[med-svn] [Git][med-team/ncbi-entrez-direct][master] 27 commits: New upstream version 13.8.20200817+dfsg
Aaron M. Ucko
gitlab at salsa.debian.org
Mon Oct 12 20:17:21 BST 2020
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-entrez-direct
Commits:
df8f55ce by Aaron M. Ucko at 2020-08-23T20:34:38-04:00
New upstream version 13.8.20200817+dfsg
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74f61e49 by Aaron M. Ucko at 2020-08-23T20:36:04-04:00
Merge tag 'upstream/13.8.20200817+dfsg' into master
Upstream version 13.8.20200817(+dfsg).
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b4f98c38 by Aaron M. Ucko at 2020-10-03T22:10:43-04:00
New upstream version 13.8.20200909+dfsg
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dca59a41 by Aaron M. Ucko at 2020-10-03T22:47:58-04:00
New upstream version 13.9.20200914+dfsg
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38017857 by Aaron M. Ucko at 2020-10-12T11:53:47-04:00
New upstream version 13.9.20200923+dfsg
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6a08323f by Aaron M. Ucko at 2020-10-12T12:01:57-04:00
New upstream version 14.0.20201007+dfsg
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2f5e6d8f by Aaron M. Ucko at 2020-10-12T12:15:50-04:00
New upstream version 14.0.20201009+dfsg
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d0a09293 by Aaron M. Ucko at 2020-10-12T14:37:09-04:00
debian/rules: Belatedly install phrase-search (as is).
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1ed60c8f by Aaron M. Ucko at 2020-10-12T14:38:01-04:00
debian/man/{download-ncbi-data,esample}.1: Correct old typos.
Transposed letters, unescaped hyphen, missing parentheses.
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128fdaf5 by Aaron M. Ucko at 2020-10-12T14:38:58-04:00
debian/efetch: Belatedly resync %ncbi_supported with current usage.
Missed -style, -revcomp, -chr_stop, -raw, and -json.
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1c3d5f93 by Aaron M. Ucko at 2020-10-12T14:41:13-04:00
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.
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b1cf2574 by Aaron M. Ucko at 2020-10-12T14:43:02-04:00
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.
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a9aefd29 by Aaron M. Ucko at 2020-10-12T14:43:06-04:00
d/copyright: Add myself [Aaron Ucko] (at NCBI) as an upstream author.
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46367231 by Aaron M. Ucko at 2020-10-12T14:43:07-04:00
debian/tests/run-unit-test: Correct gbf2xml invocation.
It ignores any arguments and reads from standard input.
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415f0e9b by Aaron M. Ucko at 2020-10-12T14:43:07-04:00
debian/copyright: Also exclude CA.pm and cacert.pm.
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bd2bdcba by Aaron M. Ucko at 2020-10-12T14:43:07-04:00
Merge tag 'upstream/13.8.20200909+dfsg' into master
Upstream version 13.8.20200909(+dfsg).
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cb2f4e7c by Aaron M. Ucko at 2020-10-12T14:43:07-04:00
debian/rules: Account for retirement of ?2?.go.
Account for retirement of dedicated g2x, j2x, and t2x binaries and of
unbuilt s2p.go.
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92ac001c by Aaron M. Ucko at 2020-10-12T14:51:46-04:00
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.
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ae60dae2 by Aaron M. Ucko at 2020-10-12T14:51:46-04:00
debian/tests/run-unit-test: Drop j2x test.
Renumber following tests accordingly.
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43b5a98f by Aaron M. Ucko at 2020-10-12T14:51:46-04:00
Merge tag 'upstream/13.9.20200914+dfsg' into master
Upstream version 13.9.20200914(+dfsg).
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104c0373 by Aaron M. Ucko at 2020-10-12T14:51:46-04:00
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.
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836dd16e by Aaron M. Ucko at 2020-10-12T14:51:46-04:00
Merge tag 'upstream/13.9.20200923+dfsg' into master
Upstream version 13.9.20200923(+dfsg).
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5b1f556d by Aaron M. Ucko at 2020-10-12T14:51:46-04:00
efetch.1: Update for new upstream release (13.9.20200923[+dfsg]).
Document new shell-only options -style master and -showgaps.
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f8f75f7d by Aaron M. Ucko at 2020-10-12T14:51:46-04:00
Merge tag 'upstream/14.0.20201007+dfsg' into master
Upstream version 14.0.20201007(+dfsg).
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71ec826d by Aaron M. Ucko at 2020-10-12T14:51:46-04:00
xtract.1: Update for new upstream release (14.0.20201007[+dfsg]).
Document new flags -ncbi2na, -ncbi4na (both Sequence Processing), and
-a2x (Data Conversion).
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40cb007b by Aaron M. Ucko at 2020-10-12T14:51:46-04:00
Merge tag 'upstream/14.0.20201009+dfsg' into master
Upstream version 14.0.20201009(+dfsg).
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1a0a45b3 by Aaron M. Ucko at 2020-10-12T15:14:48-04:00
Finalize ncbi-entrez-direct 14.0.20201009+dfsg-1 for unstable.
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30 changed files:
- README
- build.sh
- common.go
- debian/changelog
- debian/copyright
- debian/efetch
- debian/einfo
- debian/install
- debian/man/bt-link.1
- debian/man/bt-srch.1
- debian/man/download-ncbi-data.1
- debian/man/edirect.1
- debian/man/efetch.1
- + debian/man/efetch.ncbi.1
- debian/man/efilter.1
- debian/man/einfo.1
- + debian/man/einfo.ncbi.1
- debian/man/elink.1
- − debian/man/enquire.1
- debian/man/epost.1
- debian/man/esample.1
- debian/man/esearch.1
- − debian/man/g2x.1
- − debian/man/j2x.1
- debian/man/nquire.1
- + debian/man/skip-if-file-exists.1
- − debian/man/t2x.1
- debian/man/transmute.1
- debian/man/xplore.1
- debian/man/xtract.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/3ff79da3f1d0d11d2976f414edfd56adcf372b89...1a0a45b33d972a7e14864aeabc2f6ad7ec43122c
--
View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/3ff79da3f1d0d11d2976f414edfd56adcf372b89...1a0a45b33d972a7e14864aeabc2f6ad7ec43122c
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