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<h3>
Aaron M. Ucko pushed to branch master
at <a href="https://salsa.debian.org/med-team/ncbi-entrez-direct">Debian Med / ncbi-entrez-direct</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/df8f55ce159c092d8be78953eb36500876296167">df8f55ce</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-08-23T20:34:38-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 13.8.20200817+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/74f61e49a0c657d127ed38eb2c05826f60c29372">74f61e49</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-08-23T20:36:04-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge tag 'upstream/13.8.20200817+dfsg' into master
Upstream version 13.8.20200817(+dfsg).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/b4f98c385bd769e0263cc27565c03e2fca62e5ef">b4f98c38</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-03T22:10:43-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 13.8.20200909+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/dca59a415535038330a96aa25025436c49c3376b">dca59a41</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-03T22:47:58-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 13.9.20200914+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/38017857209a5177a7935985dbe5d337c1759409">38017857</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T11:53:47-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 13.9.20200923+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/6a08323ff6fe8a9704889591fe5a0bf56549a579">6a08323f</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T12:01:57-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 14.0.20201007+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/2f5e6d8fa282fb369b466bbfd17f577d4ce8ae51">2f5e6d8f</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T12:15:50-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 14.0.20201009+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/d0a092931f5d271db8cc9fe42f11afbd7693d396">d0a09293</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T14:37:09-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/rules: Belatedly install phrase-search (as is).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/1ed60c8fb714eec962520785d65f64956d87df7b">1ed60c8f</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T14:38:01-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/man/{download-ncbi-data,esample}.1: Correct old typos.
Transposed letters, unescaped hyphen, missing parentheses.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/128fdaf5c6de62cbb5dbc4913d3768849d1dd7c8">128fdaf5</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T14:38:58-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/efetch: Belatedly resync %ncbi_supported with current usage.
Missed -style, -revcomp, -chr_stop, -raw, and -json.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/1c3d5f938834cdde4e03cdb46bab1539efb78295">1c3d5f93</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T14:41:13-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Account for new ecommon setup and skip-if-file-exists script.
* debian/efetch: 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/rules:
- 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); 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.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/b1cf2574d165c760cc716c922f0c93adb43aa8d6">b1cf2574</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T14:43:02-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/man: Update for new upstream release (13.8.20200817[+dfsg]).
* efilter.1, epost.1, esearch.1: Drop -label.
* einfo.1: Per upstream, list -db after -dbs and note the possibility
of -db all.
* {einfo,efetch}.ncbi.1: Add alias pages for completeness.
* elink.1: Drop -mode ref and -label.
* enquire.1: Drop altogether (fully incorporated into nquire, albeit
on an experimental basis).
* esample.1: New -flatfile mode.
* skip-if-file-exists.1: Document new command.
* Update SEE ALSO links accordingly.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/a9aefd295f7f67b3dee4093a2f4b91448eae2f38">a9aefd29</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T14:43:06-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/copyright: Add myself [Aaron Ucko] (at NCBI) as an upstream author.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/46367231e0b495483568110c3325ba6af01410b1">46367231</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T14:43:07-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/tests/run-unit-test: Correct gbf2xml invocation.
It ignores any arguments and reads from standard input.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/415f0e9bdd2fb287bb22ab254cd2f69eee62b77c">415f0e9b</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T14:43:07-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/copyright: Also exclude CA.pm and cacert.pm.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/bd2bdcba50ba890f62d601239d2179dfb43cb951">bd2bdcba</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T14:43:07-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge tag 'upstream/13.8.20200909+dfsg' into master
Upstream version 13.8.20200909(+dfsg).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/cb2f4e7c751cd7a9330f56988476ec5e45de8485">cb2f4e7c</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T14:43:07-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/rules: Account for retirement of ?2?.go.
Account for retirement of dedicated g2x, j2x, and t2x binaries and of
unbuilt s2p.go.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/92ac001c32ec9464cc39a1816d7d0a3b42661d7e">92ac001c</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T14:51:46-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/man: Update for new upstream release (13.8.20200909[+dfsg]).
* g2x.1, j2x.1, t2x.1: Retire.
* xtract.1: Add new -c2x mode alongside -t2x.
* Update SEE ALSO links accordingly.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/ae60dae20b9172ff682e7c5b3d3940cba7e3c95d">ae60dae2</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T14:51:46-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/tests/run-unit-test: Drop j2x test.
Renumber following tests accordingly.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/43b5a98ff6182958c18afe33866bece90b8d076c">43b5a98f</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T14:51:46-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge tag 'upstream/13.9.20200914+dfsg' into master
Upstream version 13.9.20200914(+dfsg).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/104c0373a93bac90d4db4880e6927a4a720edcab">104c0373</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T14:51:46-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/man: Update for new upstream release (13.9.20200914[+dfsg]).
* efetch.1, efilter.1, einfo.1, elink.1, epost.1, esearch.1, nquire.1:
Generally document the possibility of using a shell curl-/wget-based
implementation rather than the traditional Perl implementation by
setting USE_NEW_EDIRECT.
* efetch.1: Note new shell-only -input and -forward flags, and
Perl-only status of -json flag.
* efilter.1: Note that the -q shorthand, -sort, -field, -pairs, and
-spell are all Perl-only.
* elink.1: Note shell-only -input flag, Perl-only status of -holding
and -batch, and minor differences in accepted -cmd values.
* esearch.1: Note that the shell implementation accepts all efilter
options, and that the -q shorthand, -field, and -pairs are all
Perl-only.
* nquire.1: Note shell-only -lst, -dwn, and -asp flags, Perl-only
status of -eutils, and potential differences in -ftp usage.
* xtract.1: Note addition of -fasta (Sequence Processing), rename of
-retaining to -in, and retirement of -excluding and -appending.
* Update SEE ALSO links appropriately.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/836dd16e73f50334a6bc99877c8150fae087d0d3">836dd16e</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T14:51:46-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge tag 'upstream/13.9.20200923+dfsg' into master
Upstream version 13.9.20200923(+dfsg).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/5b1f556d6aeb50b9c7dc3e257842ccc212070435">5b1f556d</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T14:51:46-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">efetch.1: Update for new upstream release (13.9.20200923[+dfsg]).
Document new shell-only options -style master and -showgaps.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/f8f75f7d7c9b453363a1e5ca32aee77de514f24d">f8f75f7d</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T14:51:46-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge tag 'upstream/14.0.20201007+dfsg' into master
Upstream version 14.0.20201007(+dfsg).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/71ec826d12fc2fd97eda64af23f026715dab8fde">71ec826d</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T14:51:46-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">xtract.1: Update for new upstream release (14.0.20201007[+dfsg]).
Document new flags -ncbi2na, -ncbi4na (both Sequence Processing), and
-a2x (Data Conversion).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/40cb007bc9632f38b9b207cacc7aeb5e511542f5">40cb007b</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T14:51:46-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge tag 'upstream/14.0.20201009+dfsg' into master
Upstream version 14.0.20201009(+dfsg).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/1a0a45b33d972a7e14864aeabc2f6ad7ec43122c">1a0a45b3</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-12T15:14:48-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Finalize ncbi-entrez-direct 14.0.20201009+dfsg-1 for unstable.
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#69e27356ef629022720d868ab0c0e3394775b6c1">
README
</a>
</li>
<li class="file-stats">
<a href="#59f81c123b3abbcb97274545796dd18706c3e106">
build.sh
</a>
</li>
<li class="file-stats">
<a href="#1588f2dbc1e98ab2c9bf8a54be702ddf2c59a3e5">
common.go
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#ca3000170e885840431dc10880df1717587a5227">
debian/efetch
</a>
</li>
<li class="file-stats">
<a href="#659f6050751ab82e34b7c0db35af70b44ca0ee3f">
debian/einfo
</a>
</li>
<li class="file-stats">
<a href="#68d8c5c6babbf5cf109b2584c454449dbff75772">
debian/install
</a>
</li>
<li class="file-stats">
<a href="#403b257c446245d31733478d185351671b2e0939">
debian/man/bt-link.1
</a>
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<a href="#7d0b610530db4e1bfd376d9728d153b250e21894">
debian/man/bt-srch.1
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<li class="file-stats">
<a href="#0d0a41c55a60d15f26c5a3fca73b899f3eec7a5b">
debian/man/download-ncbi-data.1
</a>
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<li class="file-stats">
<a href="#eb14d9a63f01ebc183cc3018aac3f0c1f31466c6">
debian/man/edirect.1
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<a href="#70c9431e40b6a76de4408359471875da0caa1e6f">
debian/man/efetch.1
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<span class="new-file">
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debian/man/efetch.ncbi.1
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</li>
<li class="file-stats">
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debian/man/efilter.1
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<a href="#b1ee2cadbc327adf9f388a4b1abde0cc1e44c3fd">
debian/man/einfo.1
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<a href="#52a0fdbe8d603aa709a003a4c4dd131c84556fce">
<span class="new-file">
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debian/man/einfo.ncbi.1
</span>
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debian/man/elink.1
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<span class="deleted-file">
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debian/man/enquire.1
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<a href="#c570c7ea4cdc5daf3aecbab418b8e6f73534b1a9">
debian/man/epost.1
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<a href="#afa6e53aacd6ef993cbc1a86b41cfb0eecfca064">
debian/man/esample.1
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<a href="#40aa9666c26a1c35f0b79326e8b20308563c0dba">
debian/man/esearch.1
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debian/man/g2x.1
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debian/man/j2x.1
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debian/man/nquire.1
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debian/man/skip-if-file-exists.1
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debian/man/t2x.1
</span>
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</li>
<li class="file-stats">
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debian/man/transmute.1
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<a href="#4b138ed9e116e230954d53a3ec7cede60089724c">
debian/man/xplore.1
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<a href="#c60765c1b932f4071ad43fe9aed248d0db4baa61">
debian/man/xtract.1
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</ul>
<h5>The diff was not included because it is too large.</h5>
</div>
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