwebpmux3 (= 1.3.2-0.3), libx11-6 (= 2:1.8.7-1), libx11-data (= 2:1.8.7-1), 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-1.3build3), libxrender1 (= 1:0.9.10-1.1), libxslt1.1 (= 1.1.35-1), libxss1 (= 1:1.2.3-1build2), libyaml-0-2 (= 0.2.5-1), libzmq5 (= 4.3.5-1), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.6.0-14.14), llvm-14 (= 1:14.0.6-16build2), llvm-14-linker-tools (= 1:14.0.6-16build2), llvm-14-runtime (= 1:14.0.6-16build2), login (= 1:4.13+dfsg1-3ubuntu1), lto-disabled-list (= 46), m4 (= 1.4.19-4), make (= 4.3-4.1build1), man-db (= 2.12.0-3), mawk (= 1.3.4.20231126-1), media-types (= 10.1.0), ncurses-base (= 6.4+20240113-1), ncurses-bin (= 6.4+20240113-1), netbase (= 6.4), openssl (= 3.0.10-1ubuntu3), pandoc (= 3.1.3+ds-2), pandoc-data (= 3.1.3-1), patch (= 2.7.6-7build2), perl (= 5.38.2-3), perl-base (= 5.38.2-3), perl-modules-5.38 (= 5.38.2-3), po-debconf (= 1.0.21+nmu1), pybuild-plugin-pyproject (= 6.20231223), python-babel-localedata (= 2.10.3-3build1), python-matplotlib-data (= 3.6.3-1ubuntu3), python-tinycss2-common (= 1.2.1-2), python3 (= 3.12.1-0ubuntu1), python3-alabaster (= 0.7.12-1), python3-all (= 3.12.1-0ubuntu1), python3-all-dev (= 3.12.1-0ubuntu1), python3-anyio (= 4.2.0-1), python3-appdirs (= 1.4.4-4), python3-argon2 (= 21.1.0-2), python3-attr (= 23.2.0-1), python3-babel (= 2.10.3-3build1), python3-bleach (= 6.1.0-2), python3-brotli (= 1.1.0-2), python3-bs4 (= 4.12.3-1), python3-build (= 0.10.0-1), python3-certifi (= 2023.11.17-1), python3-cffi-backend (= 1.16.0-2), python3-chardet (= 5.2.0+dfsg-1), python3-commonmark (= 0.9.1-4), python3-contourpy (= 1.0.7-1build2), python3-coverage (= 7.3.2-0ubuntu1), python3-cycler (= 0.11.0-1), python3-dateutil (= 2.8.2-3), python3-decorator (= 5.1.1-5), python3-defusedxml (= 0.7.1-2), python3-dev (= 3.12.1-0ubuntu1), python3-distutils (= 3.11.5-1), python3-docutils (= 0.20.1+dfsg-3), python3-entrypoints (= 0.4-2), python3-execnet (= 2.0.0-2), python3-fastjsonschema (= 2.19.0-1), python3-fonttools (= 4.46.0-1), python3-fs (= 2.4.16-3), python3-html5lib (= 1.1-3ubuntu1), python3-idna (= 3.3-2), python3-imagesize (= 1.4.1-1), python3-iniconfig (= 1.1.1-2), python3-installer (= 0.7.0+dfsg1-2), python3-isort (= 5.6.4-1), python3-jinja2 (= 3.1.2-1ubuntu1), python3-json5 (= 0.9.14-1), python3-jsonschema (= 4.10.3-2ubuntu1), python3-jupyter-client (= 8.6.0-0ubuntu1), python3-jupyter-core (= 5.3.2-1), python3-jupyter-server (= 1.23.3-2), python3-jupyter-sphinx-theme (= 0.0.6+ds1-11), python3-jupyterlab-pygments (= 0.2.2-3), python3-jupyterlab-server (= 2.25.2-1), python3-kiwisolver (= 1.4.4-1build2), python3-latexcodec (= 2.0.1-2), python3-lib2to3 (= 3.11.5-1), python3-llvmlite (= 0.41.1-1), python3-lxml (= 5.1.0-1), python3-lz4 (= 4.0.2+dfsg-1build2), python3-markupsafe (= 2.1.3-1build1), python3-matplotlib (= 3.6.3-1ubuntu3), python3-minimal (= 3.12.1-0ubuntu1), python3-mpmath (= 1.2.1-2), python3-nbclient (= 0.8.0-1), python3-nbconvert (= 6.5.3-4), python3-nbformat (= 5.9.1-1), python3-nbsphinx (= 0.8.11+ds-1), python3-numba (= 0.58.1+dfsg-1), python3-numpy (= 1:1.24.2-2), python3-numpydoc (= 1.6.0-1), python3-packaging (= 23.2-1), python3-pandas (= 1.5.3+dfsg-12), python3-pandas-lib (= 1.5.3+dfsg-12), python3-pandocfilters (= 1.5.0-1), python3-pil (= 10.2.0-1), python3-pil.imagetk (= 10.2.0-1), python3-pkg-resources (= 68.1.2-2), python3-platformdirs (= 4.1.0-1), python3-plotly (= 5.15.0+dfsg1-1), python3-pluggy (= 1.3.0-1), python3-prometheus-client (= 0.19.0+ds1-1), python3-ptyprocess (= 0.7.0-5), python3-py (= 1.11.0-2), python3-pybtex (= 0.24.0-4), python3-pybtex-docutils (= 1.0.2-1), python3-pydata-sphinx-theme (= 0.7.2-3), python3-pygments (= 2.15.1+dfsg-1), python3-pyparsing (= 3.1.1-1), python3-pyproject-hooks (= 1.0.0-2), python3-pyrsistent (= 0.18.1-1build5), python3-pytest (= 7.4.4-1), python3-pytest-cov (= 4.1.0-1), python3-pytest-xdist (= 3.4.0-1), python3-recommonmark (= 0.7.1+ds-5), python3-requests (= 2.31.0+dfsg-1ubuntu1), python3-roman (= 3.3-3), python3-scipy (= 1.10.1-7), python3-scitrack (= 2021.5.3-3), python3-send2trash (= 1.8.2-1), python3-setuptools (= 68.1.2-2), python3-six (= 1.16.0-4), python3-sniffio (= 1.3.0-2), python3-snowballstemmer (= 2.2.0-4), python3-soupsieve (= 2.5-1), python3-sphinx (= 7.2.6-3), python3-sphinx-bootstrap-theme (= 0.8.1-1), python3-sphinx-design (= 0.5.0-2), python3-sphinx-gallery (= 0.10.1-4), python3-sphinxcontrib.bibtex (= 2.6.2-1), python3-sympy (= 1.12-7), python3-tabulate (= 0.8.10-1), python3-tenacity (= 8.2.3-2), python3-terminado (= 0.18.0-1), python3-tinycss2 (= 1.2.1-2), python3-tinydb (= 3.15.2-4), python3-tk (= 3.11.5-1), python3-toml (= 0.10.2-1), python3-tomli-w (= 1.0.0-2), python3-tornado (= 6.4.0-0ubuntu1), python3-tqdm (= 4.64.1-1), python3-traitlets (= 5.5.0-2), python3-typing-extensions (= 4.7.1-2), python3-tz (= 2023.3.post1-2), python3-ufolib2 (= 0.16.0+dfsg1-1), python3-urllib3 (= 2.0.7-1), python3-webencodings (= 0.5.1-5), python3-websocket (= 1.2.3-1), python3-wheel (= 0.42.0-1), python3-yaml (= 6.0.1-2), python3-zmq (= 24.0.1-5), python3.11 (= 3.11.7-2), python3.11-dev (= 3.11.7-2), python3.11-minimal (= 3.11.7-2), python3.12 (= 3.12.1-2), python3.12-dev (= 3.12.1-2), python3.12-minimal (= 3.12.1-2), readline-common (= 8.2-3), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-2), sensible-utils (= 0.0.20), sgml-base (= 1.31), sphinx-common (= 7.2.6-3), sysvinit-utils (= 3.08-3ubuntu1), tar (= 1.35+dfsg-3), tk8.6-blt2.5 (= 2.5.3+dfsg-7), tzdata (= 2023d-1ubuntu2), unicode-data (= 15.1.0-1), util-linux (= 2.39.2-6ubuntu1), x11-common (= 1:7.7+23ubuntu2), xml-core (= 0.19), xz-utils (= 5.4.5-0.3), zlib1g (= 1:1.3.dfsg-3ubuntu1), zlib1g-dev (= 1:1.3.dfsg-3ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1706279771" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ python3-cogent3_2023.12.15a1+dfsg-1_arm64.deb --------------------------------------------- new Debian package, version 2.0. size 2030252 bytes: control archive=10827 bytes. 1248 bytes, 25 lines control 37917 bytes, 405 lines md5sums 277 bytes, 12 lines * postinst #!/bin/sh 390 bytes, 12 lines * prerm #!/bin/sh Package: python3-cogent3 Source: python-cogent Version: 2023.12.15a1+dfsg-1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 6903 Depends: python3-chardet, python3-numba, python3-numpy (>= 1:1.22.0), python3-numpy-abi9, python3-scipy, python3-scitrack, python3-tqdm, python3-typing-extensions, python3:any, python3-matplotlib, python3-pandas, python3-plotly, python3-tinydb Recommends: ncbi-blast+-legacy, dialign Suggests: python-cogent-doc 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. 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requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Type: any Build-Space: 181156 Build-Time: 13207 Distribution: noble-proposed Host Architecture: arm64 Install-Time: 2252 Job: python-cogent_2023.12.15a1+dfsg-1.dsc Machine Architecture: arm64 Package: python-cogent Package-Time: 15505 Source-Version: 2023.12.15a1+dfsg-1 Space: 181156 Status: successful Version: 2023.12.15a1+dfsg-1 -------------------------------------------------------------------------------- Finished at 2024-01-27T03:44:26Z Build needed 04:18:25, 181156k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27687842 Scanning for processes to kill in build PACKAGEBUILD-27687842