[med-svn] [Git][med-team/ncbi-entrez-direct][master] 8 commits: New upstream version 14.0.20201111+dfsg

[Aaron M. Ucko]

Aaron M. Ucko pushed to branch master at Debian Med / ncbi-entrez-direct


Commits:
6664ab8f by Aaron M. Ucko at 2020-11-11T18:10:31-05:00
New upstream version 14.0.20201111+dfsg
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762f2a82 by Aaron M. Ucko at 2020-11-11T18:11:34-05:00
Merge tag 'upstream/14.0.20201111+dfsg' into master

Upstream version 14.0.20201111(+dfsg).

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f9f458fd by Aaron M. Ucko at 2021-01-20T17:34:52-05:00
{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.

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fb9b9d3b by Aaron M. Ucko at 2021-01-24T17:11:09-05:00
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.

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0169f566 by Aaron M. Ucko at 2021-01-24T17:11:09-05:00
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.

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42f61211 by Aaron M. Ucko at 2021-01-24T17:11:09-05:00
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.

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17c58ccc by Aaron M. Ucko at 2021-01-24T17:11:27-05:00
debian/NEWS (new): Document changes to e*, nquire, and transmute.

Document switch to new e* and nquire implementations by default and
reimplementation of transmute.

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687313c8 by Aaron M. Ucko at 2021-01-24T17:15:09-05:00
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.

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30 changed files:

- README
- bt-link
- bt-srch
- build.sh
- + debian/NEWS
- debian/changelog
- debian/control
- debian/man/efetch.1
- debian/man/efilter.1
- debian/man/einfo.1
- debian/man/elink.1
- debian/man/epost.1
- debian/man/esearch.1
- debian/man/gbf2xml.1
- debian/man/nquire.1
- debian/man/transmute.1
- debian/man/xtract.1
- debian/rules
- download-ncbi-data
- ecommon.sh
- efetch
- efilter
- einfo
- elink
- epost
- esearch
- esummary
- gbf2xml
- hlp-xtract.txt
- nquire


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/3d9114ce05b1730e1373efbd116818658d584f06...687313c879979c1b562d5a6d6adbffb585acf8cd

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