[med-svn] [Git][med-team/ncbi-entrez-direct][master] 71 commits: New upstream version 19.3.20230411+dfsg

Aaron M. Ucko (@ucko) gitlab at salsa.debian.org
Thu Apr 10 04:28:00 BST 2025 


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


Commits:
e923eab8 by Aaron M. Ucko at 2024-04-21T13:19:17-04:00
New upstream version 19.3.20230411+dfsg
- - - - -
3dee7edb by Aaron M. Ucko at 2024-04-21T13:21:04-04:00
Merge tag 'upstream/19.3.20230411+dfsg'

Upstream version 19.3.20230411(+dfsg).

- - - - -
9eb801e6 by Aaron M. Ucko at 2024-04-21T13:40:35-04:00
debian/rules: Install new as-is script pmc2bioc.

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002546a5 by Aaron M. Ucko at 2024-04-21T13:41:19-04:00
debian/man: Update for new release (19.3.20230411[+dfsg]).

* pmc2bioc.1: New.
* xtract.1: Add -atr (Tag and Attribute Construction) and
  -test (Validation); clarify -att (Tag and Attribute Construction).

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126c373f by Aaron M. Ucko at 2024-04-21T13:41:38-04:00
New upstream version 19.3.20230421+dfsg
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5bd56384 by Aaron M. Ucko at 2024-04-21T13:42:00-04:00
Merge tag 'upstream/19.3.20230421+dfsg'

Upstream version 19.3.20230421(+dfsg).

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9143d21a by Aaron M. Ucko at 2024-04-21T13:56:54-04:00
elink.1: Belatedly clean up with Perl implementation gone.

-cmd:
* Drop mention of Perl-only llinkslib.
* List score in lieu of neighbor_score per upstream help.
* Fully columnize now that it's sanely possible.
* Consistently end descriptions with periods.

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62ada9ca by Aaron M. Ucko at 2024-04-21T14:15:51-04:00
debian/rules: Install new as-is script pma2apa.

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9d7c5234 by Aaron M. Ucko at 2024-04-21T14:19:59-04:00
New upstream version 19.4.20230424+dfsg
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281ddeae by Aaron M. Ucko at 2024-04-21T15:20:00-04:00
New upstream version 19.4.20230503+dfsg
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530b52e7 by Aaron M. Ucko at 2024-04-21T16:35:30-04:00
debian/man: Update for new release (19.3.20230421[+dfsg]).

* pma2apa.1: New.
* elink.1: Add -cmd edirect.
* Update SEE ALSO links as appropriate.

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c3b75719 by Aaron M. Ucko at 2024-04-21T16:35:42-04:00
Merge tag 'upstream/19.4.20230424+dfsg'

Upstream version 19.4.20230424(+dfsg).

- - - - -
3a6774de by Aaron M. Ucko at 2024-04-21T16:35:43-04:00
rules: New as-is scripts archive-taxonomy and fetch-{local,taxonomy}.

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bb521846 by Aaron M. Ucko at 2024-04-21T16:36:23-04:00
debian/man: Update for new release (19.4.20230424[+dfsg]).

* archive-taxonomy.1, fetch-local.1, fetch-taxonomy.1: New.
* Update SEE ALSO links as appropriate.

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0fedd8d5 by Aaron M. Ucko at 2024-04-21T16:36:29-04:00
Merge tag 'upstream/19.4.20230503+dfsg'

Upstream version 19.4.20230503(+dfsg).

- - - - -
a8671173 by Aaron M. Ucko at 2024-04-21T16:37:34-04:00
debian/man: Update for new release (19.4.20230503[+dfsg]).

* archive-taxonomy.1: New [-]setup mode.
* download-ncbi-data.1: New taxoninfo target.
* Add SEE ALSO links between the two.

- - - - -
a4c168ae by Aaron M. Ucko at 2024-04-21T17:54:29-04:00
New upstream version 19.5.20230508+dfsg
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ee304fb8 by Aaron M. Ucko at 2024-04-21T17:54:59-04:00
Merge tag 'upstream/19.5.20230508+dfsg'

Upstream version 19.5.20230508(+dfsg).

- - - - -
38a17ee6 by Aaron M. Ucko at 2024-04-21T17:58:30-04:00
debian/man/xtract.1: Add -decode (Character Processing).

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29102eee by Aaron M. Ucko at 2024-04-21T17:59:16-04:00
New upstream version 19.6.20230524+dfsg
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d90adda0 by Aaron M. Ucko at 2024-04-21T17:59:43-04:00
Merge tag 'upstream/19.6.20230524+dfsg'

Upstream version 19.6.20230524(+dfsg).

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09d887d5 by Aaron M. Ucko at 2024-04-21T18:03:57-04:00
debian/man/download-pmc.1: New -ftp and -http(s) options.

FTP remains the default.

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b14f7f82 by Aaron M. Ucko at 2024-04-21T18:04:09-04:00
New upstream version 19.6.20230525+dfsg
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5e2a9d8f by Aaron M. Ucko at 2024-04-21T18:04:35-04:00
Merge tag 'upstream/19.6.20230525+dfsg'

Upstream version 19.6.20230525(+dfsg).

- - - - -
7563ce30 by Aaron M. Ucko at 2024-04-21T18:06:15-04:00
New upstream version 19.7.20230531+dfsg
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04e2b8b8 by Aaron M. Ucko at 2024-04-21T18:06:39-04:00
Merge tag 'upstream/19.7.20230531+dfsg'

Upstream version 19.7.20230531(+dfsg).

- - - - -
c5ee42bc by Aaron M. Ucko at 2024-04-21T19:40:10-04:00
debian/rules: Install new as-is script ini2xml.

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ee46c534 by Aaron M. Ucko at 2024-04-21T19:43:43-04:00
New upstream version 19.7.20230602+dfsg
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2b07b0b7 by Aaron M. Ucko at 2024-04-21T19:46:40-04:00
New upstream version 19.8.20230608+dfsg
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4a812db6 by Aaron M. Ucko at 2024-04-21T19:54:24-04:00
New upstream version 19.8.20230628+dfsg
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2a41161a by Aaron M. Ucko at 2024-04-21T21:06:29-04:00
New upstream version 19.9.20230629+dfsg
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37c2521f by Aaron M. Ucko at 2024-04-21T21:07:21-04:00
New upstream version 19.9.20230706+dfsg
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00aa4c0c by Aaron M. Ucko at 2024-04-21T21:09:10-04:00
New upstream version 20.0.20230716+dfsg
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3f36eca6 by Aaron M. Ucko at 2024-04-21T21:14:12-04:00
New upstream version 20.0.20230724+dfsg
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3bca75e0 by Aaron M. Ucko at 2024-04-21T21:15:35-04:00
New upstream version 20.1.20230731+dfsg
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6120e228 by Aaron M. Ucko at 2024-04-21T21:18:50-04:00
New upstream version 20.2.20230822+dfsg
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293524fd by Aaron M. Ucko at 2024-04-21T22:21:46-04:00
debian/man: Update for new release (19.7.20230531[+dfsg]).

* ini2xml.1: New (via csv2xml.1).
* phrase-search.1: Drop -path; an environment setting is now mandatory.
* transmute.1: Add -i2x (Data Conversion).

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22a240e4 by Aaron M. Ucko at 2024-04-21T22:21:46-04:00
Merge tag 'upstream/19.7.20230602+dfsg'

Upstream version 19.7.20230602(+dfsg).

- - - - -
568ea27f by Aaron M. Ucko at 2024-04-21T22:21:47-04:00
Merge tag 'upstream/19.8.20230608+dfsg'

Upstream version 19.8.20230608(+dfsg).

- - - - -
8cea768e by Aaron M. Ucko at 2024-04-21T22:21:47-04:00
debian/man/archive-*.1: Environment settings are now mandatory.

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b2cd1226 by Aaron M. Ucko at 2024-04-21T22:21:47-04:00
Merge tag 'upstream/19.8.20230628+dfsg'

Upstream version 19.8.20230628(+dfsg).

- - - - -
8ee5b5b8 by Aaron M. Ucko at 2024-04-21T22:21:47-04:00
debian/rules: Add pmc2info (as is); drop index-pubmed (retired).

Take the opportunity to correct this changelog stanza's debian/rules
placement.

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a4d3a3de by Aaron M. Ucko at 2024-04-21T22:21:47-04:00
debian/man: Update for new release (19.8.20230628[+dfsg]).

* Substitute EDIRECT_LOCAL_{MASTER,WORKING} for traditional
  resource-specific variables (e.g. EDIRECT_PUBMED_*).
* Reflect index-pubmed's retirement, citing archive-pubmed instead as
  appropriate.
* archive-pubmed.1: Add [-]scour.
* pmc2info.1: New.
* xtract.1: Add -alpha (Character Processing).
* Update SEE ALSO accordingly.

- - - - -
fb87a703 by Aaron M. Ucko at 2024-04-21T22:21:47-04:00
Merge tag 'upstream/19.9.20230629+dfsg'

Upstream version 19.9.20230629(+dfsg).

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94015a1e by Aaron M. Ucko at 2024-04-21T22:21:47-04:00
Merge tag 'upstream/19.9.20230706+dfsg'

Upstream version 19.9.20230706(+dfsg).

- - - - -
a2ed7ef8 by Aaron M. Ucko at 2024-04-21T22:21:47-04:00
Merge tag 'upstream/20.0.20230716+dfsg'

Upstream version 20.0.20230716(+dfsg).

- - - - -
5114dffe by Aaron M. Ucko at 2024-04-21T22:21:47-04:00
archive-pmc.1: Add [-]scour, [-]ftp (default), and [-]http[s].

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ee8c019d by Aaron M. Ucko at 2024-04-21T22:21:47-04:00
Merge tag 'upstream/20.0.20230724+dfsg'

Upstream version 20.0.20230724(+dfsg).

- - - - -
5f87f02d by Aaron M. Ucko at 2024-04-21T22:21:47-04:00
Merge tag 'upstream/20.1.20230731+dfsg'

Upstream version 20.1.20230731(+dfsg).

- - - - -
55100ac3 by Aaron M. Ucko at 2024-04-21T22:21:48-04:00
Merge tag 'upstream/20.2.20230822+dfsg'

Upstream version 20.2.20230822(+dfsg).

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2a3a1c0c by Aaron M. Ucko at 2024-04-21T22:21:48-04:00
New Go dependencies: GH/goccy/go-yaml, hence GL/x/xerrors.

* debian/control: Add a B-D on golang-github-goccy-go-yaml-dev.
* debian/rules: Enable use of github.com/goccy/go-yaml
  and (indirectly, no B-D needed) golang.org/x/xerrors.

- - - - -
876dfc5d by Aaron M. Ucko at 2024-04-21T22:21:48-04:00
debian/rules: New as-is scripts gm2segs and yaml2xml.

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711b267d by Aaron M. Ucko at 2024-04-21T22:21:48-04:00
debian/man: Update for new release (20.2.20230822[+dfsg]).

* archive-pubmed.1: Add [-]stem[med].
* archive-taxonomy.1: Zap [-]zap. ;-)
* expand-current.1: Environment settings are now mandatory.
* gm2segs.1: New.
* xtract.1: Add alternative substring element construct; substitute
  -journal (String Processing) for -jour (Citation Functions).
* yaml2xml.1: New (via csv2xml.1).
* Update SEE ALSO as appropriate.

- - - - -
3ed30732 by Aaron M. Ucko at 2024-04-22T15:08:59-04:00
New upstream version 20.3.20230829+dfsg
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d02178fa by Aaron M. Ucko at 2024-04-22T15:09:42-04:00
Merge tag 'upstream/20.3.20230829+dfsg'

Upstream version 20.3.20230829(+dfsg).

- - - - -
df5cec7e by Aaron M. Ucko at 2024-04-22T15:11:53-04:00
debian/man/archive-pmc.1: Zap [-]zap. ;-)

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760893ee by Aaron M. Ucko at 2024-04-22T15:12:05-04:00
New upstream version 20.3.20230908+dfsg
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91a9b355 by Aaron M. Ucko at 2024-04-22T15:12:32-04:00
Merge tag 'upstream/20.3.20230908+dfsg'

Upstream version 20.3.20230908(+dfsg).

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6b10a700 by Aaron M. Ucko at 2024-04-22T15:19:42-04:00
xtract.1: Update for new release (20.3.20230908[+dfsg]]).

In Entrez Indexing, add -indexer and drop -indices, -article,
-abstract, -paragraph, and -stemmed.

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59d006d2 by Aaron M. Ucko at 2024-04-22T15:20:07-04:00
Merge tag 'upstream/20.4.20230911+dfsg'

Upstream version 20.4.20230911+dfsg

- - - - -
d23b8bdd by Aaron M. Ucko at 2024-04-22T15:20:07-04:00
New upstream version 20.4.20230911+dfsg
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6fa7032d by Aaron M. Ucko at 2024-04-22T16:42:47-04:00
Account for github.com/komkom/toml and its dependency tree.

* debian/control: Add a B-D on golang-github-komkom-toml-dev.
* debian/rules: Enable use of github.com/komkom/toml and (indirectly,
  no B-Ds needed) github.com/pkg/errors and
  github.com/stretchr/{objx,testify}.

- - - - -
ee90057d by Aaron M. Ucko at 2024-04-22T16:45:36-04:00
debian/man/transmute.1: Add -m2x and -y2x (Data Conversion).

- - - - -
e5ce7471 by Aaron M. Ucko at 2025-04-02T20:59:49-04:00
New upstream version 23.7.20250401+dfsg
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ba9e4e1f by Aaron M. Ucko at 2025-04-02T21:00:47-04:00
Merge tag 'upstream/23.7.20250401+dfsg'

Upstream version 23.7.20250401(+dfsg).

- - - - -
cf0775c2 by Aaron M. Ucko at 2025-04-08T22:09:12-04:00
New upstream version 23.8.20250408+dfsg
- - - - -
45e1e696 by Aaron M. Ucko at 2025-04-08T22:10:48-04:00
Merge tag 'upstream/23.8.20250408+dfsg'

Upstream version 23.8.20250408(+dfsg).

- - - - -
506169f8 by Aaron M. Ucko at 2025-04-08T22:41:33-04:00
Abandon manpages for now; note it in NEWS.

* debian/NEWS: Note that manpages are at least temporarily out of the
  picture to reduce maintenance overhead.
* debian/manpages: Rename to manpages.disabled for now.

- - - - -
5ac9ccdf by Aaron M. Ucko at 2025-04-09T23:15:04-04:00
Reflect upstream additions and removals over the past year or two.

* debian/control: Suggest golang-any for the sake of scripts that
  build specialized binaries on the fly.
* debian/install: Install new data tree to ncbi-entrez-direct; also
  throw in eutils and extern for the sake of scripts that build
  specialized binaries on the fly.
* debian/rules:
  - Install new as-is scripts bsmp2info, ecollect, filter-record, fsa2xml,
    gff-sort, gff2xml, jsonl2xml, just-top-hits, pair-at-a-time,
    print-missing-subranges, quote-grouped-elements, refseq-nm-cds,
    sort-by-length, and systematic-mutations.
  - Install all download-* and gbf2* scripts as is, including some new
    ones.
  - Install all archive-* scripts (including some new ones) and the new
    local-archive scripts xfetch, xfilter, xinfo, xlink, and xsearch with
    library-directory substitutions.
  - Reflect upstream retirement of fetch-*, index-extras, index-pubmed,
    phrase-search, and stream-pubmed, superseded by xfetch et al.

- - - - -
c4c9257e by Aaron M. Ucko at 2025-04-09T23:19:41-04:00
debian/.gitignore: Ignore .debhelper.

- - - - -
b2bd3bde by Aaron M. Ucko at 2025-04-09T23:21:38-04:00
Finalize ncbi-entrez-direct 23.8.20250408+dfsg-1 for experimental.

- - - - -


210 changed files:

- + LICENSE
- README
- align-columns
- + archive-nihocc
- + archive-nlmnlp
- + archive-nmcds
- + archive-pids
- archive-pmc
- archive-pubmed
- + archive-taxonomy
- + args2slice
- + bsmp2info
- cit2pmid
- cmd/build.sh
- cmd/edict.go
- cmd/go.mod
- cmd/go.sum
- cmd/rchive.go
- cmd/transmute.go
- cmd/xtract.go
- custom-index
- + data/unicode-ascii.txt
- help/unicode-extras.txt → data/unicode-extra.txt
- debian/.gitignore
- debian/NEWS
- debian/changelog
- debian/control
- debian/install
- debian/man/archive-pmc.1
- debian/man/archive-pubmed.1
- + debian/man/archive-taxonomy.1
- debian/man/cit2pmid.1
- debian/man/csv2xml.1
- debian/man/custom-index.1
- debian/man/download-ncbi-data.1
- debian/man/download-pmc.1
- debian/man/download-pubmed.1
- debian/man/edict.1
- debian/man/efetch.1
- debian/man/elink.1
- debian/man/expand-current.1
- + debian/man/fetch-local.1
- debian/man/fetch-pmc.1
- debian/man/fetch-pubmed.1
- + debian/man/fetch-taxonomy.1
- + debian/man/gm2segs.1
- debian/man/index-extras.1
- − debian/man/index-pubmed.1
- + debian/man/ini2xml.1
- debian/man/phrase-search.1
- debian/man/pm-collect.1
- debian/man/pm-prepare.1
- debian/man/pm-refresh.1
- + debian/man/pma2apa.1
- debian/man/pma2pme.1
- + debian/man/pmc2bioc.1
- + debian/man/pmc2info.1
- debian/man/rchive.1
- debian/man/stream-pubmed.1
- debian/man/theme-aliases.1
- debian/man/transmute.1
- debian/man/xtract.1
- + debian/man/yaml2xml.1
- debian/manpages → debian/manpages.disabled
- debian/rules
- disambiguate-nucleotides
- + download-flatfile
- download-ncbi-data
- download-ncbi-software
- download-pmc
- download-pubmed
- download-sequence
- + ecollect
- ecommon.sh
- edirect.py
- efetch
- efilter
- einfo
- elink
- epost
- esample
- esearch
- esummary
- eutils/align.go
- eutils/asn.go
- eutils/cache.go
- eutils/chan.go
- eutils/citref.go
- eutils/clean.go
- + eutils/eutils_test.go
- eutils/fasta.go
- eutils/format.go
- eutils/gbff.go
- eutils/gcode.go
- eutils/gdata.go
- eutils/go.mod
- eutils/go.sum
- eutils/hgvs.go
- eutils/index.go
- + eutils/ini.go
- + eutils/insd.go
- eutils/json.go
- eutils/merge.go
- eutils/misc.go
- eutils/molwt.go
- eutils/normal.go
- eutils/phrase.go
- eutils/poster.go
- eutils/search.go
- eutils/spdi.go
- eutils/table.go
- + eutils/text.go
- + eutils/toml.go
- + eutils/transmute_test.go
- eutils/trie.go
- eutils/utils.go
- eutils/valid.go
- eutils/xml.go
- + eutils/xparse.go
- eutils/xplore.go
- + eutils/xtract_test.go
- + eutils/yaml.go
- expand-current
- + extern/build.sh
- + extern/prep-finish.go
- + extern/prep-geneinfo.go
- + extern/prep-generif.go
- + extern/prep-nihocc.go
- + extern/prep-nlmnlp.go
- + extern/prep-taxoninfo.go
- − fetch-pmc
- − fetch-pubmed
- filter-columns
- index-pubmed → filter-genbank
- + filter-record
- + fsa2xml
- fuse-segments
- + gbf2facds
- + gbf2fsa
- + gbf2info
- + gff-sort
- + gff2xml
- + gm2segs
- help/efetch-help.txt
- help/efilter-help.txt
- help/einfo-errors.txt
- help/elink-help.txt
- help/nquire-help.txt
- help/phrase-search-extras.txt
- help/phrase-search-help.txt
- help/rchive-help.txt
- help/transmute-help.txt
- help/tst-efetch.txt
- help/tst-elink.txt
- help/tst-esearch.txt
- help/tst-esummary.txt
- help/xtract-examples.txt
- help/xtract-help.txt
- help/xtract-unix.txt
- hgvs2spdi
- idx-auid
- + idx-doi
- + idx-errors
- + idx-grant
- idx-stemmed
- − index-extras
- + ini2xml
- join-into-groups-of
- + jsonl2xml
- + just-top-hits
- nhance.sh
- nquire
- + pair-at-a-time
- − phrase-search
- + pm-clean
- pm-prepare
- pm-refresh
- + pm-setup
- + pma2apa
- + pmc2bioc
- + pmc2info
- print-columns
- + print-missing-subranges
- + quote-grouped-elements
- rchive
- + refseq-nm-cds
- snp2tbl
- + sort-by-length
- − stream-pubmed
- + systematic-mutations
- tbl2prod
- test-edirect
- test-eutils
- test-pmc-index
- test-pubmed-index
- − theme-aliases
- + toml2xml
- transmute
- + xcommon.sh
- + xfetch
- + xfetch.ini
- + xfilter
- + xinfo
- + xlink
- xml2fsa
- xml2tbl
- + xsearch
- xtract
- xy-plot
- + yaml2xml


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View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/1845bd9aafe987fae9686c818e78be07885e7210...b2bd3bdec504f146bbee134bc8da276511e25265

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