[med-svn] [Git][med-team/ncbi-entrez-direct][master] 161 commits: New upstream version 14.7.20210306+dfsg
Aaron M. Ucko (@ucko)
gitlab at salsa.debian.org
Tue Feb 14 03:41:37 GMT 2023
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-entrez-direct
Commits:
80fd4329 by Aaron M. Ucko at 2022-01-17T15:36:22-05:00
New upstream version 14.7.20210306+dfsg
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1c3b39b2 by Aaron M. Ucko at 2022-01-17T19:56:40-05:00
New upstream version 14.7.20210317+dfsg
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157b9786 by Aaron M. Ucko at 2023-01-23T20:16:02-05:00
New upstream version 14.8.20210324+dfsg
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6ac53edf by Aaron M. Ucko at 2023-01-23T20:22:22-05:00
New upstream version 14.8.20210413+dfsg
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2825701b by Aaron M. Ucko at 2023-01-23T20:56:07-05:00
New upstream version 14.9.20210414+dfsg
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b6f2cabf by Aaron M. Ucko at 2023-01-23T20:57:36-05:00
New upstream version 14.9.20210426+dfsg
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781e4a40 by Aaron M. Ucko at 2023-01-24T20:36:59-05:00
New upstream version 15.0.20210428+dfsg
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7189238e by Aaron M. Ucko at 2023-01-26T19:46:24-05:00
New upstream version 15.0.20210517+dfsg
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bf3e6c27 by Aaron M. Ucko at 2023-01-27T18:00:07-05:00
Merge tag 'upstream/14.7.20210306+dfsg'
Upstream version 14.7.20210306(+dfsg).
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06013334 by Aaron M. Ucko at 2023-01-27T18:08:30-05:00
New upstream version 15.1.20210519+dfsg
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97e7c035 by Aaron M. Ucko at 2023-01-28T23:05:30-05:00
debian/{efetch,einfo}: Belatedly resync %ncbi_supported.
Add explicit -ext(ernal) and efetch's -plus, -reverse, and -minus
aliases (all undocumented).
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9b28b8ac by Aaron M. Ucko at 2023-01-28T23:06:05-05:00
debian/control: Downgrade or remove Perl-related dependencies.
With the old EUtils wrappers fully gone, only two specialized scripts
still use Perl at all, and neither uses libwww-perl.
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0f9b43df by Aaron M. Ucko at 2023-01-28T23:06:21-05:00
debian/man/{nquire,transmute,xml2tbl}.1: Fix long-standing buglets.
* nquire.1: Belatedly fix typo in -get's usage; belatedly add "URL
Additions" and "Miscellaneous" subsections rather than letting "File
Downloads" nominally run on.
* transmute.1: Belatedly list xml2tbl in SEE ALSO.
* xml2tbl.1: Belatedly list transmute in SEE ALSO.
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9313dd4e by Aaron M. Ucko at 2023-01-28T23:06:37-05:00
debian/{examples,rules}: Reflect upstream retirements and moves.
* examples: Reflect upstream retirement of nearly everything (leaving
only test-pubmed-index). To be fair, 14.6.20210224+dfsg-2 had
relegated many files to examples in anticipation of their retirement.
* rules:
- Reflect upstream retirement of eaddress, ecitmatch, econtact,
edirutil, enotify, entrez-phrase-search, eproxy, espell, ftp-cp,
ftp-ls, and protein-neighbors.
- Reflect new Go layout -- application code now in cmd/, library code
split from common.go to eutils/*.go.
- Belatedly ensure bin/ exists in the bin/%.sh pattern rule, which has
become the first to need it with the retirement of STD_WRAPPERS.
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081c90db by Aaron M. Ucko at 2023-01-30T20:22:48-05:00
New upstream version 15.1.20210525+dfsg
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be558636 by Aaron M. Ucko at 2023-01-30T21:07:19-05:00
New upstream version 15.2.20210601+dfsg
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d2c807a2 by Aaron M. Ucko at 2023-01-30T21:36:27-05:00
New upstream version 15.2.20210615+dfsg
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a1ee6c9f by Aaron M. Ucko at 2023-01-30T22:35:15-05:00
New upstream version 15.3.20210617+dfsg
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6f845428 by Aaron M. Ucko at 2023-01-30T22:44:02-05:00
New upstream version 15.3.20210707+dfsg
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cb7efd6b by Aaron M. Ucko at 2023-01-31T20:03:25-05:00
debian/man/{efilter,transmute}.1: Belatedly clean up formatting.
Not worth rebasing fully (which might require further splitting).
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ecb71a8e by Aaron M. Ucko at 2023-01-31T20:05:13-05:00
debian/man: Update for new release (14.7.20210306[+dfsg]).
* {eaddress,ecitmatch,econtact,edirutil,enotify,entrez-phrase-search,
eproxy,espell,ftp-cp,ftp-ls,protein-neighbors}.1: Retire.
* edirect.1: Drop SYNOPSIS references to retired wrappers.
* transmute.1: -format's fmt parameter may no longer be "copy", but is
evidently optional.
* Generally drop SEE ALSO references to retired scripts.
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65d1c24c by Aaron M. Ucko at 2023-01-31T20:05:49-05:00
Merge tag 'upstream/14.7.20210317+dfsg'
Upstream version 14.7.20210317(+dfsg).
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e55c159b by Aaron M. Ucko at 2023-01-31T21:40:06-05:00
debian/rules: Update list of as-is scripts for new release.
* Add filter-table, print-columns, and sort-table.
* Retire eblast.
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feb9c7f1 by Aaron M. Ucko at 2023-01-31T21:46:44-05:00
debian/man: Update for new release (14.7.20210317[+dfsg]).
* eblast.1: Retire.
* {filter-table,print-columns,sort-table}.1: Document new commands.
* Update SEE ALSO accordingly.
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fc190fba by Aaron M. Ucko at 2023-01-31T21:47:29-05:00
Merge tag 'upstream/14.8.20210324+dfsg'
Upstream version 14.8.20210324(+dfsg).
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09ef8750 by Aaron M. Ucko at 2023-01-31T21:47:29-05:00
debian/man/nquire.1: Update for new release (14.8.20210324[+dfsg]).
Add -dir.
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4a90722c by Aaron M. Ucko at 2023-01-31T21:47:29-05:00
Merge tag 'upstream/14.8.20210413+dfsg'
Upstream version 14.8.20210413(+dfsg).
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1783fe1c by Aaron M. Ucko at 2023-01-31T21:48:23-05:00
debian/man/esample.1: Update for new release (14.8.20210413[+dfsg]).
Add -hgvs.
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0aeac7c1 by Aaron M. Ucko at 2023-01-31T21:48:42-05:00
Merge tag 'upstream/14.9.20210414+dfsg'
Upstream version 14.9.20210414(+dfsg).
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7147487e by Aaron M. Ucko at 2023-01-31T21:48:42-05:00
Merge tag 'upstream/14.9.20210426+dfsg'
Upstream version 14.9.20210426(+dfsg).
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d3eaeeae by Aaron M. Ucko at 2023-01-31T21:50:10-05:00
New as-is scripts hgvs2spdi, snp2hgvs, snp2tbl, and spdi2prod.
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fead4206 by Aaron M. Ucko at 2023-01-31T21:51:36-05:00
debian/man: Update for new release (14.9.20210426[+dfsg]).
* hgvs2spdi.1, snp2hgvs.1, snp2tbl.1, spdi2prod.1: New commands.
* transmute.1: New -lower option for -replace and -extract; cds2prot
-trim now removes trailing *s, not just Xs.
* Update SEE ALSO accordingly.
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1df6fb1c by Aaron M. Ucko at 2023-01-31T21:51:51-05:00
Merge tag 'upstream/15.0.20210428+dfsg'
Upstream version 15.0.20210428(+dfsg).
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200fac25 by Aaron M. Ucko at 2023-01-31T21:51:51-05:00
debian/rules: Reflect upstream retirement of edirect.
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b3ce724b by Aaron M. Ucko at 2023-01-31T21:55:45-05:00
debian/man: Update for new release (15.0.20210428[+dfsg]).
Reflect retirement of old Perl edirect script in favor of shell
implementations of its subcommands.
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bdeae160 by Aaron M. Ucko at 2023-01-31T21:56:02-05:00
debian/{efetch,einfo}: Resync %ncbi_supported (Perl impl. gone).
Drop options available only through the Perl implementation:
* For both, -api_key, -silent, -verbose, -compact, -http(s), and -alias.
* For efetch, also -showgi, -nogi, and -pipe.
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6e8382cc by Aaron M. Ucko at 2023-01-31T21:56:03-05:00
Merge tag 'upstream/15.0.20210517+dfsg'
Upstream version 15.0.20210517(+dfsg).
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e21067ba by Aaron M. Ucko at 2023-01-31T21:56:42-05:00
d/rules: Add as-is scripts csv2xml, json2xml, spdi2tbl, and tbl2xml.
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5978cc07 by Aaron M. Ucko at 2023-01-31T21:56:52-05:00
Install transmute's new asn2xml wrapper to /u/l/n-e-d/bin.
* debian/README.Debian (new): Document asn2xml's status.
* debian/install: Install transmute's asn2xml convenience wrapper to
/usr/lib/ncbi-entrez-direct/bin. Installing it to /usr/bin would
conflict with ncbi-tools-bin without special tricks like an
efetch/einfo-style wrapper, which would be overkill here; those names
were primary entry points all along, whereas this wrapper is merely
shorthand without even any internal use.
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4064ffdf by Aaron M. Ucko at 2023-01-31T21:57:31-05:00
debian/rules: Have esummary run efetch.ncbi directly
... so the wrapper can't interfere with its dedicated -help output.
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d6688ef1 by Aaron M. Ucko at 2023-01-31T21:57:41-05:00
debian/man/{align-columns,gbf2xml,transmute}.1: Split up.
align-columns and gbf2xml remain wrappers for transmute, but some
additional *2xml wrappers will be joining them, and the result would
otherwise be unwieldy.
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21df8e36 by Aaron M. Ucko at 2023-01-31T21:57:42-05:00
debian/man: Update for new release (15.0.20210517[+dfsg]).
* csv2xml.1, json2xml.1, spdi2tbl.1, tbl2xml.1: Document new commands.
* efetch.1: Drop -examples and undocumented esummary options.
* gbf2xml.1: Subsume into csv2xml.1, which also covers the new
json2xml and tbl2xml wrappers.
* nquire.1: Document newly official URL shortcuts: -ncbi, -eutils,
-pubchem.
* transmute.1: Move Sequence Comparison (-diff) down to between
Variation Processing and String Transformations per -help; add
-codons (with suboptions -nuc, -prot, -frame, and -three).
* Update SEE ALSO references accordingly.
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1d153d8e by Aaron M. Ucko at 2023-01-31T21:57:42-05:00
debian/efetch: Resync %ncbi_supported (drop -example/s and -error/s)
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6871688f by Aaron M. Ucko at 2023-01-31T21:57:42-05:00
Merge tag 'upstream/15.1.20210519+dfsg'
Upstream version 15.1.20210519(+dfsg).
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f8f5186f by Aaron M. Ucko at 2023-01-31T21:58:31-05:00
Merge tag 'upstream/15.1.20210525+dfsg'
Upstream version 15.1.20210525(+dfsg).
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b49f9e57 by Aaron M. Ucko at 2023-01-31T21:58:50-05:00
debian/man: Update for new release (15.1.20210525[+dfsg]).
* {phrase-search,rchive}.1: Add -title; clarify that -exact is more general.
* xtract.1: Add -includes (String Constraints) and -article (Entrez Indexing).
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7b74de4d by Aaron M. Ucko at 2023-01-31T21:59:39-05:00
Merge tag 'upstream/15.2.20210601+dfsg'
Upstream version 15.2.20210601(+dfsg).
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4c210d5b by Aaron M. Ucko at 2023-01-31T22:01:14-05:00
debian/rules: Install new as-is script custom-index.
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753dd9c4 by Aaron M. Ucko at 2023-01-31T22:01:21-05:00
debian/examples: Add index-author-num.
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8f8d07b6 by Aaron M. Ucko at 2023-01-31T22:04:24-05:00
debian/man: Update for new release (15.2.20210601[+dfsg]).
* custom-index.1: Document new script.
* Update SEE ALSO references accordingly.
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571b46a3 by Aaron M. Ucko at 2023-01-31T22:04:39-05:00
Merge tag 'upstream/15.2.20210615+dfsg'
Upstream version 15.2.20210615(+dfsg).
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b0272a98 by Aaron M. Ucko at 2023-01-31T22:04:47-05:00
debian/rules: Stop temporarily moving aside go.mod and go.sum
... no longer shipped.
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2919aec2 by Aaron M. Ucko at 2023-01-31T22:04:49-05:00
.gitignore: Stop ignoring "saved", no longer needed.
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d9dcb38f by Aaron M. Ucko at 2023-01-31T22:04:54-05:00
debian/examples: Replace index-author-num by idx-*.
idx-author-num is now idx-words, and has been joined by idx-authors.
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fc3f33f8 by Aaron M. Ucko at 2023-01-31T22:04:59-05:00
debian/man: Update for new release (15.2.20210615[+dfsg]).
* custom-index.1: Update helper example details.
* transmute.1: Replace -format's -separate by -combine (Customized XML
Reformatting).
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7c67fb6c by Aaron M. Ucko at 2023-01-31T22:05:18-05:00
Merge tag 'upstream/15.3.20210617+dfsg'
Upstream version 15.3.20210617(+dfsg).
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71dcc8ce by Aaron M. Ucko at 2023-01-31T22:05:19-05:00
transmute.1: Update for new release (15.3.20210617[+dfsg]).
* Add -search [-circular] (Sequence Processing).
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1173e3a5 by Aaron M. Ucko at 2023-01-31T22:06:27-05:00
Merge tag 'upstream/15.3.20210707+dfsg'
Upstream version 15.3.20210707(+dfsg).
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872e3b56 by Aaron M. Ucko at 2023-01-31T22:19:10-05:00
debian/rules: Add as-is script disambiguate-nucleotides.
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150ad72d by Aaron M. Ucko at 2023-01-31T22:20:53-05:00
debian/man: Update for new release (15.3.20210707[+dfsg]).
* align-columns.1: Update synopsis per transmute.1.
* efilter.1: Add -source select (Sequence Filters).
* transmute.1: Add -align's -w and -a m/M suboptions (Pretty-Printing);
move -search to a new Sequence Searching subsection between Variation
Processing and String Transformations per upstream -help and document
it in more detail; add Text Searching (-find [-relaxed]) right after.
* Update SEE ALSO references accordingly.
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cdc07f33 by Aaron M. Ucko at 2023-01-31T22:29:01-05:00
New upstream version 15.4.20210715+dfsg
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5b92901d by Aaron M. Ucko at 2023-01-31T22:29:51-05:00
Merge tag 'upstream/15.4.20210715+dfsg'
Upstream version 15.4.20210715(+dfsg).
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708bfaf7 by Aaron M. Ucko at 2023-01-31T22:31:57-05:00
debian/rules: Fold BASH_SCRIPTS into AS_IS_SCRIPTS.
It was already down to index-extras, which now explicitly specifies
#!/bin/bash. In retrospect, it should have also included
download-ncbi-data, but that's good now too.
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7b240f55 by Aaron M. Ucko at 2023-01-31T22:32:55-05:00
New upstream version 15.4.20210802+dfsg
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73de5f45 by Aaron M. Ucko at 2023-01-31T22:33:28-05:00
Merge tag 'upstream/15.4.20210802+dfsg'
Upstream version 15.4.20210802(+dfsg).
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a85f58cd by Aaron M. Ucko at 2023-02-01T22:17:27-05:00
.gitignore, debian/rules: Reinstate cmd/go.{mod,sum} handling.
This reverts commits b0272a986c0ca34809f97a65c08ee73ab491fba3 and
2919aec22acc3ac73f4d54dcf0a4545d336985b4.
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97cc0488 by Aaron M. Ucko at 2023-02-01T22:52:12-05:00
debian/rules: Install new as-is script xml2fsa.
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c1994a0c by Aaron M. Ucko at 2023-02-01T22:54:58-05:00
New upstream version 15.5.20210806+dfsg
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5d2fe4f3 by Aaron M. Ucko at 2023-02-01T23:28:09-05:00
debian/man: Update for new release (15.4.20210802[+dfsg]).
* transmute.1: Add -counts (Sequence Comparison); -search has
additional -protein and -top flags (Sequence Searching); -find has
additional -sensitive flag (Text Searching); add -relax (new Letters
plus Digits subsection between String Transformations and Customized
XML Reformatting).
* xml2fsa.1: Document new command.
* Update SEE ALSO references accordingly.
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8d12115d by Aaron M. Ucko at 2023-02-01T23:28:33-05:00
Merge tag 'upstream/15.5.20210806+dfsg'
Upstream version 15.5.20210806(+dfsg).
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62adf638 by Aaron M. Ucko at 2023-02-01T23:28:33-05:00
d/rules: New as-is scripts download-ncbi-software and fuse-ranges.
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6177c749 by Aaron M. Ucko at 2023-02-01T23:28:49-05:00
New upstream version 15.5.20210827+dfsg
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30831c79 by Aaron M. Ucko at 2023-02-02T23:00:54-05:00
xtract.1: Fix an old paste-o in Special -element Operations.
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1b520e76 by Aaron M. Ucko at 2023-02-02T23:01:09-05:00
debian/man: Update for new release (15.5.20210806[+dfsg]).
* download-ncbi-software.1, fuse-ranges.1: Document new commands.
* Update SEE ALSO references accordingly.
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6155d323 by Aaron M. Ucko at 2023-02-02T23:01:09-05:00
Merge tag 'upstream/15.5.20210827+dfsg'
Upstream version 15.5.20210827(+dfsg).
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b00e5e43 by Aaron M. Ucko at 2023-02-02T23:01:09-05:00
d/rules: + as-is scripts blst2tkns, find-in-gene, split-at-intron.
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1609c89f by Aaron M. Ucko at 2023-02-02T23:01:09-05:00
debian/man: Update for new release (15.5.20210827[+dfsg]).
* blst2tkns.1, find-in-gene.1, split-at-intron.1: Document new commands.
* download-ncbi-software.1: Add (-)datasets and (-)sra-toolkit.
* efilter.1: Add -keyword purpose and -purpose baseline/targeted (both
under Sequence Filters).
* xtract.1: Add ~ (Special -element Operations); update -fasta details
(Sequence Processing).
* Update SEE ALSO references accordingly.
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5d2dc8e4 by Aaron M. Ucko at 2023-02-03T10:27:11-05:00
New upstream version 15.6.20210831+dfsg
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6e4cf93c by Aaron M. Ucko at 2023-02-03T10:28:00-05:00
Merge tag 'upstream/15.6.20210831+dfsg'
Upstream version 15.6.20210831(+dfsg).
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39f7d138 by Aaron M. Ucko at 2023-02-03T10:32:19-05:00
d/man/efilter.1: Belatedly add -pub medline and -pub published.
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a7b03e26 by Aaron M. Ucko at 2023-02-03T10:39:06-05:00
d/rules: Account for direct use of github.com/rainycape/unidecode.
No more need to pass it off as github.com/fiam/gounidecode/unidecode.
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1ab54106 by Aaron M. Ucko at 2023-02-03T10:41:25-05:00
efilter.1: Update for new release (15.6.20210831[+dfsg]).
Add new -pub types retracted and retraction.
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b74e3f37 by Aaron M. Ucko at 2023-02-03T10:42:03-05:00
New upstream version 15.6.20210908+dfsg
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253f0862 by Aaron M. Ucko at 2023-02-03T10:43:42-05:00
Merge tag 'upstream/15.6.20210908+dfsg'
Upstream version 15.6.20210908(+dfsg).
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59ac1c03 by Aaron M. Ucko at 2023-02-03T11:14:45-05:00
debian/rules: filter-table is now filter-columns (as-is script).
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b1f7c01f by Aaron M. Ucko at 2023-02-03T11:21:46-05:00
debian/{install,rules}: Account for help text split-out.
* debian/install: Install help files to /usr/lib/ncbi-entrez-direct/help.
* debian/rules: Account for split out of help texts for ecommon scripts,
nquire, and remaining Go binaries. In particular, factor out and
generalize the logic to tweak scripts, extend it to nquire, and treat
compiled binaries uniformly.
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188e553d by Aaron M. Ucko at 2023-02-03T14:30:30-05:00
debian/man: Update for new release (15.6.20210908[+dfsg]).
* filter-columns.1: Rename from filter-table.1.
* Update SEE ALSO references accordingly.
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367531f3 by Aaron M. Ucko at 2023-02-03T14:32:01-05:00
New upstream version 15.7.20210909+dfsg
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c5b641af by Aaron M. Ucko at 2023-02-03T14:32:51-05:00
Merge tag 'upstream/15.7.20210909+dfsg'
Upstream version 15.7.20210909(+dfsg).
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5edeecbc by Aaron M. Ucko at 2023-02-03T14:37:31-05:00
debian/{efetch,einfo}: Recognize new common -immediate flag.
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862181d9 by Aaron M. Ucko at 2023-02-03T14:39:16-05:00
debian/man/xtract.1: Add -backward as of 15.7.20210909[+dfsg].
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49c58f7c by Aaron M. Ucko at 2023-02-03T14:39:35-05:00
New upstream version 15.7.20210914+dfsg
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821467c2 by Aaron M. Ucko at 2023-02-03T14:41:55-05:00
Merge tag 'upstream/15.7.20210914+dfsg'
Upstream version 15.7.20210914(+dfsg).
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869e988c by Aaron M. Ucko at 2023-02-03T14:47:33-05:00
debian/man: Update for new release (15.7.20210914[+dfsg]).
* transmute.1: Add standalone -upper and -lower (new Case subsection,
between String Transformations and Protein).
* xtract.1: Move -year and -doi out of String Processing to a new
Miscellaneous Functions subsection and -translate to a new Value
Transformation subsection, with the pair landing between Text
Processing and Regular Expressions; rename the remainder of String
Processing to Character Processing.
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c55a7f5b by Aaron M. Ucko at 2023-02-03T17:18:21-05:00
New upstream version 15.8.20210915+dfsg
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bf4adcf6 by Aaron M. Ucko at 2023-02-03T17:19:05-05:00
Merge tag 'upstream/15.8.20210915+dfsg'
Upstream version 15.8.20210915(+dfsg).
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d47c8baf by Aaron M. Ucko at 2023-02-03T17:28:39-05:00
debian/rules: Replace as-is script spdi2prod by tbl2prod.
The existing snp2tbl and spdi2tbl can take care of the initial steps.
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89db409a by Aaron M. Ucko at 2023-02-03T17:29:08-05:00
debian/man: Update for new release (15.8.20210915[+dfsg]).
* Reflect replacement of spdi2prod by a tbl2prod that can pair with
either snp2tbl or spdi2tbl.
- - - - -
a7cd8583 by Aaron M. Ucko at 2023-02-03T17:30:13-05:00
New upstream version 15.8.20210923+dfsg
- - - - -
de9cf625 by Aaron M. Ucko at 2023-02-03T17:30:47-05:00
Merge tag 'upstream/15.8.20210923+dfsg'
Upstream version 15.8.20210923(+dfsg).
- - - - -
1aec124d by Aaron M. Ucko at 2023-02-05T14:29:52-05:00
debian/rules: New as-is script uniq-columns.
- - - - -
43d25808 by Aaron M. Ucko at 2023-02-05T14:30:47-05:00
debian/man: Update for new release (15.8.20210923[+dfsg]).
* elink.1: Note where -cited and -cites get their data.
* uniq-columns.1: Document new command.
* -xtract.1: + -author (Character Processing).
- - - - -
7ff17579 by Aaron M. Ucko at 2023-02-05T14:33:30-05:00
New upstream version 15.9.20210924+dfsg
- - - - -
1e18a81b by Aaron M. Ucko at 2023-02-05T16:46:26-05:00
Merge tag 'upstream/15.9.20210924+dfsg'
Upstream version 15.9.20210924(+dfsg).
- - - - -
a818c5bb by Aaron M. Ucko at 2023-02-05T16:47:21-05:00
New upstream version 15.9.20210929+dfsg
- - - - -
49321616 by Aaron M. Ucko at 2023-02-05T16:49:30-05:00
Merge tag 'upstream/15.9.20210929+dfsg'
Upstream version 15.9.20210929(+dfsg).
- - - - -
198e8945 by Aaron M. Ucko at 2023-02-05T16:51:06-05:00
debian/rules: New as-is script gene2range.
- - - - -
8254da25 by Aaron M. Ucko at 2023-02-05T16:54:44-05:00
debian/man/find-in-gene.1: Fix paste-o in NAME.
- - - - -
07f041f3 by Aaron M. Ucko at 2023-02-05T18:29:37-05:00
debian/man: Update for new release (15.9.20210929[+dfsg]).
* find-in-gene: Note input format change.
* gene2range: New command.
* Update SEE ALSO references accordingly.
- - - - -
ed504d41 by Aaron M. Ucko at 2023-02-05T18:30:49-05:00
New upstream version 16.0.20211001+dfsg
- - - - -
85b4bad3 by Aaron M. Ucko at 2023-02-05T18:31:25-05:00
Merge tag 'upstream/16.0.20211001+dfsg'
Upstream version 16.0.20211001(+dfsg).
- - - - -
f76f7b62 by Aaron M. Ucko at 2023-02-05T18:33:57-05:00
debian/rules: New as-is script fuse-segments.
- - - - -
799e9cf6 by Aaron M. Ucko at 2023-02-05T18:41:02-05:00
debian/man: Update for new release (16.0.20211001[+dfsg]).
* fuse-segments.1: New command.
* transmute.1: New -extract options -1-based and -0-based (Sequence Editing).
* Update SEE ALSO references accordingly.
- - - - -
b1eb2ebc by Aaron M. Ucko at 2023-02-05T18:44:21-05:00
New upstream version 16.0.20211004+dfsg
- - - - -
cd3bc970 by Aaron M. Ucko at 2023-02-05T18:44:57-05:00
Merge tag 'upstream/16.0.20211004+dfsg'
Upstream version 16.0.20211004(+dfsg).
- - - - -
eda7bf39 by Aaron M. Ucko at 2023-02-05T18:50:00-05:00
Reflect uniq-columns -> uniq-table name change.
- - - - -
d1cd5e91 by Aaron M. Ucko at 2023-02-05T18:52:12-05:00
debian/man/fuse-segments.1: Document input format generalization.
- - - - -
0b3e191f by Aaron M. Ucko at 2023-02-05T18:53:10-05:00
New upstream version 16.1.20211012+dfsg
- - - - -
74043b37 by Aaron M. Ucko at 2023-02-05T18:53:49-05:00
Merge tag 'upstream/16.1.20211012+dfsg'
Upstream version 16.1.20211012(+dfsg).
- - - - -
ccc2d580 by Aaron M. Ucko at 2023-02-06T22:12:12-05:00
debian/{efetch,einfo}: Recognize new common -express flag.
- - - - -
d9d34859 by Aaron M. Ucko at 2023-02-06T22:12:38-05:00
debian/man: Update for new release (16.1.20211012[+dfsg]).
* efetch.1: New -express and -immediate flags (Miscellaneous).
* xtract.1: New -self flag (Processing Flags).
- - - - -
16bea89a by Aaron M. Ucko at 2023-02-06T22:17:27-05:00
New upstream version 16.1.20211020+dfsg
- - - - -
8bf48363 by Aaron M. Ucko at 2023-02-06T22:18:18-05:00
Merge tag 'upstream/16.1.20211020+dfsg'
Upstream version 16.1.20211020(+dfsg).
- - - - -
9a096e33 by Aaron M. Ucko at 2023-02-07T21:29:10-05:00
New upstream version 16.2.20211022+dfsg
- - - - -
d764ba6a by Aaron M. Ucko at 2023-02-07T21:30:18-05:00
Merge tag 'upstream/16.2.20211022+dfsg'
Upstream version 16.2.20211022(+dfsg).
- - - - -
31ebe584 by Aaron M. Ucko at 2023-02-07T21:33:53-05:00
d/man/transmute.1: Fix typos in json2xml and gbf2xml annotations.
- - - - -
9f51e1ba by Aaron M. Ucko at 2023-02-07T21:34:26-05:00
d/man/transmute.1: Update for new release (16.2.20211022[+dfsg]).
* Add -j2x -nest element (Pretty-Printing).
- - - - -
feb250a8 by Aaron M. Ucko at 2023-02-07T21:35:35-05:00
New upstream version 16.2.20211103+dfsg
- - - - -
e1c1b89d by Aaron M. Ucko at 2023-02-07T21:36:15-05:00
Merge tag 'upstream/16.2.20211103+dfsg'
Upstream version 16.2.20211103(+dfsg).
- - - - -
4a6ca870 by Aaron M. Ucko at 2023-02-07T22:53:08-05:00
Arrange to install the new edirect.py via dh_python3.
* debian/control: To accommodate dh_python3, add build dependencies on
both dh-python and python3, and recommend ${python3:Depends} rather
than merely suggesting python. (Recommends is overkill, but the
weakest dh_python3 accepts.)
* debian/ncbi-entrez-direct.pyinstall (new): List debian/edirect.py.
* debian/rules:
- Additionally enable the python3 build system.
- Transiently supply a non-executable(!) copy of edirect.py in debian/.
- - - - -
fb026cb2 by Aaron M. Ucko at 2023-02-07T22:54:25-05:00
debian/.gitignore: Add more ignores per Python handling.
Additionally ignore edirect.py (a transient non-executable copy) and
ncbi-entrez-direct.*.debhelper.
- - - - -
244cee56 by Aaron M. Ucko at 2023-02-07T22:56:09-05:00
New upstream version 16.3.20211215+dfsg
- - - - -
38d4c197 by Aaron M. Ucko at 2023-02-07T22:56:49-05:00
Merge tag 'upstream/16.3.20211215+dfsg'
Upstream version 16.3.20211215(+dfsg).
- - - - -
c3b1f24a by Aaron M. Ucko at 2023-02-08T20:16:45-05:00
debian/man/transmute.1: Belated fixups.
* Properly (albeit somewhat hackishly) label String Transformation
subsubsections -- Case wound up at the top level, and the others
were unmarked altogether.
* Escape hyphens in -encode64 and -decode64 descriptions.
- - - - -
8249bf2a by Aaron M. Ucko at 2023-02-08T21:23:44-05:00
debian/man: Update for new release (16.3.20211215[+dfsg]).
* archive-pubmed.1: Note addition of MeSH tree.
* efilter.1: Assembly Filters (-status latest/replaced) between SNP
Filters and Biosystems Filters.
* nquire.1: Rename -pubchem to -pugrest; add a similar -pugview.
* transmute.1: Accent (-plain) in String Transformation between Base64
and Case.
- - - - -
abc75b54 by Aaron M. Ucko at 2023-02-08T21:26:48-05:00
New upstream version 16.4.20211217+dfsg
- - - - -
1a4a6351 by Aaron M. Ucko at 2023-02-08T21:27:37-05:00
Merge tag 'upstream/16.4.20211217+dfsg'
Upstream version 16.4.20211217(+dfsg).
- - - - -
f10d5a66 by Aaron M. Ucko at 2023-02-08T21:28:36-05:00
New upstream version 16.4.20211222+dfsg
- - - - -
47cc4be9 by Aaron M. Ucko at 2023-02-08T21:29:09-05:00
Merge tag 'upstream/16.4.20211222+dfsg'
Upstream version 16.4.20211222(+dfsg).
- - - - -
7e49c039 by Aaron M. Ucko at 2023-02-08T22:21:52-05:00
New upstream version 16.5.20220103+dfsg
- - - - -
bdb53a06 by Aaron M. Ucko at 2023-02-08T22:22:36-05:00
Merge tag 'upstream/16.5.20220103+dfsg'
Upstream version 16.5.20220103(+dfsg).
- - - - -
3a7e8f73 by Aaron M. Ucko at 2023-02-08T22:24:06-05:00
New upstream version 16.5.20220114+dfsg
- - - - -
6a46ad1d by Aaron M. Ucko at 2023-02-08T22:24:45-05:00
Merge tag 'upstream/16.5.20220114+dfsg'
Upstream version 16.5.20220114(+dfsg).
- - - - -
b62e9ca7 by Aaron M. Ucko at 2023-02-08T22:37:13-05:00
debian/rules: New as-is script pma2pme.
- - - - -
bc8a7dd9 by Aaron M. Ucko at 2023-02-08T22:41:15-05:00
New upstream version 16.6.20220208+dfsg
- - - - -
960708ba by Aaron M. Ucko at 2023-02-08T22:45:23-05:00
debian/man: Update for new release (16.5.20220114[+dfsg]).
* pma2pme.1: Document new command.
* xtract.1: Add "." (Special -element Operations) and -month
(Miscellaneous Functions).
* Update SEE ALSO references accordingly.
- - - - -
d3ec8d00 by Aaron M. Ucko at 2023-02-08T22:45:24-05:00
Merge tag 'upstream/16.6.20220208+dfsg'
Upstream version 16.6.20220208(+dfsg).
- - - - -
faeb5aa2 by Aaron M. Ucko at 2023-02-10T17:35:47-05:00
Belatedly reflect pm-index's second mandatory argument.
Add corresponding SEE ALSO references with download-ncbi-data, and
reduce debian/changelog's already incomplete description of belated
changes to focus on highlights, this very much included.
- - - - -
9c09aa13 by Aaron M. Ucko at 2023-02-11T23:13:10-05:00
debian/man: Somewhat belatedly acknowledge optional extra indexing.
* index-pubmed.1: New -extras flag.
* pm-index.1: New optional boolean extras argument.
* xtract.1: -e2index now takes a boolean.
- - - - -
b7f00795 by Aaron M. Ucko at 2023-02-11T23:14:53-05:00
d/man/pma2pme.1: Slightly belatedly document author-format options.
- - - - -
1ee4485c by Aaron M. Ucko at 2023-02-11T23:23:05-05:00
debian/man: Update for new release (16.6.20220208[+dfsg]).
* {archive,index}-pubmed.1, pm-stash.1: Document new (-)pma2pme / (-)asn[(.)1]
option.
* efetch.1: Document that esummary takes -mode too.
* pma2pme.1: Document new (-)xml and (-)asn options, and that existing
options can take hyphens too.
* xtract.1: New options -acc, -oct, and -hex (Numeric Processing), and
-basic, -simple, and -prose (reinstated String Processing, to which
-plain and -author have moved); update -author's description.
- - - - -
35277b19 by Aaron M. Ucko at 2023-02-11T23:28:52-05:00
New upstream version 16.6.20220228+dfsg
- - - - -
f4b8dad8 by Aaron M. Ucko at 2023-02-11T23:33:14-05:00
Merge tag 'upstream/16.6.20220228+dfsg'
Upstream version 16.6.20220228(+dfsg).
- - - - -
0d1deb36 by Aaron M. Ucko at 2023-02-12T21:52:26-05:00
d/rules: +{combine,difference}-uid-lists ds2pme gfb2ref ref2pmid
All as-is.
- - - - -
91b833f6 by Aaron M. Ucko at 2023-02-12T22:58:49-05:00
debian/man: More belated tuneups.
* efilter.1: SEE ALSO intersect-uid-lists.
* fetch-pubmed.1: Drop spurious outer brackets in OPTIONS for -strict/-mixed.
* filter-stop-words.1: Escape hyphens in SEE ALSO.
* transmute.1: GenBank -> GenBank/GenPept (-g2x, Data Conversion)
* word-at-a-time.1: SEE ALSO filter-stop-words.
- - - - -
e562eb83 by Aaron M. Ucko at 2023-02-12T23:16:19-05:00
debian/man: Update for new release (16.6.20220228[+dfsg]).
* {combine,difference}-uid-lists.1, ds2pme.1, gbf2ref.1, ref2pmid.1:
Document new commands.
* csv2xml.1: Cover gbf2ref.
* {fetch,stream}-pubmed.1: Add -asn/-xml.
* phrase-search.1: Drop -master alias for -path; add -words and -pairs.
* transmute.1: Add -g2r (Data Conversion).
* xtract.1: Add -page, -auth, -trim, and -wct (all Miscellaneous
Functions) and JSON Record (Special -element Operations)
* Update SEE ALSO links accordingly.
- - - - -
65bf9150 by Aaron M. Ucko at 2023-02-13T22:23:20-05:00
Standards-Version: 4.6.2 (already compliant).
- - - - -
4b158e0a by Aaron M. Ucko at 2023-02-13T22:27:49-05:00
debian/control: Drop golang-any constraint; clean up whitespace.
- - - - -
6ccb994b by Aaron M. Ucko at 2023-02-13T22:29:08-05:00
debian/rules: Remove trailing whitespace.
- - - - -
58017cbf by Aaron M. Ucko at 2023-02-13T22:29:37-05:00
Avoid explicitly specifying -Wl,--as-needed linker flag.
Changes-By: lintian-brush
Fixes: lintian: debian-rules-uses-as-needed-linker-flag
See-also: https://lintian.debian.org/tags/debian-rules-uses-as-needed-linker-flag.html
- - - - -
5c08c81d by Aaron M. Ucko at 2023-02-13T22:34:31-05:00
Finalize ncbi-entrez-direct 16.6.20220228+dfsg-1 for unstable.
Still carefully catching up, but this is at least a specialized leaf
package.
- - - - -
19 changed files:
- README
- accn-at-a-time
- align-columns
- amino-acid-composition
- archive-pubmed
- + asn2xml
- − asp-cp
- − asp-ls
- between-two-genes
- + blst2tkns
- − bt-context.txt
- − bt-link
- − bt-load
- − bt-save
- − bt-srch
- − build.sh
- + cmd/build.sh
- + cmd/go.mod
- + cmd/go.sum
The diff was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/a24923ff4982291dfadebe8589c50d4dba0156c2...5c08c81d23be73dd3892b6c7b9ac057347e4a1f7
--
View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/a24923ff4982291dfadebe8589c50d4dba0156c2...5c08c81d23be73dd3892b6c7b9ac057347e4a1f7
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