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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/6664ab8ff1b879364e5ce944b95f874a36d89e6b">6664ab8f</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-11-11T18:10:31-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 14.0.20201111+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/762f2a829b9c26f77800b65a616578605dade9f9">762f2a82</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-11-11T18:11:34-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge tag 'upstream/14.0.20201111+dfsg' into master
Upstream version 14.0.20201111(+dfsg).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/f9f458fd71a6d6732d033f62d04ff608491fae52">f9f458fd</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2021-01-20T17:34:52-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">{nquire,xtract}.1: Belatedly correct minor documentation errors.
* nquire.1: Belatedly correct paste-o in description of shell
implementation (which does not in fact use itself!).
* xtract.1: Belatedly retire two old flags from OPTIONS: -require and
-exclude (the entire Phrase Filtering subsection) went away in
8.70.20180511[+ds] in favor of -select, but the associated man page
update accidentally removed them only from SYNOPSIS.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/fb9b9d3b87264804e0ae956170a9619f4258f96c">fb9b9d3b</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2021-01-24T17:11:09-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">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 script
under /usr/lib -- it's formally an implementation detail of transmute
-x2j, and would otherwise conflict with libxml-compile-perl.) Tweak
the 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.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/0169f5668db5b915ee359499f26a35cf13dd9301">0169f566</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2021-01-24T17:11:09-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update Depends and Suggests for new release (14.0.20201111[+dfsg]).
- 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.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/42f612111d1f9034ddefb180587797b954f02035">42f61211</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2021-01-24T17:11:09-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/man/*.1: Update for new release (14.0.20201111[+dfsg]).
* efetch.1, efilter.1, einfo.1, elink.1, epost.1, esearch.1, nquire.1:
Reflect switch to shell implementation by default.
* efetch.1: -json is no longer Perl-only.
* efilter.1: New -division flag (under Sequence Filters).
* gbf2ml.1: Reflect move from xtract to transmute.
* transmute.1: Document incorporation of some functionality factored
out of xtract (detailed below) and a total rework of the scripted
functionality (now in shell rather than Perl).
* xtract.1:
- New -unix option (under Documentation).
- Retire options that migrated to transmute: -unicode, -script,
-mathml (all from Reformat XML), and the entirety of
Modification (-filter), Efetch Normalization (-normalize), and
Data Conversion (-j2x, -a2x, -t2x, and -g2x).
- Correct description of -encode (XML, not URL) per -help.
- Rename Miscellaneous to Output Organization per -help.
- Move Record Selection and Record Rearrangement above Reformatting
per -help.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/17c58cccb6e7a12269842be8d76c7a948ffde82b">17c58ccc</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2021-01-24T17:11:27-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/NEWS (new): Document changes to e*, nquire, and transmute.
Document switch to new e* and nquire implementations by default and
reimplementation of transmute.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/687313c879979c1b562d5a6d6adbffb585acf8cd">687313c8</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2021-01-24T17:15:09-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Finalize ncbi-entrez-direct 14.0.20201111+dfsg-1 for unstable.
It's not the latest release, but enough of a milestone to merit an
individual upload anyway.
</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="#c5a4dd6ddcc86cb31503fafc67cc034f5ea47cab">
bt-link
</a>
</li>
<li class="file-stats">
<a href="#bc07c5224c450ededa3d43825734a71367dae6ff">
bt-srch
</a>
</li>
<li class="file-stats">
<a href="#59f81c123b3abbcb97274545796dd18706c3e106">
build.sh
</a>
</li>
<li class="file-stats">
<a href="#b3f55b8d9783f2ed27acfd1f0fe06dfc461e2aba">
<span class="new-file">
+
debian/NEWS
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#70c9431e40b6a76de4408359471875da0caa1e6f">
debian/man/efetch.1
</a>
</li>
<li class="file-stats">
<a href="#fbb2dec58c54b6eaa486cdb89fc56bbe5f220e30">
debian/man/efilter.1
</a>
</li>
<li class="file-stats">
<a href="#b1ee2cadbc327adf9f388a4b1abde0cc1e44c3fd">
debian/man/einfo.1
</a>
</li>
<li class="file-stats">
<a href="#5d7cbf1438498bd5cbb95095d12c0d883b6b02b2">
debian/man/elink.1
</a>
</li>
<li class="file-stats">
<a href="#c570c7ea4cdc5daf3aecbab418b8e6f73534b1a9">
debian/man/epost.1
</a>
</li>
<li class="file-stats">
<a href="#40aa9666c26a1c35f0b79326e8b20308563c0dba">
debian/man/esearch.1
</a>
</li>
<li class="file-stats">
<a href="#479365981cee26484156e41e35daaa0e65bff582">
debian/man/gbf2xml.1
</a>
</li>
<li class="file-stats">
<a href="#f66b2f258243857b3a8567d328ade1df1cc5db3a">
debian/man/nquire.1
</a>
</li>
<li class="file-stats">
<a href="#e49162a15ac33ba88a04e53b8fdc162601186481">
debian/man/transmute.1
</a>
</li>
<li class="file-stats">
<a href="#c60765c1b932f4071ad43fe9aed248d0db4baa61">
debian/man/xtract.1
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#729f73e52899dfa90ecad046f733a8f9dd86e211">
download-ncbi-data
</a>
</li>
<li class="file-stats">
<a href="#546ec4d28ff21f5987364bea47f5f9aa843b6d85">
ecommon.sh
</a>
</li>
<li class="file-stats">
<a href="#7089ac196cd936d06fa2abbca64b9ed09d4a5b42">
efetch
</a>
</li>
<li class="file-stats">
<a href="#0d041160c873be73247b39ab4a93ae3fff7842e9">
efilter
</a>
</li>
<li class="file-stats">
<a href="#6905e20db6a4588d2be3a1099fcb8fbc775ea36a">
einfo
</a>
</li>
<li class="file-stats">
<a href="#83237eb0da0ab95daa4de5951c8e611ee5e4ffe7">
elink
</a>
</li>
<li class="file-stats">
<a href="#9528dde7c71e2e013ebd6028faefca86b22cae6f">
epost
</a>
</li>
<li class="file-stats">
<a href="#e03f493277c65e85da1208a04e61b44112617168">
esearch
</a>
</li>
<li class="file-stats">
<a href="#f14411a4a819cce75189aaa462d0bd81ca820e65">
esummary
</a>
</li>
<li class="file-stats">
<a href="#a3bf962e151b57ecc4bab8772c24123436f0bf1b">
gbf2xml
</a>
</li>
<li class="file-stats">
<a href="#f555edcfb71bb400c39b45118f326189205574d8">
hlp-xtract.txt
</a>
</li>
<li class="file-stats">
<a href="#0aae011363caa6b0a509245f540cbd08b70f0d78">
nquire
</a>
</li>
</ul>
<h5>The diff was not included because it is too large.</h5>
</div>
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