ncbi-entrez-direct (19.2.20230331+dfsg-1) experimental; urgency=medium * New upstream point release, still to experimental. * debian/man/xtract.1: Update for new release. -- Aaron M. Ucko Fri, 31 Mar 2023 17:53:02 -0400 ncbi-entrez-direct (19.2.20230330+dfsg-1) experimental; urgency=medium * New upstream incremental release; initially uploading to experimental to be extra sure the changes are all safe. * debian/control: Belatedly suggest unzip. * debian/examples: List new scripts blst2gm and gm2ranges here, at least for now. * debian/man/{archive-pubmed,download-ncbi-data}.1: Update for new release. -- Aaron M. Ucko Thu, 30 Mar 2023 23:26:38 -0400 ncbi-entrez-direct (19.0.20230216+dfsg-2) unstable; urgency=medium * Upload to unstable. (Don't read too much into the version number difference -- upstream has a low threshold for bumping the second component, and has been keeping it to a single digit. Also, many of the code changes are refactoring and similar formalities, and as previously noted this is a specialized leaf package.) -- Aaron M. Ucko Wed, 01 Mar 2023 18:11:52 -0500 ncbi-entrez-direct (19.0.20230216+dfsg-1) experimental; urgency=medium * New upstream release; uploading to experimental, at least for now. * debian/control: Add B-Ds on golang-github-gin-gonic-gin-dev and golang-github-klauspost-pgzip-dev. * debian/{efetch,einfo}: Recognize new common flags -verbose and -tranquil. * debian/install: Install new nhance.sh helper to /usr/lib/n-e-d. * debian/man/{archive-pubmed,combine-uid-lists,csv2xml,download-ncbi-data, download-pubmed,download-sequence,efilter,esearch,fetch-pubmed, index-pubmed,nquire,phrase-search,pm-collect,pm-prepare,pm-stash,rchive, ref2pmid,transmute,xtract}.1: Update for new release. * debian/man/{asn2ref,cit2pmid,edict,scn2xml}.1: Document new commands. * debian/man/{pm-index,pm-invert,pm-merge,pm-promote,pm-stash}.1: Retire. * debian/rules: - Account for use of github.com/gin-gonic/gin and its dependency tree and of github.com/klauspost/pgzip and its dependency github.com/klauspost/compress. - Install new as-is scripts archive-pmc, asn2ref, cit2pmid, download-pmc, fetch-pmc, and scn2xml. - Install new binary edict, unwrapped. -- Aaron M. Ucko Sun, 26 Feb 2023 16:55:42 -0500 ncbi-entrez-direct (16.6.20220228+dfsg-2) unstable; urgency=medium * debian/tests/control: Depend on libxml-simple-perl for the private script behind transmute -x2j. -- Aaron M. Ucko Tue, 14 Feb 2023 07:47:26 -0500 ncbi-entrez-direct (16.6.20220228+dfsg-1) unstable; urgency=medium * New(er) upstream release. (Still carefully catching up, but this is at least a specialized leaf package.) * debian/.gitignore: Additionally ignore edirect.py (a transient non-executable copy) and ncbi-entrez-direct.*.debhelper. * debian/README.Debian (new): Document asn2xml's status. * 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. - 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.) - Standards-Version: 4.6.2 (already compliant). - Drop golang-any constraint, satisfied even in oldstable. - Clean up whitespace (a hard tab slipped in at one point). * debian/{efetch,einfo}: - Resync %ncbi_supported; in particular, belatedly add explicit -ext(ernal) and efetch's -plus, -reverse, and -minus aliases (all undocumented). - Recognize new common -immediate and -express flags. * debian/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. - Add idx-*. * 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. - Install help files to /usr/lib/ncbi-entrez-direct/help. * debian/man/*.1: Various belated corrections and formal cleanups. In particular, fix typos in nquire.1 and xtract.1 and note that pm-index takes a second mandatory argument these days. * 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. * debian/man/{blst2tkns,combine-uid-lists,csv2xml,custom-index, difference-uid-lists,disambiguate-nucleotides,download-ncbi-software, ds2pme,filter-columns,find-in-gene,fuse-ranges,fuse-segments,gbf2ref, hgvs2spdi,json2xml,pma2pme,print-columns,ref2pmid,snp2hgvs,snp2tbl, sort-table,spdi2tbl,split-at-introns,tbl2prod,tbl2xml,uniq-table, xml2fsa}.1: Document new commands, with csv2xml.1 now covering all *2xml wrappers and gbf2ref. * debian/man/{archive-pubmed,download-ncbi-data,download-pubmed, download-sequence,efetch,efilter,einfo,elink,epost,esample,esearch, exclude-uid-lists,fetch-pubmed,filter-stop-words,gene2range,index-extras, index-pubmed,intersect-uid-lists,nquire,phrase-search,pm-index,pm-stash, rchive,reorder-columns,run-ncbi-converter,sort-table,stream-pubmed, transmute,word-at-a-time,xml2tbl,xtract}.1: Update for new release. * debian/man/{eaddress,eblast,ecitmatch,econtact,edirect,edirutil,enotify, entrez-phrase-search,eproxy,espell,ftp-cp,ftp-ls,protein-neighbors}.1: Retire. * debian/ncbi-entrez-direct.pyinstall (new): List debian/edirect.py. * debian/rules: - Reflect upstream retirement of eaddress, eblast, ecitmatch, econtact, edirect, 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. - Install new as-is scripts blst2tkns, combine-uid-lists, csv2xml, custom-index, difference-uid-lists, disambiguate-nucleotides, download-ncbi-software, ds2pme, filter-columns, find-in-gene, fuse-ranges, fuse-segments, gbf2ref, gene2range, hgvs2spdi, json2xml, pma2pme, print-columns, ref2pmid, snp2hgvs, snp2tbl, sort-table, spdi2tbl, split-at-intron, tbl2prod, tbl2xml, uniq-table, and xml2fsa. - Have esummary run efetch.ncbi directly so the wrapper can't interfere with its dedicated -help output. - 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.) - Account for direct use of github.com/rainycape/unidecode (no more need to pass it off as github.com/fiam/gounidecode/unidecode). - 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. - Additionally enable the python3 build system. - Transiently supply a non-executable(!) copy of edirect.py in debian/. - Remove trailing whitespace. - Avoid explicitly specifying -Wl,--as-needed linker flag. -- Aaron M. Ucko Mon, 13 Feb 2023 22:34:31 -0500 ncbi-entrez-direct (14.6.20210224+dfsg-7) unstable; urgency=medium * Team upload. * Revert "Pass right location of gopsutil/mem" + gopsutil reverted their import-path change -- Nilesh Patra Fri, 24 Jun 2022 21:11:32 +0530 ncbi-entrez-direct (14.6.20210224+dfsg-6) unstable; urgency=medium * Team upload. * d/rules: Pass right location of gopsutil/mem (Closes: #1013608) + gopsutil had been upgraded to new major upstream release with changed location, updated accordingly -- Nilesh Patra Fri, 24 Jun 2022 20:39:41 +0530 ncbi-entrez-direct (14.6.20210224+dfsg-5) unstable; urgency=high * debian/rules: - Force traditional GOPATH mode (GO111MODULE=off) to avoid needing to produce proper offline go.mod and go.sum files, which turned out not to be nearly as straightforward as I'd hoped. It's not clear how much longer this option will be available, but it works in 1.16 and from what I gather even 1.17 after all. (Closes: #995349.) - Substitute .../klauspost/cpuid/v2 for .../klauspost/cpuid as needed. - Set CGO_{C,CPP,CXX,F,LD}FLAGS from (hardened) dpkg-supplied flags. (See #951262.) -- Aaron M. Ucko Sun, 03 Oct 2021 20:28:46 -0400 ncbi-entrez-direct (14.6.20210224+dfsg-4) unstable; urgency=medium * debian/{efetch,einfo}: Refresh %ncbi_supported, taking care to include undocumented options. (In particular, ncbi-blast+'s get_species_taxids uses efetch's undocumented -docsum shorthand.) (Closes: #990741.) -- Aaron M. Ucko Thu, 08 Jul 2021 17:36:20 -0400 ncbi-entrez-direct (14.6.20210224+dfsg-3) unstable; urgency=medium * debian/man/eblast.1: Extend deprecation notice to eblast. * debian/man/protein-neighbors.1: Note that eblast is now deprecated too. -- Aaron M. Ucko Sat, 13 Mar 2021 22:24:07 -0500 ncbi-entrez-direct (14.6.20210224+dfsg-2) unstable; urgency=medium * debian/{examples,install,rules}: Relegate obsolescent short-lived specialized content to examples: bt-*, fetch-extras, index-themes, and xplore. All came along after buster (which had 10.9.20190219+ds-1) and will be absent from future upstream releases, so there's no sense in having them appear in /usr/bin in bullseye only to disappear fully in the next stable Debian release. * debian/man: Drop corresponding man pages and references thereto. * debian/man/{eaddress,ecitmatch,econtact,edirect,edirutil,enotify, entrez-phrase-search,eproxy,espell,ftp-cp,ftp-ls,protein-neighbors}.1: Mark as deprecated (somewhat speculatively in the case of edirect), with suggestions for alternatives in most cases. All of these commands have been around for a while, so they can remain in /usr/bin for bullseye. -- Aaron M. Ucko Sun, 07 Mar 2021 16:26:20 -0500 ncbi-entrez-direct (14.6.20210224+dfsg-1) unstable; urgency=medium * New upstream point release. * debian/man/esample.1: Update for new release. -- Aaron M. Ucko Wed, 24 Feb 2021 21:14:35 -0500 ncbi-entrez-direct (14.6.20210209+dfsg-1) unstable; urgency=medium * New upstream release. * debian/man/{transmute,xtract}.1: Update for new release. * debian/man/xtract.1: Tune hyphenation under -insd. -- Aaron M. Ucko Fri, 12 Feb 2021 12:31:49 -0500 ncbi-entrez-direct (14.6.20210203+dfsg-2) unstable; urgency=medium * Standards-Version: 4.5.1 (routine-update) * Add salsa-ci file (routine-update) * Drop alternative build-dependency on unavailable golang-1.10-go -- even stable has golang-go 1.11, which I've confirmed to work here. -- Aaron M. Ucko Sat, 06 Feb 2021 22:52:01 -0500 ncbi-entrez-direct (14.6.20210203+dfsg-1) unstable; urgency=medium * New upstream release. * debian/man/{edirect,efetch,efilter,esample,nquire,transmute,xtract}.1: Update for new release. * debian/man/transmute.1: - Fully document new (as of 14.0.20201111[+dfsg]) -format suboptions -xml, -doctype, -comment, and -cdata, half of which turn out to take arguments. - Reformat mode descriptions more compactly. -- Aaron M. Ucko Sat, 06 Feb 2021 22:06:37 -0500 ncbi-entrez-direct (14.0.20201111+dfsg-1) unstable; urgency=medium * New upstream release. (Not the latest, but enough of a milestone to merit an individual upload anyway.) * debian/NEWS (new): Document switch to new e* and nquire implementations by default and reimplementation of transmute. * debian/control: - Add curl | wget to Depends now that nquire defaults to using the shell (vs. Perl) implementation; leave Perl dependencies alone for the sake of other major scripts, and curl as a specific suggestion for the sake of download-ncbi-data and index-extras. - Suggest libxml2-utils and python3 for specific transmute modes. * debian/man/{efetch,efilter,einfo,elink,epost,esearch,gbf2xml,nquire, transmute,xtract}.1: Update for new release. * debian/man/nquire.1: Belatedly correct paste-o in description of shell implementation (which does not in fact use itself!). * debian/man/xtract.1: Belatedly retire two old flags from OPTIONS in addition to SYNOPSIS. * debian/rules: Reflect transmute-related changes -- it's gone from a trivial wrapper around the legacy edirect Perl script to a combination of a Go executable factored out of xtract, a non-trivial shell wrapper that handles several cases outside Go, and an xml2json Perl script cribbed from edirect. - Install that xml2json under /usr/lib -- it's formally an implementation detail of transmute -x2j, and would otherwise conflict with libxml-compile-perl. - Tweak the transmute wrapper to run python3 rather than versionless python for json.tool. - Retain the new portion of upstream's xtract wrapper that delegates factored-out functionality to transmute. - To facilitate some of those changes, add a PKG_BIN_DIR macro. -- Aaron M. Ucko Sun, 24 Jan 2021 17:14:03 -0500 ncbi-entrez-direct (14.0.20201030+dfsg-1) unstable; urgency=medium * New upstream release. * debian/man/efetch.1: Update for new release. -- Aaron M. Ucko Sun, 01 Nov 2020 21:24:40 -0500 ncbi-entrez-direct (14.0.20201015+dfsg-1) unstable; urgency=medium * New upstream release. * debian/man/xtract.1: Update for new release. -- Aaron M. Ucko Mon, 19 Oct 2020 21:37:21 -0400 ncbi-entrez-direct (14.0.20201009+dfsg-1) unstable; urgency=medium * New upstream release. * debian/copyright: - Add myself (at NCBI) as an upstream author. - Also exclude CA.pm and cacert.pm. * debian/efetch: - Belatedly resync %ncbi_supported with current usage (missed -style, -revcomp, -chr_stop, -raw, and -json). - 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/man/{bt-link,bt-srch,download-ncbi-data,edirect,efetch,efilter, einfo,elink,epost,esample,esearch,j2x,nquire,t2x,transmute,xplore, xtract}.1: Update for new release. * debian/man/{download-ncbi-data,esample}.1: Correct old typos (transposed letters, unescaped hyphen, missing parentheses). * debian/man/{einfo,efetch}.ncbi.1: Add alias pages for completeness. * debian/man/enquire.1: Retire per full incorporation of enquire into nquire, albeit on an experimental basis. * debian/man/{g2x,j2x,t2x}.1: Retire. * debian/man/skip-if-file-exists.1: Document new command. * debian/rules: - Belatedly install phrase-search (as is). - 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); retirement of dedicated g2x, j2x, and t2x binaries and of unbuilt s2p.go; 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. * debian/tests/run-unit-test: - Correct gbf2xml invocation. (It ignores any arguments and reads from standard input.) - Drop j2x test; renumber following tests accordingly. -- Aaron M. Ucko Mon, 12 Oct 2020 15:14:47 -0400 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 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 Sun, 28 Jun 2020 21:11:51 -0400 ncbi-entrez-direct (13.7.20200615+dfsg-1) unstable; urgency=medium * New upstream release. * debian/man/{bt-link,bt-srch,download-ncbi-data,edirect,fetch-extras, index-extras,index-pubmed,j2x,nquire,phrase-search,rchive,t2x,xplore, xtract}.1: Update for new release. * debian/man/{enquire,index-themes,theme-aliases}.1: Document new commands. * debian/man/nquire.1: Belatedly note FTP support in NAME and DESCRIPTION; correct formatting of SEE ALSO header; formally adjust SEE ALSO order (accidentally not quite sorted). * debian/rules: Account for new as-is script enquire, bash script index-themes, and sourceable theme-aliases. * debhelper-compat 13 (routine-update) -- Aaron M. Ucko Sun, 28 Jun 2020 17:28:59 -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 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 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 Sun, 02 Feb 2020 22:02:43 -0500 ncbi-entrez-direct (10.9.20190219+ds-1) unstable; urgency=medium * New upstream point release. * debian/man/xtract.1: Update accordingly (adding -is-within). -- Aaron M. Ucko Tue, 26 Feb 2019 21:28:41 -0500 ncbi-entrez-direct (10.9.20190205+ds-1) unstable; urgency=medium * New upstream release. * debian/man/{archive-pubmed,download-pubmed,edirect,efilter, entrez-phrase-search,esearch,espell,fetch-pubmed,index-pubmed, phrase-search,rchive,stream-pubmed,transmute,xtract}.1: Update accordingly. * debian/man/{local-phrase-search,pm-{clean,current,erase,log,repack,uids, verify}}.1: Retire per the corresponding scripts. * debian/rules: Stop installing retired scripts local-phrase-search and (implicitly) pm-{clean,current,erase,log,repack,uids,verify}. -- Aaron M. Ucko Wed, 06 Feb 2019 22:51:27 -0500 ncbi-entrez-direct (10.5.20181204+ds-2) unstable; urgency=medium * debian/control: Actually build-depend on dh-golang. -- Aaron M. Ucko Wed, 05 Dec 2018 22:05:20 -0500 ncbi-entrez-direct (10.5.20181204+ds-1) unstable; urgency=medium * New upstream release. * (debian/).gitignore: Update per GOPATH change. * debian/control: - Build-depend on dh-golang, golang-github-dataence-porter2-dev, golang-github-fatih-color-dev, golang-github-klauspost-cpuid-dev, golang-github-rainycape-unidecode-dev, and golang-github-shirou-gopsutil-dev. - Set Built-Using (with the help of dh-golang). - Bump minimum Go version to 1.10 for strings.Builder. - Depend on libxml-simple-perl. - Repoint Vcs-{Browser,Git} at salsa.debian.org. - Rules-Requires-Root: no (confirmed safe). - Standards-Version: 4.2.1 (compliant at this point). * debian/examples: Remove local storage/indexing scripts (considered official enough for /usr/bin at this point), leaving only asp-* and has-asp, which promote non-free software; add test-pubmed-index. * debian/man/{archive-pubmed,download-pubmed,download-sequence,eblast, fetch-pubmed,index-pubmed,intersect-uid-lists,(local-)phrase-search, pm-clean,pm-erase,pm-invert,pm-log,pm-merge,pm-prepare,pm-promote, pm-refresh,pm-repack,pm-stash,pm-uids,pm-verify,protein-neighbors,rchive, stream-pubmed,transmute}.1: Document newly added tools. * debian/man/{edirect,nquire,xtract}.1: Fix old documentation bugs. * debian/man/{efetch,efilter,elink,entrez-phrase-search,ftp-cp,ftp-ls, nquire,xtract}.1: Update for new release. * debian/rules: - Change (autopopulated) GOPATH to meet dh-golang's expectations. - Belatedly run dh --with=golang to populate (misc:)Built-Using. - Clean up remaining cruft from when Go support was optional. - Pull github.com/surgebase/porter2 (aka gh.c/dataence/porter2), github.com/fatih/color (along with its dependencies github.com/mattn/go-{colorable,isatty}), github.com/klauspost/cpuid, github.com/rainycape/unidecode (aliased, per rchive.go's expectations, to github.com/fiam/gounidecode/unidecode), github.com/shirou/gopsutil (along with its dependency golang.org/x/sys/unix), and our ersatz github.com/pbnjay/memory into the path. (The rainycape version of unidecode has the key advantages of being fresher and already packaged for Debian.) - Build rchive.go in addition to xtract.go; build both against a common.go factored out of xtract.go. - Install run-ncbi-converter (accidentally left off earlier). - Flip Perl scripts back to running via /usr/bin/perl (from /usr/bin/env perl). - Enforce use of Go version 1.10 or newer, even if the default is older. - Install local storage/indexing scripts to /usr/bin. (Closes: #901028.) - Install new eblast wrapper (corresponding to new -blast mode) and protein-neighbors script. * debian/vendor/github.com/pbnjay/memory/memory.go: New wrapper around github.com/shirou/gopsutil/mem, filling in for a different third-party library that lacks a declared license. -- Aaron M. Ucko Wed, 05 Dec 2018 21:19:35 -0500 ncbi-entrez-direct (7.40.20170928+ds-1) unstable; urgency=medium * New upstream release. * debian/control: Unconditionalize Go build dependencies. * debian/examples: Add several new scripts for experimental local record storage, which may migrate to /usr/bin when they're more mature. * debian/man/{efilter,esearch,xtract}.1: Update for new release. * debian/rules: Remove fallback logic to install the old Perl implementation of xtract, now retired upstream. * Standards-Version: 4.1.1 (already compliant). -- Aaron M. Ucko Fri, 06 Oct 2017 17:52:27 -0400 ncbi-entrez-direct (6.90.20170705+ds-2) unstable; urgency=medium * debian/rules: Rework Go-related logic to accommodate builds on (non-release) architectures on which I've had to conditionalize out the relevant build dependencies. -- Aaron M. Ucko Thu, 06 Jul 2017 22:25:05 -0400 ncbi-entrez-direct (6.90.20170705+ds-1) unstable; urgency=medium * New upstream release. * debian/compat: Advance to debhelper 10. * debian/control: - Advance debhelper build dependency accordingly. - Reinstate architecture qualifiers for Go build dependencies on the basis of experimental build logs. - Standards-Version: 4.0.0 (already compliant). * debian/man/{ftp-cp,gbf2xml}.1: Correct syntax for optional filenames. * debian/man/xtract.1: Update for new release. -- Aaron M. Ucko Wed, 05 Jul 2017 22:12:35 -0400 ncbi-entrez-direct (6.80.20170608+ds-1) experimental; urgency=medium * New upstream release. * debian/man/ftp-cp.1: Update accordingly. * Install the new asp-ls script as an example (alongside asp-cp) and the new gbf2xml script as an executable; give gbf2xml a man page. -- Aaron M. Ucko Fri, 09 Jun 2017 18:01:55 -0400 ncbi-entrez-direct (6.70.20170508+ds-1) experimental; urgency=medium * New upstream release. * debian/man/xtract.1: Update accordingly. * debian/control: - Tighten Go dependencies to require Go 1.8 for sort.Slice. - Add a dependency on golang-golang-x-text-dev, also newly necessary. - Remove architecture qualifiers for now. (This *is* for experimental.) * debian/rules: - Build with /usr/lib/go-1.8/bin/go if necessary (notably, for backports). - Establish a local GOPATH with a symlink to .../golang.org/x/text. - Run go build -v now that there are third-party libraries to incorporate. * debian/.gitignore: Ignore debian/gopath. * debian/examples: Install the new asp-cp script as an example, since it requires non-free Aspera tools. -- Aaron M. Ucko Mon, 29 May 2017 21:28:44 -0400 ncbi-entrez-direct (6.10.20170123+ds-2) UNRELEASED; urgency=medium * debian/e{fetch,info}: Correct help text to cite our man pages too. (They didn't yet exist when I originally wrote these wrappers.) * debian/man/xtract.1: Fix an old typo (esapes vs. escapes). -- Aaron M. Ucko Mon, 29 May 2017 15:41:49 -0400 ncbi-entrez-direct (6.10.20170123+ds-1) unstable; urgency=medium * New upstream release. * Resolve conflicts by diverting acedb-other's efetch and epub-utils' einfo to efetch.acedb and einfo.epub respectively (and likewise for their man pages) and deploying wrapper scripts that try to figure out which implementation the user intended to run. (Proper usage differs radically, so ambiguity is unlikely to be an issue in practice.) * Add man pages for all commands. -- Aaron M. Ucko Tue, 24 Jan 2017 21:56:00 -0500 ncbi-entrez-direct (6.00.20170105+ds-1) unstable; urgency=medium * New upstream release. * debian/control: Canonicalize per cme. * debian/copyright: Likewise; also, correct placement of Files-Excluded. -- Aaron M. Ucko Thu, 05 Jan 2017 22:27:51 -0500 ncbi-entrez-direct (5.90.20161221+ds-4) unstable; urgency=medium * debian/control: Remove annotations from conflicts here. (Oops.) -- Aaron M. Ucko Sat, 24 Dec 2016 23:48:49 -0500 ncbi-entrez-direct (5.90.20161221+ds-3) unstable; urgency=medium * debian/control: - Build-Depends: Correct syntax for multiple exclusions. - Conflicts: acedb-other (over efetch), epub-utils (over einfo). -- Aaron M. Ucko Sat, 24 Dec 2016 23:25:29 -0500 ncbi-entrez-direct (5.90.20161221+ds-2) unstable; urgency=medium * .gitignore: Account for files created outside debian/ at build time. * debian/control: - Set debian-med as maintainer, and myself as uploader. - Don't build depend on golang-any on architectures on which it's currently uninstallable. * debian/rules: If building xtract.go fails for any reason, fall back on installing the original Perl implementation. * debian/source/options: single-debian-patch. * xtract.pl: Don't insist on -fallback. -- Aaron M. Ucko Sat, 24 Dec 2016 22:43:40 -0500 ncbi-entrez-direct (5.90.20161221+ds-1) unstable; urgency=low * Initial release. (Closes: #810949.) -- Aaron M. Ucko Fri, 23 Dec 2016 16:35:19 -0500