-
ncbi-entrez-direct (13.7.20200713+dfsg-1) unstable; urgency=medium
* New upstream release.
* debian/man/{accn-at-a-time,g2x}.1: Document new commands.
* debian/man/{gbf2xml,word-at-a-time,xtract}.1: Update for new release.
* debian/rules:
- Account for new as-is script accn-at-a-time, new Go executable g2x, and
gbf2xml's switch from a Perl script to an as-is script (wrapping xtract).
- Belatedly arrange to tweak enquire, whose --ca* options won't do here.
-- Aaron M. Ucko <email address hidden> Tue, 14 Jul 2020 22:17:15 -0400
-
ncbi-entrez-direct (13.7.20200615+dfsg-2) unstable; urgency=medium
* debian/rules: Install ftp-cp, ftp-ls, nquire, and transmute as simple
wrappers for edirect (with no .pl suffix) now that they're no longer
independent Perl scripts (as of 12.3.20191024[+ds]), fixing a
regression caught by autopkgtest.
* debian/tests/run-unit-test: Correct invocation of filter-stop-words
(which ignores its arguments and reads from standard input).
-- Aaron M. Ucko <email address hidden> Sun, 28 Jun 2020 21:11:51 -0400
-
ncbi-entrez-direct (13.1.20200102+dfsg-1) unstable; urgency=medium
* New upstream release.
* .gitignore: Ignore new "saved" directory.
* debian/control: Suggest curl (for index-extras).
* debian/copyright: Add *.pdf (sourceless) to Files-Excluded.
* debian/examples: Remove Scripps BioThings support, now considered official
enough (mentioned in README, albeit as experimental).
* debian/install: Install bt-*.txt and hlp-*.txt (bt-context.txt and
hlp-xtract.txt at present) to a new /usr/lib/ncbi-entrez-direct directory.
* debian/man/{archive-pubmed,download-ncbi-data,edirect,efetch,elink,esample,
esearch,ftp-cp,fetch-pubmed,ftp-ls,index-pubmed,j2x,join-into-groups-of,
nquire,phrase-search,rchive,sort-uniq-count,transmute,xtract}.1: Update for
new release.
* debian/man/{bt-link,bt-load,bt-save,bt-srch,expand-current,fetch-extras,
t2x,xplore}.1: Document new commands.
* debian/man/efetch.1: Correct old paste-o in -chr_stop's description.
* debian/man/fetch-pubmed.1: Belatedly wordsmith description of -path.
* debian/man/index-extras.1: Rename from index-bioc.1 and update.
* debian/man/nquire.1: Belatedly drop accidental self-referential SEE ALSO.
* debian/man/xtract.1: Explicitly mark suboptions as such; belatedly resync
-indices' description.
* debian/rules:
- Account for new as-is scripts expand-current and fetch-extras; 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); for new Go executable t2x; and for rename of as-is script
index-bioc to index-extras (which moreover needs its interpreter
specification corrected to #!/bin/bash via a new generic mechanism).
- Move the xtract binary from /usr/bin to /usr/lib/ncbi-entrez-direct (so
it can find hlp-xtract.txt) and substitute a wrapper script.
- Broaden .../x/sys/unix to .../x/sys in GOLIBSRC(_). (Closes: #963439.)
- 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.)
* debian/watch: Change repack suffix to +dfsg due to the additional need
to exclude sourceless PDF documents.
-- Aaron M. Ucko <email address hidden> Sun, 21 Jun 2020 22:32:39 -0400
-
ncbi-entrez-direct (12.0.20190816+ds-2) unstable; urgency=medium
* Team upload
* Add autopkgtests
-- Pranav Ballaney <email address hidden> Wed, 06 May 2020 19:11:16 +0530
-
ncbi-entrez-direct (12.0.20190816+ds-1) unstable; urgency=medium
[ Aaron M. Ucko ]
* New upstream release. (Not fully caught up, but uploading anyway to
address an FTBFS bug that turned up.)
* debian/control:
- Build-depend on github-gedex-inflector-dev.
- Declare a nominal XS-Go-Import-Path to placate dh-golang.
* debian/examples: Install BioThings support as examples for now: bt-*
(including one data file currently expected to live alongside scripts)
and xplore.
* debian/man/{download-ncbi-data,esample,exclude-uid-lists,index-bioc,j2x,
pm-collect,xml2tbl}.1: Document new commands.
* debian/man/{download-{pubmed,sequence},efetch,efilter,esearch,fetch-pubmed,
ftp-{cp,ls},index-pubmed,intersect-uid-lists,nquire,pm-index,rchive,
transmute,xtract}.1: Update for new release.
* debian/man/download-sequence.1: Fix copy-and-paste error (wrong name
left in DESCRIPTION).
* debian/rules:
- Belatedly use FIX_PERL_SHEBANG for bin/edirect.
- Factor out GH and GL macros for github.com and golang.org respectively.
- Factor out a pattern rule for building Go executables (and a
supporting rule for the gounidecode compatibility symlink).
- Add $(GH)/gedex/inflector to GOLIBSRC_ (for xtract).
- Account for new download script download-ncbi-data; as-is scripts
esample, exclude-uid-lists, index-bioc, pm-collect, and xml2tbl; and Go
executable j2x (which does not use common.go).
- Set GOCACHE to avoid needing a writable (or simply existent!) HOME;
wipe the cache in override_dh_auto_clean. (Closes: 947995.)
* .gitignore: Ignore the new go-cache tree.
[ Andreas Tille ]
* d/watch: simplify + version=4
* Standards-Version: 4.5.0 (routine-update)
* debhelper-compat 12 (routine-update)
-- Aaron M. Ucko <email address hidden> Sun, 02 Feb 2020 22:02:43 -0500
