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|
ncbi-entrez-direct (14.6.20210209+dfsg-1) UNRELEASED; urgency=medium
* New upstream release. (NOT RELEASED YET.)
* debian/man/{transmute,xtract}.1: Update for new release.
* debian/man/xtract.1: Tune hyphenation under -insd.
-- Aaron M. Ucko <ucko@debian.org> Fri, 12 Feb 2021 12:27:00 -0500
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 <ucko@debian.org> Sat, 06 Feb 2021 22:52:01 -0500
ncbi-entrez-direct (14.6.20210203+dfsg-1) unstable; urgency=medium
* New upstream release.
* debian/man/{edirect,efetch,efilter,esample,nquire,transmute,xtract}.1:
Update for new release.
* debian/man/transmute.1:
- Fully document new (as of 14.0.20201111[+dfsg]) -format suboptions
-xml, -doctype, -comment, and -cdata, half of which turn out to take
arguments.
- Reformat mode descriptions more compactly.
-- Aaron M. Ucko <ucko@debian.org> Sat, 06 Feb 2021 22:06:37 -0500
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 <ucko@debian.org> Sun, 24 Jan 2021 17:14:03 -0500
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 <ucko@debian.org> Sun, 01 Nov 2020 21:24:40 -0500
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 <ucko@debian.org> Mon, 19 Oct 2020 21:37:21 -0400
ncbi-entrez-direct (14.0.20201009+dfsg-1) unstable; urgency=medium
* New upstream release.
* debian/copyright:
- Add myself (at NCBI) as an upstream author.
- Also exclude CA.pm and cacert.pm.
* debian/efetch:
- Belatedly resync %ncbi_supported with current usage
(missed -style, -revcomp, -chr_stop, -raw, and -json).
- Additionally recognize -input and -forward, as supported by the new
shell implementation.
* debian/{efetch,einfo}: Substitute e*.ncbi for edirect -*, now that the
NCBI implementations won't necessarily boil down to edirect one-liners.
* debian/install: Install ecommon.sh to /usr/lib/ncbi-entrez-direct.
* debian/man/{bt-link,bt-srch,download-ncbi-data,edirect,efetch,efilter,
einfo,elink,epost,esample,esearch,j2x,nquire,t2x,transmute,xplore,
xtract}.1: Update for new release.
* debian/man/{download-ncbi-data,esample}.1: Correct old typos
(transposed letters, unescaped hyphen, missing parentheses).
* debian/man/{einfo,efetch}.ncbi.1: Add alias pages for completeness.
* debian/man/enquire.1: Retire per full incorporation of enquire into
nquire, albeit on an experimental basis.
* debian/man/{g2x,j2x,t2x}.1: Retire.
* debian/man/skip-if-file-exists.1: Document new command.
* debian/rules:
- Belatedly install phrase-search (as is).
- Account for new internal ecommon.sh sourceable; transformation of
efetch, efilter, einfo, elink, epost, esearch, and esummary to
ecommon.sh-based scripts (that still wrap Perl edirect by default,
though); full incorporation of enquire (curl-/wget-based) as an
experimental alternate mode for nquire (previously a pure edirect
wrapper); retirement of dedicated g2x, j2x, and t2x binaries and of
unbuilt s2p.go; and new as-is script skip-if-file-exists.
- For efetch and einfo, install the upstream scripts with .ncbi
extensions, since they won't necessarily reduce to edirect
one-liners.
* debian/tests/run-unit-test:
- Correct gbf2xml invocation. (It ignores any arguments and reads
from standard input.)
- Drop j2x test; renumber following tests accordingly.
-- Aaron M. Ucko <ucko@debian.org> Mon, 12 Oct 2020 15:14:47 -0400
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 <ucko@debian.org> Tue, 14 Jul 2020 22:17:15 -0400
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 <ucko@debian.org> Sun, 28 Jun 2020 21:11:51 -0400
ncbi-entrez-direct (13.7.20200615+dfsg-1) unstable; urgency=medium
* New upstream release.
* debian/man/{bt-link,bt-srch,download-ncbi-data,edirect,fetch-extras,
index-extras,index-pubmed,j2x,nquire,phrase-search,rchive,t2x,xplore,
xtract}.1: Update for new release.
* debian/man/{enquire,index-themes,theme-aliases}.1: Document new commands.
* debian/man/nquire.1: Belatedly note FTP support in NAME and DESCRIPTION;
correct formatting of SEE ALSO header; formally adjust SEE ALSO order
(accidentally not quite sorted).
* debian/rules: Account for new as-is script enquire, bash script
index-themes, and sourceable theme-aliases.
* debhelper-compat 13 (routine-update)
-- Aaron M. Ucko <ucko@debian.org> Sun, 28 Jun 2020 17:28:59 -0400
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 <ucko@debian.org> Sun, 21 Jun 2020 22:32:39 -0400
ncbi-entrez-direct (12.0.20190816+ds-2) unstable; urgency=medium
* Team upload
* Add autopkgtests
-- Pranav Ballaney <ballaneypranav@gmail.com> Wed, 06 May 2020 19:11:16 +0530
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 <ucko@debian.org> Sun, 02 Feb 2020 22:02:43 -0500
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 <ucko@debian.org> Tue, 26 Feb 2019 21:28:41 -0500
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 <ucko@debian.org> Wed, 06 Feb 2019 22:51:27 -0500
ncbi-entrez-direct (10.5.20181204+ds-2) unstable; urgency=medium
* debian/control: Actually build-depend on dh-golang.
-- Aaron M. Ucko <ucko@debian.org> Wed, 05 Dec 2018 22:05:20 -0500
ncbi-entrez-direct (10.5.20181204+ds-1) unstable; urgency=medium
* New upstream release.
* (debian/).gitignore: Update per GOPATH change.
* debian/control:
- Build-depend on dh-golang, golang-github-dataence-porter2-dev,
golang-github-fatih-color-dev, golang-github-klauspost-cpuid-dev,
golang-github-rainycape-unidecode-dev, and
golang-github-shirou-gopsutil-dev.
- Set Built-Using (with the help of dh-golang).
- Bump minimum Go version to 1.10 for strings.Builder.
- Depend on libxml-simple-perl.
- Repoint Vcs-{Browser,Git} at salsa.debian.org.
- Rules-Requires-Root: no (confirmed safe).
- Standards-Version: 4.2.1 (compliant at this point).
* debian/examples: Remove local storage/indexing scripts (considered
official enough for /usr/bin at this point), leaving only asp-* and
has-asp, which promote non-free software; add test-pubmed-index.
* debian/man/{archive-pubmed,download-pubmed,download-sequence,eblast,
fetch-pubmed,index-pubmed,intersect-uid-lists,(local-)phrase-search,
pm-clean,pm-erase,pm-invert,pm-log,pm-merge,pm-prepare,pm-promote,
pm-refresh,pm-repack,pm-stash,pm-uids,pm-verify,protein-neighbors,rchive,
stream-pubmed,transmute}.1: Document newly added tools.
* debian/man/{edirect,nquire,xtract}.1: Fix old documentation bugs.
* debian/man/{efetch,efilter,elink,entrez-phrase-search,ftp-cp,ftp-ls,
nquire,xtract}.1: Update for new release.
* debian/rules:
- Change (autopopulated) GOPATH to meet dh-golang's expectations.
- Belatedly run dh --with=golang to populate (misc:)Built-Using.
- Clean up remaining cruft from when Go support was optional.
- Pull github.com/surgebase/porter2 (aka gh.c/dataence/porter2),
github.com/fatih/color (along with its dependencies
github.com/mattn/go-{colorable,isatty}), github.com/klauspost/cpuid,
github.com/rainycape/unidecode (aliased, per rchive.go's expectations,
to github.com/fiam/gounidecode/unidecode), github.com/shirou/gopsutil
(along with its dependency golang.org/x/sys/unix), and our ersatz
github.com/pbnjay/memory into the path. (The rainycape version of
unidecode has the key advantages of being fresher and already packaged
for Debian.)
- Build rchive.go in addition to xtract.go; build both against a
common.go factored out of xtract.go.
- Install run-ncbi-converter (accidentally left off earlier).
- Flip Perl scripts back to running via /usr/bin/perl (from
/usr/bin/env perl).
- Enforce use of Go version 1.10 or newer, even if the default is older.
- Install local storage/indexing scripts to /usr/bin. (Closes: #901028.)
- Install new eblast wrapper (corresponding to new -blast mode) and
protein-neighbors script.
* debian/vendor/github.com/pbnjay/memory/memory.go: New wrapper around
github.com/shirou/gopsutil/mem, filling in for a different third-party
library that lacks a declared license.
-- Aaron M. Ucko <ucko@debian.org> Wed, 05 Dec 2018 21:19:35 -0500
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 <ucko@debian.org> Fri, 06 Oct 2017 17:52:27 -0400
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 <ucko@debian.org> Thu, 06 Jul 2017 22:25:05 -0400
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 <ucko@debian.org> Wed, 05 Jul 2017 22:12:35 -0400
ncbi-entrez-direct (6.80.20170608+ds-1) experimental; urgency=medium
* New upstream release.
* debian/man/ftp-cp.1: Update accordingly.
* Install the new asp-ls script as an example (alongside asp-cp) and
the new gbf2xml script as an executable; give gbf2xml a man page.
-- Aaron M. Ucko <ucko@debian.org> Fri, 09 Jun 2017 18:01:55 -0400
ncbi-entrez-direct (6.70.20170508+ds-1) experimental; urgency=medium
* New upstream release.
* debian/man/xtract.1: Update accordingly.
* debian/control:
- Tighten Go dependencies to require Go 1.8 for sort.Slice.
- Add a dependency on golang-golang-x-text-dev, also newly necessary.
- Remove architecture qualifiers for now. (This *is* for experimental.)
* debian/rules:
- Build with /usr/lib/go-1.8/bin/go if necessary (notably, for backports).
- Establish a local GOPATH with a symlink to .../golang.org/x/text.
- Run go build -v now that there are third-party libraries to incorporate.
* debian/.gitignore: Ignore debian/gopath.
* debian/examples: Install the new asp-cp script as an example, since it
requires non-free Aspera tools.
-- Aaron M. Ucko <ucko@debian.org> Mon, 29 May 2017 21:28:44 -0400
ncbi-entrez-direct (6.10.20170123+ds-2) UNRELEASED; urgency=medium
* debian/e{fetch,info}: Correct help text to cite our man pages too.
(They didn't yet exist when I originally wrote these wrappers.)
* debian/man/xtract.1: Fix an old typo (esapes vs. escapes).
-- Aaron M. Ucko <ucko@debian.org> Mon, 29 May 2017 15:41:49 -0400
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 <ucko@debian.org> Tue, 24 Jan 2017 21:56:00 -0500
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 <ucko@debian.org> Thu, 05 Jan 2017 22:27:51 -0500
ncbi-entrez-direct (5.90.20161221+ds-4) unstable; urgency=medium
* debian/control: Remove annotations from conflicts here. (Oops.)
-- Aaron M. Ucko <ucko@debian.org> Sat, 24 Dec 2016 23:48:49 -0500
ncbi-entrez-direct (5.90.20161221+ds-3) unstable; urgency=medium
* debian/control:
- Build-Depends: Correct syntax for multiple exclusions.
- Conflicts: acedb-other (over efetch), epub-utils (over einfo).
-- Aaron M. Ucko <ucko@debian.org> Sat, 24 Dec 2016 23:25:29 -0500
ncbi-entrez-direct (5.90.20161221+ds-2) unstable; urgency=medium
* .gitignore: Account for files created outside debian/ at build time.
* debian/control:
- Set debian-med as maintainer, and myself as uploader.
- Don't build depend on golang-any on architectures on
which it's currently uninstallable.
* debian/rules: If building xtract.go fails for any reason, fall back on
installing the original Perl implementation.
* debian/source/options: single-debian-patch.
* xtract.pl: Don't insist on -fallback.
-- Aaron M. Ucko <ucko@debian.org> Sat, 24 Dec 2016 22:43:40 -0500
ncbi-entrez-direct (5.90.20161221+ds-1) unstable; urgency=low
* Initial release. (Closes: #810949.)
-- Aaron M. Ucko <ucko@debian.org> Fri, 23 Dec 2016 16:35:19 -0500
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