[med-svn] [Git][med-team/ncbi-entrez-direct][master] 15 commits: New upstream version 23.8.20250429+dfsg
Aaron M. Ucko (@ucko)
gitlab at salsa.debian.org
Mon May 26 17:02:56 BST 2025
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-entrez-direct
Commits:
18ae4204 by Aaron M. Ucko at 2025-05-01T23:00:11-04:00
New upstream version 23.8.20250429+dfsg
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48271b21 by Aaron M. Ucko at 2025-05-18T22:19:05-04:00
New upstream version 23.9.20250512+dfsg
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708ecd27 by Aaron M. Ucko at 2025-05-18T22:22:04-04:00
Merge tag 'upstream/23.9.20250512+dfsg'
Upstream version 23.9.20250512(+dfsg).
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a2bef797 by Aaron M. Ucko at 2025-05-18T22:25:18-04:00
New upstream version 23.9.20250518+dfsg
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ef3a430c by Aaron M. Ucko at 2025-05-18T22:25:48-04:00
Merge tag 'upstream/23.9.20250518+dfsg'
Upstream version 23.9.20250518(+dfsg).
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8533ada9 by Aaron M. Ucko at 2025-05-23T15:04:55-04:00
New upstream version 23.9.20250520+dfsg
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c94e203e by Aaron M. Ucko at 2025-05-23T15:05:52-04:00
Merge tag 'upstream/23.9.20250520+dfsg'
Upstream version 23.9.20250520(+dfsg).
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7c5fb8e0 by Aaron M. Ucko at 2025-05-23T15:06:37-04:00
New upstream version 24.0.20250522+dfsg
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7e9ef643 by Aaron M. Ucko at 2025-05-23T15:07:11-04:00
Merge tag 'upstream/24.0.20250522+dfsg'
Upstream version 24.0.20250522(+dfsg).
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a382716c by Aaron M. Ucko at 2025-05-23T15:34:36-04:00
Make *.ini available in /etc/ncbi and (indirectly) /u/s/n-e-d.
* debian/install: Install *.ini to /etc/ncbi.
* debian/links: Symlink them into /usr/lib/ncbi-entrez-direct.
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fc5c88a3 by Aaron M. Ucko at 2025-05-23T15:43:03-04:00
debian/rules: Pull out previously missed [EX]COMMON_SCRIPTS.
Move ecollect to ECOMMON_SCRIPTS and cit2pmid, pm-clean, pm-prepare,
and pm-setup to XCOMMON_SCRIPTS, in all cases from AS_IS_SCRIPTS, so
they know to look in /usr/lib/ncbi-entrez-direct as needed, at minimum
for [ex]common.sh.
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08f679c6 by Aaron M. Ucko at 2025-05-25T21:55:17-04:00
New upstream version 24.0.20250523+dfsg
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5b160b69 by Aaron M. Ucko at 2025-05-25T21:55:47-04:00
Merge tag 'upstream/24.0.20250523+dfsg'
Upstream version 24.0.20250523(+dfsg).
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ef863917 by Aaron M. Ucko at 2025-05-26T11:55:02-04:00
Bring manpages back up to date and install them again.
* Substitute EDIRECT_LOCAL_ARCHIVE for EDIRECT_LOCAL_MASTER.
* Update and symmetrize SEE ALSO, bypassing csv2xml's aliases.
* Various minor copy-editing; in particular, always escape - as needed.
* archive-{nihocc,nlmnlp,nmcds,pids}.1: New since last overall update
(for 20.4.20230911[+dfsg]).
* archive-pmc.1: Add (-)download, (-)verify, (-)missing, (-)stem(med),
(-)scrap, (-)erase, (-)zap, and -info; drop -path and -temp/-work(ing)
(already absent from SYNOPSIS); update (-)scour's scope.
* archive-pubmed.1: Add (-)download, (-)verify, (-)missing, (-)scrap,
(-)erase), (-)zap, and -info; drop (-)pma2pme/(-)asn([.]1),
(-)stem(med), (-)biocoll/(-)extras/(-)bioconcepts/(-)generifs, and
(-)nihocc; update (-)scour's scope.
* archive-taxonomy.1: Add (-)scour, (-)erase, (-)zap, and -info; drop
-setup.
* {args2slice,bsmp2info}.1: New since last overall update.
* cit2pmid.1: Refer to new xsearch -exact rather than old phrase-search.
* csv2xml.1: Add fsa2xml (transmute -f2x) and toml2xml (transmute -m2x);
move yaml2xml down for correct alphabetical ordering.
* {download-flatfile,ecollect}.1: New since last overall update.
* efetch.1 (-mode): Add binary; substitute asn for asn.1.
* elink.1: Add -command uid.
* esample.1: Add -gff.
* fetch-*.1: Delete (command gone upstream since last overall update).
* {filter-{genbank,record},fsa2xml,gbf2{facds,fsa,info,tbl},gff-sort,
gff2xml}.1: New since last overall update.
* gm2segs.1: Note that -1-based is default.
* index-extras.1: Delete (command gone upstream since last overall update).
* join-into-groups-of.1: There's now a default group size, namely 10,000.
* {jsonl2xml,just-top-hits}.1: New since last overall update.
* nquire.1: Add -datasets (https://api.ncbi.nlm.nih.gov/datasets/v2alpha).
* pair-at-a-time.1: New since last overall update.
* phrase-search.1: Delete (command gone upstream since last overall update).
* pm-clean.1: New since last overall update.
* pm-prepare.1: Take -db rather than explicit directory names; note
broadened scope.
* pm-setup.1: New since last overall update.
* {print-missing-subranges,quote-grouped-elements,refseq-nm-cds,
sort-by-length}.1: New since last overall update.
* stream-pubmed.1: Delete (command gone upstream since last overall update).
* systematic-mutations.1: New since last overall update.
* theme-aliases.1: Delete (command gone upstream since last overall update).
* transmute.1:
- Add -f2p, -m2x (toml2xml), -txf (filter-record), -f2x (fsa2xml), and
-gbf (filter-genbank), all under Data Conversion except -f2p
(under Pretty-Printing).
- Under -align (Pretty-Printing), add -a w.
- Under -extract (Sequence Editing), note that -1-based and -0-based
are mutually exclusive and consistently list all subarguments or
none as appropriate.
- Under -cds2prot (Sequence Processing), add -all (as an alternative
to -frame), -between, -circular, -orf, and -max, and rename -code
to -gcode.
- Under -molwt (Sequence Processing), add -fmet as an alternative to
-met.
* {xfetch,xfilter,xinfo,xlink,xsearch}.1: New since last overall update.
* xtract.1:
- Add -mimics, -excludes, and -consists-of (String Constraints);
FASTA Parsable Fields (-bkt); -even and -odd (Element Selection);
-geo, -hrm, -rms, -sqt, -lge, -lg2, and -log (Numeric [Integer]
Processing, with a newly clarified title); -split and -pentamers
(Text Processing); -accession and -numeric (Citation Functions);
-cds2prot (Nucleotide Processing, split from Sequence Processing);
-molwt-m/-f and -pept (Protein Processing, likewise split); and
-insdx (Command Generator).
- Drop -e2index (Entrez Indexing).
- Include -revcomp, -nucleic, and -ncbi{2,4}na in split-out
Nucleotide Processing and -molwt in split-out Protein Processing.
* debian/manpages: Rename back from manpages.disabled.
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c627bfbb by Aaron M. Ucko at 2025-05-26T11:58:00-04:00
Finalize ncbi-entrez-direct 24.0.20250523+dfsg-1 for unstable.
Note that as with 19.0.20230216(+dfsg), the nominal major version bump
isn't as meaningful as it might appear.
- - - - -
131 changed files:
- README
- archive-pids
- archive-pmc
- archive-pubmed
- cmd/go.mod
- cmd/go.sum
- cmd/rchive.go
- cmd/transmute.go
- cmd/xtract.go
- debian/changelog
- debian/install
- + debian/links
- debian/man/accn-at-a-time.1
- debian/man/align-columns.1
- + debian/man/archive-nihocc.1
- + debian/man/archive-nlmnlp.1
- + debian/man/archive-nmcds.1
- + debian/man/archive-pids.1
- debian/man/archive-pmc.1
- debian/man/archive-pubmed.1
- debian/man/archive-taxonomy.1
- + debian/man/args2slice.1
- debian/man/asn2ref.1
- debian/man/between-two-genes.1
- + debian/man/bsmp2info.1
- debian/man/cit2pmid.1
- debian/man/combine-uid-lists.1
- debian/man/csv2xml.1
- debian/man/custom-index.1
- debian/man/difference-uid-lists.1
- debian/man/disambiguate-nucleotides.1
- + debian/man/download-flatfile.1
- debian/man/download-ncbi-data.1
- debian/man/download-pmc.1
- debian/man/download-pubmed.1
- debian/man/download-sequence.1
- debian/man/ds2pme.1
- + debian/man/ecollect.1
- debian/man/edict.1
- debian/man/efetch.1
- debian/man/efetch.ncbi.1
- debian/man/efilter.1
- debian/man/einfo.ncbi.1
- debian/man/elink.1
- debian/man/epost.1
- debian/man/esample.1
- debian/man/esearch.1
- debian/man/esummary.1
- debian/man/exclude-uid-lists.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/filter-columns.1
- + debian/man/filter-genbank.1
- + debian/man/filter-record.1
- debian/man/filter-stop-words.1
- + debian/man/fsa2xml.1
- + debian/man/gbf2facds.1
- + debian/man/gbf2fsa.1
- + debian/man/gbf2info.1
- + debian/man/gbf2tbl.1
- debian/man/gene2range.1
- + debian/man/gff-sort.1
- + debian/man/gff2xml.1
- debian/man/gm2segs.1
- − debian/man/index-extras.1
- debian/man/intersect-uid-lists.1
- debian/man/join-into-groups-of.1
- + debian/man/jsonl2xml.1
- + debian/man/just-top-hits.1
- debian/man/nquire.1
- + debian/man/pair-at-a-time.1
- − debian/man/phrase-search.1
- + debian/man/pm-clean.1
- debian/man/pm-prepare.1
- debian/man/pm-refresh.1
- + debian/man/pm-setup.1
- debian/man/pma2apa.1
- debian/man/pma2pme.1
- debian/man/pmc2bioc.1
- debian/man/pmc2info.1
- debian/man/print-columns.1
- + debian/man/print-missing-subranges.1
- + debian/man/quote-grouped-elements.1
- debian/man/rchive.1
- debian/man/ref2pmid.1
- + debian/man/refseq-nm-cds.1
- debian/man/reorder-columns.1
- debian/man/snp2tbl.1
- + debian/man/sort-by-length.1
- debian/man/sort-table.1
- debian/man/sort-uniq-count-rank.1
- debian/man/sort-uniq-count.1
- debian/man/spdi2tbl.1
- − debian/man/stream-pubmed.1
- + debian/man/systematic-mutations.1
- − debian/man/theme-aliases.1
- debian/man/transmute.1
- debian/man/uniq-table.1
- debian/man/word-at-a-time.1
- + debian/man/xfetch.1
- + debian/man/xfilter.1
- + debian/man/xinfo.1
- + debian/man/xlink.1
- debian/man/xml2fsa.1
- debian/man/xml2tbl.1
- + debian/man/xsearch.1
- debian/man/xtract.1
- debian/man/xy-plot.1
- debian/manpages.disabled → debian/manpages
- debian/rules
- ecommon.sh
- efetch
- einfo
- eutils/eutils_test.go
- eutils/format.go
- eutils/go.mod
- eutils/go.sum
- eutils/misc.go
- eutils/utils.go
- eutils/xplore.go
- gbf2info
- help/tst-elink.txt
- help/xtract-help.txt
- nquire
- xcommon.sh
- xfetch
- xlink
- + xlink.ini
The diff was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/83771ff4ebea759e23b002809ce9bacd89760c51...c627bfbbb1ce6d7958f078d2820c1b30d92f12c3
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View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/83771ff4ebea759e23b002809ce9bacd89760c51...c627bfbbb1ce6d7958f078d2820c1b30d92f12c3
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