Change log for ncbi-entrez-direct package in Ubuntu

123 of 23 results
Published in hirsute-proposed on 2021-02-25
ncbi-entrez-direct (14.6.20210224+dfsg-1) unstable; urgency=medium

  * New upstream point release.
  * debian/man/esample.1: Update for new release.

 -- Aaron M. Ucko <email address hidden>  Wed, 24 Feb 2021 21:14:35 -0500
Published in hirsute-release on 2021-02-13
Deleted in hirsute-proposed (Reason: moved to Release)
ncbi-entrez-direct (14.6.20210209+dfsg-1) unstable; urgency=medium

  * New upstream release.
  * debian/man/{transmute,xtract}.1: Update for new release.
  * debian/man/xtract.1: Tune hyphenation under -insd.

 -- Aaron M. Ucko <email address hidden>  Fri, 12 Feb 2021 12:31:49 -0500
Superseded in hirsute-release on 2021-02-13
Deleted in hirsute-proposed on 2021-02-14 (Reason: moved to Release)
ncbi-entrez-direct (14.6.20210203+dfsg-2) unstable; urgency=medium

  * Standards-Version: 4.5.1 (routine-update)
  * Add salsa-ci file (routine-update)
  * Drop alternative build-dependency on unavailable golang-1.10-go --
    even stable has golang-go 1.11, which I've confirmed to work here.

 -- Aaron M. Ucko <email address hidden>  Sat, 06 Feb 2021 22:52:01 -0500
Superseded in hirsute-release on 2021-02-07
Deleted in hirsute-proposed on 2021-02-08 (Reason: moved to Release)
ncbi-entrez-direct (14.0.20201111+dfsg-1) unstable; urgency=medium

  * New upstream release.  (Not the latest, but enough of a milestone
    to merit an individual upload anyway.)
  * debian/NEWS (new): Document switch to new e* and nquire
    implementations by default and reimplementation of transmute.
  * debian/control:
    - Add curl | wget to Depends now that nquire defaults to using the
      shell (vs. Perl) implementation; leave Perl dependencies alone for
      the sake of other major scripts, and curl as a specific suggestion
      for the sake of download-ncbi-data and index-extras.
    - Suggest libxml2-utils and python3 for specific transmute modes.
  * debian/man/{efetch,efilter,einfo,elink,epost,esearch,gbf2xml,nquire,
    transmute,xtract}.1: Update for new release.
  * debian/man/nquire.1: Belatedly correct paste-o in description of shell
    implementation (which does not in fact use itself!).
  * debian/man/xtract.1: Belatedly retire two old flags from OPTIONS
    in addition to SYNOPSIS.
  * debian/rules: Reflect transmute-related changes -- it's gone from a
    trivial wrapper around the legacy edirect Perl script to a combination
    of a Go executable factored out of xtract, a non-trivial shell wrapper
    that handles several cases outside Go, and an xml2json Perl script
    cribbed from edirect.
    - Install that xml2json under /usr/lib -- it's formally an
      implementation detail of transmute -x2j, and would otherwise
      conflict with libxml-compile-perl.
    - Tweak the transmute wrapper to run python3 rather than versionless
      python for json.tool.
    - Retain the new portion of upstream's xtract wrapper that delegates
      factored-out functionality to transmute.
    - To facilitate some of those changes, add a PKG_BIN_DIR macro.

 -- Aaron M. Ucko <email address hidden>  Sun, 24 Jan 2021 17:14:03 -0500
Superseded in hirsute-release on 2021-01-25
Deleted in hirsute-proposed on 2021-01-26 (Reason: moved to Release)
ncbi-entrez-direct (14.0.20201030+dfsg-1) unstable; urgency=medium

  * New upstream release.
  * debian/man/efetch.1: Update for new release.

 -- Aaron M. Ucko <email address hidden>  Sun, 01 Nov 2020 21:24:40 -0500
Superseded in hirsute-release on 2020-11-02
Deleted in hirsute-proposed on 2020-11-03 (Reason: moved to Release)
ncbi-entrez-direct (14.0.20201015+dfsg-1) unstable; urgency=medium

  * New upstream release.
  * debian/man/xtract.1: Update for new release.

 -- Aaron M. Ucko <email address hidden>  Mon, 19 Oct 2020 21:37:21 -0400
Superseded in hirsute-release on 2020-10-29
Published in groovy-release on 2020-07-15
Deleted in groovy-proposed (Reason: moved to Release)
ncbi-entrez-direct (13.7.20200713+dfsg-1) unstable; urgency=medium

  * New upstream release.
  * debian/man/{accn-at-a-time,g2x}.1: Document new commands.
  * debian/man/{gbf2xml,word-at-a-time,xtract}.1: Update for new release.
  * debian/rules:
    - Account for new as-is script accn-at-a-time, new Go executable g2x, and
      gbf2xml's switch from a Perl script to an as-is script (wrapping xtract).
    - Belatedly arrange to tweak enquire, whose --ca* options won't do here.

 -- Aaron M. Ucko <email address hidden>  Tue, 14 Jul 2020 22:17:15 -0400
Superseded in groovy-release on 2020-07-15
Deleted in groovy-proposed on 2020-07-17 (Reason: moved to Release)
ncbi-entrez-direct (13.7.20200615+dfsg-2) unstable; urgency=medium

  * debian/rules: Install ftp-cp, ftp-ls, nquire, and transmute as simple
    wrappers for edirect (with no .pl suffix) now that they're no longer
    independent Perl scripts (as of 12.3.20191024[+ds]), fixing a
    regression caught by autopkgtest.
  * debian/tests/run-unit-test: Correct invocation of filter-stop-words
    (which ignores its arguments and reads from standard input).

 -- Aaron M. Ucko <email address hidden>  Sun, 28 Jun 2020 21:11:51 -0400
Superseded in groovy-release on 2020-06-29
Deleted in groovy-proposed on 2020-06-30 (Reason: moved to Release)
ncbi-entrez-direct (13.1.20200102+dfsg-1) unstable; urgency=medium

  * New upstream release.
  * .gitignore: Ignore new "saved" directory.
  * debian/control: Suggest curl (for index-extras).
  * debian/copyright: Add *.pdf (sourceless) to Files-Excluded.
  * debian/examples: Remove Scripps BioThings support, now considered official
    enough (mentioned in README, albeit as experimental).
  * debian/install: Install bt-*.txt and hlp-*.txt (bt-context.txt and
    hlp-xtract.txt at present) to a new /usr/lib/ncbi-entrez-direct directory.
  * debian/man/{archive-pubmed,download-ncbi-data,edirect,efetch,elink,esample,
    esearch,ftp-cp,fetch-pubmed,ftp-ls,index-pubmed,j2x,join-into-groups-of,
    nquire,phrase-search,rchive,sort-uniq-count,transmute,xtract}.1: Update for
    new release.
  * debian/man/{bt-link,bt-load,bt-save,bt-srch,expand-current,fetch-extras,
    t2x,xplore}.1: Document new commands.
  * debian/man/efetch.1: Correct old paste-o in -chr_stop's description.
  * debian/man/fetch-pubmed.1: Belatedly wordsmith description of -path.
  * debian/man/index-extras.1: Rename from index-bioc.1 and update.
  * debian/man/nquire.1: Belatedly drop accidental self-referential SEE ALSO.
  * debian/man/xtract.1: Explicitly mark suboptions as such; belatedly resync
    -indices' description.
  * debian/rules:
    - Account for new as-is scripts expand-current and fetch-extras; for newly
      official Scripps BioThings scripts bt-link, bt-load, bt-save, bt-srch,
      and xplore (some of which need tweaking to look for bt-context.txt in the
      right place); for new Go executable t2x; and for rename of as-is script
      index-bioc to index-extras (which moreover needs its interpreter
      specification corrected to #!/bin/bash via a new generic mechanism).
    - Move the xtract binary from /usr/bin to /usr/lib/ncbi-entrez-direct (so
      it can find hlp-xtract.txt) and substitute a wrapper script.
    - Broaden .../x/sys/unix to .../x/sys in GOLIBSRC(_).  (Closes: #963439.)
    - Temporarily move new go.mod, go.sum, and s2p.go files to a "saved"
      directory to keep them from interfering with the build process.  (They
      don't necessarily deserve outright exclusion, even with repacking
      already in use.)
  * debian/watch: Change repack suffix to +dfsg due to the additional need
    to exclude sourceless PDF documents.

 -- Aaron M. Ucko <email address hidden>  Sun, 21 Jun 2020 22:32:39 -0400
Superseded in groovy-release on 2020-06-22
Deleted in groovy-proposed on 2020-06-23 (Reason: moved to Release)
ncbi-entrez-direct (12.0.20190816+ds-2) unstable; urgency=medium

  * Team upload
  * Add autopkgtests

 -- Pranav Ballaney <email address hidden>  Wed, 06 May 2020 19:11:16 +0530
Superseded in groovy-release on 2020-05-07
Published in focal-release on 2020-02-03
Deleted in focal-proposed (Reason: moved to Release)
ncbi-entrez-direct (12.0.20190816+ds-1) unstable; urgency=medium

  [ Aaron M. Ucko ]
  * New upstream release.  (Not fully caught up, but uploading anyway to
    address an FTBFS bug that turned up.)
  * debian/control:
    - Build-depend on github-gedex-inflector-dev.
    - Declare a nominal XS-Go-Import-Path to placate dh-golang.
  * debian/examples: Install BioThings support as examples for now: bt-*
    (including one data file currently expected to live alongside scripts)
    and xplore.
  * debian/man/{download-ncbi-data,esample,exclude-uid-lists,index-bioc,j2x,
    pm-collect,xml2tbl}.1: Document new commands.
  * debian/man/{download-{pubmed,sequence},efetch,efilter,esearch,fetch-pubmed,
    ftp-{cp,ls},index-pubmed,intersect-uid-lists,nquire,pm-index,rchive,
    transmute,xtract}.1: Update for new release.
  * debian/man/download-sequence.1: Fix copy-and-paste error (wrong name
    left in DESCRIPTION).
  * debian/rules:
    - Belatedly use FIX_PERL_SHEBANG for bin/edirect.
    - Factor out GH and GL macros for github.com and golang.org respectively.
    - Factor out a pattern rule for building Go executables (and a
      supporting rule for the gounidecode compatibility symlink).
    - Add $(GH)/gedex/inflector to GOLIBSRC_ (for xtract).
    - Account for new download script download-ncbi-data; as-is scripts
      esample, exclude-uid-lists, index-bioc, pm-collect, and xml2tbl; and Go
      executable j2x (which does not use common.go).
    - Set GOCACHE to avoid needing a writable (or simply existent!) HOME;
      wipe the cache in override_dh_auto_clean.  (Closes: 947995.)
  * .gitignore: Ignore the new go-cache tree.

  [ Andreas Tille ]
  * d/watch: simplify + version=4
  * Standards-Version: 4.5.0 (routine-update)
  * debhelper-compat 12 (routine-update)

 -- Aaron M. Ucko <email address hidden>  Sun, 02 Feb 2020 22:02:43 -0500
Superseded in focal-release on 2020-02-03
Obsolete in eoan-release on 2020-12-29
Deleted in eoan-proposed on 2020-12-29 (Reason: moved to release)
ncbi-entrez-direct (10.9.20190219+ds-1build2) eoan; urgency=medium

  * Rebuild against new default golang 1.11.

 -- Gianfranco Costamagna <email address hidden>  Wed, 01 May 2019 09:37:11 +0200
Superseded in eoan-release on 2019-05-01
Deleted in eoan-proposed on 2019-05-02 (Reason: moved to release)
ncbi-entrez-direct (10.9.20190219+ds-1build1) eoan; urgency=medium

  * Rebuild against new default golang 1.11.

 -- Gianfranco Costamagna <email address hidden>  Wed, 01 May 2019 09:37:11 +0200
Superseded in eoan-release on 2019-05-01
Deleted in eoan-proposed on 2019-05-02 (Reason: moved to release)
ncbi-entrez-direct (10.9.20190219+ds-1) unstable; urgency=medium

  * New upstream point release.
  * debian/man/xtract.1: Update accordingly (adding -is-within).

 -- Aaron M. Ucko <email address hidden>  Tue, 26 Feb 2019 21:28:41 -0500
Superseded in eoan-release on 2019-04-21
Obsolete in disco-release on 2020-07-14
Deleted in disco-proposed on 2020-07-14 (Reason: moved to release)
ncbi-entrez-direct (10.9.20190205+ds-1) unstable; urgency=medium

  * New upstream release.
  * debian/man/{archive-pubmed,download-pubmed,edirect,efilter,
    entrez-phrase-search,esearch,espell,fetch-pubmed,index-pubmed,
    phrase-search,rchive,stream-pubmed,transmute,xtract}.1: Update
    accordingly.
  * debian/man/{local-phrase-search,pm-{clean,current,erase,log,repack,uids,
    verify}}.1: Retire per the corresponding scripts.
  * debian/rules: Stop installing retired scripts local-phrase-search and
    (implicitly) pm-{clean,current,erase,log,repack,uids,verify}.

 -- Aaron M. Ucko <email address hidden>  Wed, 06 Feb 2019 22:51:27 -0500
Superseded in disco-release on 2019-02-07
Deleted in disco-proposed on 2019-02-08 (Reason: moved to release)
ncbi-entrez-direct (10.5.20181204+ds-2) unstable; urgency=medium

  * debian/control: Actually build-depend on dh-golang.

 -- Aaron M. Ucko <email address hidden>  Wed, 05 Dec 2018 22:05:20 -0500
Superseded in disco-release on 2018-12-06
Obsolete in cosmic-release on 2020-07-13
Published in bionic-release on 2017-11-03
Deleted in bionic-proposed (Reason: moved to release)
ncbi-entrez-direct (7.40.20170928+ds-1) unstable; urgency=medium

  * New upstream release.
  * debian/control: Unconditionalize Go build dependencies.
  * debian/examples: Add several new scripts for experimental local record
    storage, which may migrate to /usr/bin when they're more mature.
  * debian/man/{efilter,esearch,xtract}.1: Update for new release.
  * debian/rules: Remove fallback logic to install the old Perl
    implementation of xtract, now retired upstream.
  * Standards-Version: 4.1.1 (already compliant).

 -- Aaron M. Ucko <email address hidden>  Fri, 06 Oct 2017 17:52:27 -0400
Superseded in bionic-release on 2017-11-03
Obsolete in artful-release on 2020-07-10
Deleted in artful-proposed on 2020-07-10 (Reason: moved to release)
ncbi-entrez-direct (6.90.20170705+ds-2) unstable; urgency=medium

  * debian/rules: Rework Go-related logic to accommodate builds on
    (non-release) architectures on which I've had to conditionalize out
    the relevant build dependencies.

 -- Aaron M. Ucko <email address hidden>  Thu, 06 Jul 2017 22:25:05 -0400
Superseded in artful-release on 2017-07-07
Deleted in artful-proposed on 2017-07-09 (Reason: moved to release)
ncbi-entrez-direct (6.90.20170705+ds-1) unstable; urgency=medium

  * New upstream release.
  * debian/compat: Advance to debhelper 10.
  * debian/control:
    - Advance debhelper build dependency accordingly.
    - Reinstate architecture qualifiers for Go build dependencies on the
      basis of experimental build logs.
    - Standards-Version: 4.0.0 (already compliant).
  * debian/man/{ftp-cp,gbf2xml}.1: Correct syntax for optional filenames.
  * debian/man/xtract.1: Update for new release.

 -- Aaron M. Ucko <email address hidden>  Wed, 05 Jul 2017 22:12:35 -0400
Superseded in artful-release on 2017-07-06
Obsolete in zesty-release on 2018-06-22
Deleted in zesty-proposed on 2018-06-22 (Reason: moved to release)
ncbi-entrez-direct (6.10.20170123+ds-1) unstable; urgency=medium

  * New upstream release.
  * Resolve conflicts by diverting acedb-other's efetch and epub-utils'
    einfo to efetch.acedb and einfo.epub respectively (and likewise for
    their man pages) and deploying wrapper scripts that try to figure out
    which implementation the user intended to run.  (Proper usage differs
    radically, so ambiguity is unlikely to be an issue in practice.)
  * Add man pages for all commands.

 -- Aaron M. Ucko <email address hidden>  Tue, 24 Jan 2017 21:56:00 -0500
Superseded in zesty-release on 2017-01-25
Deleted in zesty-proposed on 2017-01-26 (Reason: moved to release)
ncbi-entrez-direct (6.00.20170105+ds-1) unstable; urgency=medium

  * New upstream release.
  * debian/control: Canonicalize per cme.
  * debian/copyright: Likewise; also, correct placement of Files-Excluded.

 -- Aaron M. Ucko <email address hidden>  Thu, 05 Jan 2017 22:27:51 -0500
Superseded in zesty-release on 2017-01-06
Deleted in zesty-proposed on 2017-01-07 (Reason: moved to release)
ncbi-entrez-direct (5.90.20161221+ds-4) unstable; urgency=medium

  * debian/control: Remove annotations from conflicts here.  (Oops.)

 -- Aaron M. Ucko <email address hidden>  Sat, 24 Dec 2016 23:48:49 -0500
Superseded in zesty-release on 2016-12-25
Deleted in zesty-proposed on 2016-12-26 (Reason: moved to release)
ncbi-entrez-direct (5.90.20161221+ds-1) unstable; urgency=low

  * Initial release.  (Closes: #810949.)

 -- Aaron M. Ucko <email address hidden>  Fri, 23 Dec 2016 16:35:19 -0500
123 of 23 results