[med-svn] [Git][med-team/ncbi-entrez-direct][master] 70 commits: New upstream version 12.1.20190819+ds

Aaron M. Ucko gitlab at salsa.debian.org
Mon Jun 22 03:41:59 BST 2020 


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


Commits:
b2fdbc6f by Aaron M. Ucko at 2020-02-09T15:08:38-05:00
New upstream version 12.1.20190819+ds
- - - - -
3e3c15d2 by Aaron M. Ucko at 2020-02-09T15:10:50-05:00
New upstream version 12.1.20190829+ds
- - - - -
ec277b42 by Aaron M. Ucko at 2020-02-09T16:19:45-05:00
New upstream version 12.2.20190909+ds
- - - - -
85689605 by Aaron M. Ucko at 2020-02-09T17:19:55-05:00
New upstream version 12.2.20191011+ds
- - - - -
63cee944 by Aaron M. Ucko at 2020-03-22T15:53:19-04:00
New upstream version 12.3.20191015+ds
- - - - -
d621f5b6 by Aaron M. Ucko at 2020-03-22T16:29:27-04:00
New upstream version 12.3.20191024+ds
- - - - -
a312eefb by Aaron M. Ucko at 2020-04-27T19:49:53-04:00
New upstream version 12.4.20191028+ds
- - - - -
9278fc9c by Aaron M. Ucko at 2020-04-27T20:02:40-04:00
New upstream version 12.4.20191105+ds
- - - - -
9465701b by Aaron M. Ucko at 2020-04-27T20:29:55-04:00
New upstream version 12.5.20191106+ds
- - - - -
0091def1 by Aaron M. Ucko at 2020-05-07T09:58:33-04:00
Merge tag 'upstream/12.1.20190819+ds'

Upstream version 12.1.20190819(+ds).

- - - - -
ccfdc823 by Aaron M. Ucko at 2020-05-07T09:58:33-04:00
Belated manpage fixes following 12.0.20190816+ds-1 upload.

* efetch.1: Correct old paste-o in -chr_stop's description.
* fetch-pubmed.1: Wordsmith description of -path.
* nquire.1: Drop accidental self-referential SEE ALSO.
* xtract.1: Belatedly resync -indices' description.

- - - - -
26a1c7aa by Aaron M. Ucko at 2020-05-07T09:58:33-04:00
Merge tag 'upstream/12.1.20190829+ds'

Upstream version 12.1.20190829(+ds).

- - - - -
c5a4dc29 by Aaron M. Ucko at 2020-05-07T09:58:33-04:00
d/rules (AS_IS_SCRIPTS): +expand-current, index-bioc -> index-extras

Account for new as-is script expand-current and for rename of as-is
script index-bioc to index-extras.

- - - - -
2b6d3822 by Aaron M. Ucko at 2020-05-07T09:58:33-04:00
debian/man: Update for new release (12.1.20190829[+ds]).

* download-ncbi-data.1: Document new (-)generif, (-)oa-list,
  and (-)oa-book flags.
* expand-current.1: Document new command.
* index-extras.1: Rename from index-bioc.1; document additional
  GeneRifs coverage.
* Update SEE ALSO references as appropriate.

- - - - -
6abffec9 by Aaron M. Ucko at 2020-05-07T09:58:33-04:00
Merge tag 'upstream/12.2.20190909+ds'

Upstream version 12.2.20190909+ds

- - - - -
4b9518ed by Aaron M. Ucko at 2020-05-07T09:58:33-04:00
debian/rules: Account for new mistagged bash script index-themes.

To that end, add a new generic mechanism akin to the one used for Perl
scripts.

- - - - -
0082086d by Aaron M. Ucko at 2020-05-07T09:58:33-04:00
debian/control: Suggest curl (for index-themes).

- - - - -
20c392a4 by Aaron M. Ucko at 2020-05-07T09:58:34-04:00
debian/man: Update for new release (12.2.20190909[+ds]).

* index-themes.1: Document new command.
* Update SEE ALSO references as appropriate.

- - - - -
3b41ece1 by Aaron M. Ucko at 2020-05-07T09:58:34-04:00
Merge tag 'upstream/12.2.20191011+ds'

Upstream version 12.2.20191011+ds

- - - - -
0a0cebb7 by Aaron M. Ucko at 2020-05-07T09:58:34-04:00
d/rules: +fetch-extras (as-is); index-extras subsumes index-themes.

List the merged index-extras in BASH_SCRIPTS rather than AS_IS_SCRIPTS
because it has the same unflagged bashism as index-themes did.

- - - - -
1bb46bb0 by Aaron M. Ucko at 2020-05-07T09:58:34-04:00
debian/man: Update for new release (12.2.20191011[+ds]).

* download-ncbi-data.1: Note expansion of (-)bioconcepts
  and (-)generif actions.
* fetch-extras.1: Document new command.
* index-extras.1: Document incorporation of index-themes.
* index-themes.1: Retire.
* phrase-search.1: Mode now mandatory; -search gone; -terms added;
  -query moved up per -help.
* xtract.1: New flags -is-{before,after} (String Constraints), -mul,
  -div, -mod (Numeric Processing), -chain (String Processing),
  -sort (new Record Rearrangement section), and -t2x (Data Conversion).
* Update SEE ALSO accordingly.

- - - - -
8f6014e4 by Aaron M. Ucko at 2020-05-07T09:58:34-04:00
Merge tag 'upstream/12.3.20191015+ds'

Upstream version 12.3.20191015(+ds).

- - - - -
d6e9bb1d by Aaron M. Ucko at 2020-05-07T09:58:34-04:00
xtract.1: Explicitly mark -format's and -j2x's suboptions as such..

Prepare for giving the same treatment to -t2x, which now takes suboptions
(partially overlapping with -j2x's) ahead of positional arguments.

- - - - -
1e6b950e by Aaron M. Ucko at 2020-05-07T09:58:34-04:00
debian/man: Update for new release (12.3.20191015[+ds]).

* nquire.1: Note that -get now takes an optional immediate URL (with
  no need to add -url explicitly).
* xtract.1: Note new -t2x usage, with set and record wrappers now
  coming in via -set and -rec suboptions as with -j2x, and joined
  by a new -skip suboption.

- - - - -
cccbd8f1 by Aaron M. Ucko at 2020-05-07T09:58:34-04:00
Merge tag 'upstream/12.3.20191024+ds'

Upstream version 12.3.20191024(+ds).

- - - - -
54434f7e by Aaron M. Ucko at 2020-05-07T09:59:59-04:00
Install Scripps BioThings support (bt-*, xplore) as non-examples.

* debian/examples: Remove Scripps BioThings support, now considered official
  enough (mentioned in README, albeit as experimental).
* debian/install: Install bt-*.txt (bt-context.txt at present) to a new
  /usr/share/ncbi-entrez-direct directory.
* debian/rules: Account 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).

Man pages to follow, as part of this release's general roundup.

- - - - -
17d49dd0 by Aaron M. Ucko at 2020-05-07T10:00:04-04:00
debian/man: Update for new release (12.3.20191024[+ds]).

* bt-{link,load,save-search}.1, xtract.1: Document new commands.
* {edirect,ftp-cp,ftp-ls,nquire,transmute}.1: Note consolidation of
  ftp-cp, ftp-ls, nquire, and transmute into edirect.
* elink.1: Add PubMed Citation Lookup (-cited and -cites).
* xtract.1: Note new -t2x suboptions -lower, -upper, and -indent;
  tweak -t2x suboption formatting.
* Update SEE ALSO links accordingly.

- - - - -
fc9ceedb by Aaron M. Ucko at 2020-05-07T10:00:05-04:00
Merge tag 'upstream/12.4.20191028+ds'

Upstream version 12.4.20191028(+ds).

- - - - -
45439b44 by Aaron M. Ucko at 2020-05-07T10:00:05-04:00
phrase-search.1: Document new -filter option (12.4.20191028[+ds]).

- - - - -
e7298718 by Aaron M. Ucko at 2020-05-07T10:00:05-04:00
Merge tag 'upstream/12.4.20191105+ds'

Upstream version 12.4.20191105(+ds).

- - - - -
650386ec by Aaron M. Ucko at 2020-05-07T10:00:05-04:00
debian/man: Update for new release (12.4.20191105[+ds]).

* efetch.1: Add -revcomp; clarify -strand (both under Sequence Range).
* xtract.1: Add -flush in opposition to -indent for -t2x (Data Conversion).

- - - - -
6141f5c8 by Aaron M. Ucko at 2020-05-07T10:00:05-04:00
Merge tag 'upstream/12.5.20191106+ds'

Upstream version 12.5.20191106(+ds).

- - - - -
67fc1222 by Aaron M. Ucko at 2020-05-07T10:00:05-04:00
efetch.1: + Subset Retrieval (-start/-stop) for 12.5.20191106[+ds].

- - - - -
f9809abb by Aaron M. Ucko at 2020-06-21T20:59:58-04:00
Prepare to exclude sourceless PDF documents.

* debian/copyright: Add *.pdf (sourceless) to Files-Excluded.
* debian/watch: Change repack suffix to +dfsg due to the additional need
  to exclude sourceless PDF documents.

- - - - -
c0499509 by Aaron M. Ucko at 2020-06-21T21:22:08-04:00
New upstream version 12.5.20191115+dfsg
- - - - -
ef43537b by Aaron M. Ucko at 2020-06-21T21:24:01-04:00
Merge tag 'upstream/12.5.20191115+dfsg'

Upstream version 12.5.20191115(+dfsg).

- - - - -
574a8cb3 by Aaron M. Ucko at 2020-06-21T21:26:36-04:00
debian/rules: Account for new Go executable t2x.

Man page to follow as part of a general roundup, as usual.

- - - - -
b495131a by Aaron M. Ucko at 2020-06-21T21:28:23-04:00
New upstream version 12.6.20191115+dfsg
- - - - -
08ac1e5a by Aaron M. Ucko at 2020-06-21T21:31:10-04:00
debian/man: Update for new release (12.5.20191115[+dfsg]).

* t2x.1: Document new command.
* transmute.1: Reflect radical change in -help coverage.
* Update SEE ALSO sections accordingly.

- - - - -
97687271 by Aaron M. Ucko at 2020-06-21T21:31:15-04:00
Merge tag 'upstream/12.6.20191115+dfsg'

Upstream version 12.6.20191115(+dfsg).

- - - - -
b647e6d0 by Aaron M. Ucko at 2020-06-21T21:32:15-04:00
New upstream version 12.6.20191120+dfsg
- - - - -
43c1b3ec by Aaron M. Ucko at 2020-06-21T21:33:20-04:00
Merge tag 'upstream/12.6.20191120+dfsg'

Upstream version 12.6.20191120(+dfsg).

- - - - -
eadb6ca8 by Aaron M. Ucko at 2020-06-21T21:34:15-04:00
New upstream version 12.7.20191121+dfsg
- - - - -
d7d9a879 by Aaron M. Ucko at 2020-06-21T21:35:06-04:00
Merge tag 'upstream/12.7.20191121+dfsg'

Upstream version 12.7.20191121(+dfsg).

- - - - -
25bcd429 by Aaron M. Ucko at 2020-06-21T21:36:15-04:00
New upstream version 12.7.20191128+dfsg
- - - - -
f6d88b18 by Aaron M. Ucko at 2020-06-21T21:36:30-04:00
Merge tag 'upstream/12.7.20191128+dfsg'

Upstream version 12.7.20191128(+dfsg).

- - - - -
ba88aee1 by Aaron M. Ucko at 2020-06-21T21:37:23-04:00
xtract.1: + -molwt (Sequence Processing), as of 12.7.20191128(+dfsg).

- - - - -
dd510e97 by Aaron M. Ucko at 2020-06-21T21:38:31-04:00
New upstream version 12.8.20191202+dfsg
- - - - -
75c4a359 by Aaron M. Ucko at 2020-06-21T21:39:06-04:00
Merge tag 'upstream/12.8.20191202+dfsg'

Upstream version 12.8.20191202(+dfsg).

- - - - -
a6ceb93e by Aaron M. Ucko at 2020-06-21T21:39:43-04:00
debian/man: Update for new release (12.8.20191202[+dfsg]).

* esample.1: New -docsum mode.
* xtract.1: -synopsis (Summary) now takes optional arguments (-leaf
  and/or a delimiter).

- - - - -
e3f68491 by Aaron M. Ucko at 2020-06-21T21:40:32-04:00
New upstream version 12.8.20191206+dfsg
- - - - -
ad47134d by Aaron M. Ucko at 2020-06-21T21:40:47-04:00
Merge tag 'upstream/12.8.20191206+dfsg'

Upstream version 12.8.20191206(+dfsg).

- - - - -
e1d2e252 by Aaron M. Ucko at 2020-06-21T21:42:13-04:00
Tweak installation structure so xtract can find hlp-xtract.txt.

* Generally change /usr/share/ncbi-entrez-direct to /usr/lib/n-e-d.
* debian/install: Install hlp-*.txt (hlp-xtract.txt) there too.
* debian/rules:
  - Adjust corresponding macro name from SHARE_DIR to LIB_DIR accordingly..
  - Move the xtract binary there from /usr/bin (so it can find
    hlp-xtract.txt) and substitute a wrapper script.

- - - - -
48724785 by Aaron M. Ucko at 2020-06-21T21:42:35-04:00
debian/man: Update for new release (12.8.20191206[+dfsg]).

* index-pubmed.1: Add new (mutually exclusive) options -collect,
  -index, -invert, -merge, and -promote.
* xtract.1: Rename -in to -using; add -adding and -merging (all under
  Record Selection).

- - - - -
3204ceab by Aaron M. Ucko at 2020-06-21T21:44:01-04:00
New upstream version 12.9.20191209+dfsg
- - - - -
8031da83 by Aaron M. Ucko at 2020-06-21T21:44:51-04:00
Merge tag 'upstream/12.9.20191209+dfsg'

Upstream version 12.9.20191209(+dfsg).

- - - - -
b940c298 by Aaron M. Ucko at 2020-06-21T21:45:29-04:00
New upstream version 12.9.20191213+dfsg
- - - - -
82e9dd7e by Aaron M. Ucko at 2020-06-21T21:45:44-04:00
Merge tag 'upstream/12.9.20191213+dfsg'

Upstream version 12.9.20191213(+dfsg).

- - - - -
0dae7ccd by Aaron M. Ucko at 2020-06-21T21:46:13-04:00
xtract.1: + -fwd/-awd (Format C11n) as of 12.9.20191213(+dfsg).

- - - - -
2789ed8d by Aaron M. Ucko at 2020-06-21T21:47:53-04:00
New upstream version 13.0.20191216+dfsg
- - - - -
8ded343e by Aaron M. Ucko at 2020-06-21T21:48:21-04:00
Merge tag 'upstream/13.0.20191216+dfsg'

Upstream version 13.0.20191216(+dfsg).

- - - - -
bb5309be by Aaron M. Ucko at 2020-06-21T21:49:03-04:00
debian/man: Update for new release (13.0.20191216[+dfsg]).

* xtract.1: Add new sections XML Generation (existing -wrp, -plg,
  -elg, -fwd, and -awd) between Format Customization and Element
  Selection; and Frequency Table (new -histogram) and Entrez
  Indexing (existing -e2index and -indices) between Command Generator
  and Miscellaneous.
* Update SEE ALSO sections appropriately.

- - - - -
4a689f4c by Aaron M. Ucko at 2020-06-21T21:50:21-04:00
rules: Broaden .../x/sys/unix to .../x/sys in GOLIBSRC(_) (#963439)

- - - - -
a45f7aa8 by Aaron M. Ucko at 2020-06-21T21:51:10-04:00
New upstream version 13.0.20191223+dfsg
- - - - -
2a6b2753 by Aaron M. Ucko at 2020-06-21T21:51:33-04:00
Merge tag 'upstream/13.0.20191223+dfsg'

Upstream version 13.0.20191223(+dfsg).

- - - - -
8b440ba5 by Aaron M. Ucko at 2020-06-21T21:52:39-04:00
New upstream version 13.1.20200102+dfsg
- - - - -
a6b47fc9 by Aaron M. Ucko at 2020-06-21T21:53:13-04:00
Merge tag 'upstream/13.1.20200102+dfsg'

Upstream version 13.1.20200102(+dfsg).

- - - - -
857d6d3a by Aaron M. Ucko at 2020-06-21T22:37:08-04:00
Temporarily move go.mod, go.sum, and s2p.go aside.

* .gitignore: Ignore new "saved" directory.
* debian/rules: 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.)

- - - - -
e0d49d99 by Aaron M. Ucko at 2020-06-21T22:37:08-04:00
xtract.1: Update for new release (13.1.20200102[+dfsg]).

In Record Selection, replace -using/-adding/-merging with
-retaining/-excluding/-appending (where -retaining and -appending are
simply new names for -using and -merging respectively, -adding is
gone, and -excluding is new).

- - - - -
2448c2ad by Aaron M. Ucko at 2020-06-21T22:37:08-04:00
Finalize ncbi-entrez-direct 13.1.20200102+dfsg-1 for unstable.

Still several months behind, but precipitated by #963439.

- - - - -


30 changed files:

- .gitignore
- README
- archive-pubmed
- asp-ls
- bt-link
- bt-srch
- build.sh
- common.go
- debian/changelog
- debian/control
- debian/copyright
- debian/examples
- debian/install
- debian/man/archive-pubmed.1
- + debian/man/bt-link.1
- + debian/man/bt-load.1
- + debian/man/bt-save.1
- + debian/man/bt-srch.1
- debian/man/download-ncbi-data.1
- debian/man/edirect.1
- debian/man/efetch.1
- debian/man/elink.1
- debian/man/esample.1
- debian/man/esearch.1
- + debian/man/expand-current.1
- + debian/man/fetch-extras.1
- debian/man/fetch-pubmed.1
- debian/man/ftp-cp.1
- debian/man/ftp-ls.1
- debian/man/index-bioc.1 → debian/man/index-extras.1


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/c55e0fb48ac36a6af2a2b10d9335af5377c3d53a...2448c2ad8ec6b1b23da8cc84ded2874bf696395c

-- 
View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/c55e0fb48ac36a6af2a2b10d9335af5377c3d53a...2448c2ad8ec6b1b23da8cc84ded2874bf696395c
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200622/997c94df/attachment-0001.html>

More information about the debian-med-commit mailing list