[med-svn] [Git][med-team/ncbi-entrez-direct][master] 192 commits: New upstream version 7.50.20171030+ds
Aaron M. Ucko
gitlab at salsa.debian.org
Thu Dec 6 02:26:03 GMT 2018
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-entrez-direct
Commits:
6d9a2bdf by Aaron M. Ucko at 2018-04-20T00:54:51Z
New upstream version 7.50.20171030+ds
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d5f02970 by Aaron M. Ucko at 2018-04-20T01:19:16Z
New upstream version 7.50.20171106+ds
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bf93c6d4 by Aaron M. Ucko at 2018-04-20T01:25:09Z
New upstream version 7.60.20171113+ds
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4b133077 by Aaron M. Ucko at 2018-04-24T00:56:15Z
New upstream version 7.60.20171115+ds
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a4d597cd by Aaron M. Ucko at 2018-04-24T01:13:10Z
New upstream version 7.70.20171212+ds
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aae18034 by Aaron M. Ucko at 2018-05-20T20:08:48Z
New upstream version 7.70.20180111+ds
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d8c5e54a by Aaron M. Ucko at 2018-05-20T20:27:09Z
New upstream version 7.80.20180112+ds
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3c9ebe37 by Aaron M. Ucko at 2018-05-20T20:30:39Z
New upstream version 7.80.20180126+ds
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b034e258 by Aaron M. Ucko at 2018-05-20T21:39:36Z
New upstream version 7.90.20180126+ds
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654906d9 by Aaron M. Ucko at 2018-05-20T21:53:50Z
New upstream version 7.90.20180216+ds
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dc54a3ed by Aaron M. Ucko at 2018-05-21T00:36:50Z
New upstream version 8.00.20180220+ds
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82eaec5c by Aaron M. Ucko at 2018-09-17T01:21:52Z
New upstream version 8.00.20180301+ds
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2a1518f5 by Aaron M. Ucko at 2018-10-07T20:56:00Z
New upstream version 8.10.20180305+ds
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27a43b81 by Aaron M. Ucko at 2018-10-07T21:05:50Z
New upstream version 8.20.20180312+ds
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22a294a6 by Aaron M. Ucko at 2018-10-07T23:46:04Z
New upstream version 8.20.20180323+ds
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41f5399f by Aaron M. Ucko at 2018-10-08T00:41:37Z
New upstream version 8.30.20180402+ds
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f163b209 by Aaron M. Ucko at 2018-10-08T00:46:40Z
New upstream version 8.30.20180405+ds
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11738bde by Aaron M. Ucko at 2018-10-08T00:50:52Z
New upstream version 8.40.20180406+ds
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1685ca47 by Aaron M. Ucko at 2018-10-08T00:52:54Z
New upstream version 8.40.20180412+ds
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2521ed6e by Aaron M. Ucko at 2018-10-08T00:57:20Z
New upstream version 8.50.20180413+ds
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995c4cea by Aaron M. Ucko at 2018-10-08T01:04:37Z
New upstream version 8.50.20180418+ds
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4e1f4937 by Aaron M. Ucko at 2018-10-08T02:37:42Z
New upstream version 8.60.20180425+ds
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c47a43fe by Aaron M. Ucko at 2018-10-08T02:44:52Z
New upstream version 8.60.20180426+ds
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eaa1fbd7 by Aaron M. Ucko at 2018-10-08T14:58:56Z
New upstream version 8.70.20180511+ds
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72455211 by Aaron M. Ucko at 2018-10-08T17:46:34Z
New upstream version 8.70.20180524+ds
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f3b8d085 by Aaron M. Ucko at 2018-10-08T18:02:37Z
New upstream version 8.80.20180529+ds
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0e2a4b54 by Aaron M. Ucko at 2018-10-08T18:15:31Z
New upstream version 8.80.20180531+ds
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d953ca16 by Aaron M. Ucko at 2018-10-08T18:19:17Z
New upstream version 8.90.20180604+ds
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7e812e67 by Aaron M. Ucko at 2018-10-08T18:28:03Z
New upstream version 8.90.20180605+ds
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a918bd99 by Aaron M. Ucko at 2018-10-08T20:27:42Z
New upstream version 9.00.20180606+ds
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988e3cdb by Aaron M. Ucko at 2018-10-08T20:34:35Z
New upstream version 9.10.20180618+ds
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d0ea746d by Aaron M. Ucko at 2018-10-08T20:42:53Z
New upstream version 9.20.20180622+ds
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1e9fdde9 by Aaron M. Ucko at 2018-10-08T21:54:36Z
New upstream version 9.20.20180702+ds
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84f7360b by Aaron M. Ucko at 2018-10-08T22:11:48Z
New upstream version 9.30.20180705+ds
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f738fe01 by Aaron M. Ucko at 2018-10-08T22:31:49Z
New upstream version 9.30.20180706+ds
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07019d66 by Aaron M. Ucko at 2018-10-09T00:51:06Z
New upstream version 9.40.20180716+ds
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d534b48b by Aaron M. Ucko at 2018-10-09T00:55:43Z
New upstream version 9.40.20180718+ds
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86be8637 by Aaron M. Ucko at 2018-10-09T00:58:20Z
New upstream version 9.50.20180727+ds
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ec21b7bd by Aaron M. Ucko at 2018-10-09T01:33:44Z
New upstream version 9.50.20180731+ds
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e8a4f0e7 by Aaron M. Ucko at 2018-10-09T01:36:44Z
New upstream version 9.60.20180809+ds
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52dc1594 by Aaron M. Ucko at 2018-11-11T22:20:04Z
New upstream version 9.70.20180816+ds
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b8cd919f by Aaron M. Ucko at 2018-11-11T22:36:10Z
New upstream version 9.70.20180824+ds
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f981f7fc by Aaron M. Ucko at 2018-11-11T23:20:06Z
New upstream version 9.80.20180904+ds
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11b7d6b9 by Aaron M. Ucko at 2018-11-12T02:18:53Z
New upstream version 9.80.20180907+ds
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4b1cbbaf by Aaron M. Ucko at 2018-11-12T02:20:47Z
New upstream version 9.90.20180917+ds
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39e7b278 by Aaron M. Ucko at 2018-11-12T02:24:01Z
New upstream version 9.90.20180925+ds
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2642ceaf by Aaron M. Ucko at 2018-11-12T02:53:26Z
New upstream version 10.0.20180927+ds
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6044751a by Aaron M. Ucko at 2018-11-12T20:44:00Z
New upstream version 10.0.20181004+ds
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6a684bba by Aaron M. Ucko at 2018-11-15T01:16:08Z
New upstream version 10.1.20181009+ds
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5124630a by Aaron M. Ucko at 2018-11-15T01:27:52Z
New upstream version 10.1.20181012+ds
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5eda9bea by Aaron M. Ucko at 2018-11-15T01:36:48Z
New upstream version 10.2.20181015+ds
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4be5a0fe by Aaron M. Ucko at 2018-11-15T01:52:55Z
New upstream version 10.2.20181018+ds
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dd366b3e by Aaron M. Ucko at 2018-11-15T01:55:33Z
New upstream version 10.3.20181024+ds
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a04cc894 by Aaron M. Ucko at 2018-11-15T02:06:16Z
New upstream version 10.3.20181102+ds
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73b810c5 by Aaron M. Ucko at 2018-11-19T02:39:43Z
New upstream version 10.4.20181106+ds
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975b8bd2 by Aaron M. Ucko at 2018-11-19T02:48:48Z
New upstream version 10.4.20181114+ds
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05fa9ed0 by Aaron M. Ucko at 2018-12-03T03:46:43Z
New upstream version 10.5.20181121+ds
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fc4d55da by Aaron M. Ucko at 2018-12-03T03:48:26Z
New upstream version 10.5.20181130+ds
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0ad84a2b by Aaron M. Ucko at 2018-12-05T18:52:48Z
New upstream version 10.5.20181204+ds
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ef01f43b by Aaron M. Ucko at 2018-12-05T21:03:59Z
Merge tag 'upstream/7.50.20171030+ds'
Upstream version 7.50.20171030(+ds).
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a0fb4858 by Aaron M. Ucko at 2018-12-05T21:03:59Z
Belatedly populate Built-Using with the help of dh-golang.
* (debian/).gitignore: Update per GOPATH change.
* debian/control: Build-depend on dh-golang; use it to set Built-Using.
* debian/rules:
- Change (autopopulated) GOPATH to meet dh-golang's expectations.
- Run dh --with=golang to populate (misc:)Built-Using.
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37a7ac78 by Aaron M. Ucko at 2018-12-05T21:03:59Z
debian/man/nquire.1: Belatedly correct -eutils SYNOPSIS entry.
nquire -eutils has always required a name.
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d688ce8b by Aaron M. Ucko at 2018-12-05T21:03:59Z
debian/man/xtract.1: Belatedly add Parent/Child element option.
It's been around all along, but accidentally slipped through the
cracks earlier.
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115faa66 by Aaron M. Ucko at 2018-12-05T21:03:59Z
debian/man/edirect.1: Somewhat belatedly document NCBI_API_KEY.
edirect has supported this environment variable since October of 2017.
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137a9603 by Aaron M. Ucko at 2018-12-05T21:03:59Z
d/rules: Clean up remaining cruft from when Go support was optional.
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f560267a by Aaron M. Ucko at 2018-12-05T21:03:59Z
debian/man/{efetch,xtract}.1: Update for new release.
* efetch: Add -style.
* xtract:
- Add -med, -bin, -bit, -position outer/inner/all, and -element
examples Range and Substring.
- Move Phrase filtering down.
- Drop -skip.
- Resynchronize example exploration object.
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719a9f86 by Aaron M. Ucko at 2018-12-05T21:03:59Z
debian/examples: Add prepare-stash.
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7343e59b by Aaron M. Ucko at 2018-12-05T21:03:59Z
Merge tag 'upstream/7.50.20171106+ds'
Upstream version 7.50.20171106(+ds).
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203adfd1 by Aaron M. Ucko at 2018-12-05T21:03:59Z
debian/examples: Add get-stash-uids.
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e4b1e6a8 by Aaron M. Ucko at 2018-12-05T21:03:59Z
Merge tag 'upstream/7.60.20171113+ds'
Upstream version 7.60.20171113(+ds).
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9134e03b by Aaron M. Ucko at 2018-12-05T21:03:59Z
Build rchive.go, which requires a third-party unidecode package.
* debian/control: Build-depend on golang-github-rainycape-unidecode-dev.
* debian/rules:
- Pull github.com/rainycape/unidecode into the path, with the additional
alias github.com/fiam/gounidecode/unidecode to match rchive.go's
expectations. (The rainycape version 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.
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b127c0dd by Aaron M. Ucko at 2018-12-05T21:03:59Z
debian/man: Update for new release (7.60.20171113[+ds-1]).
* {efetch,ftp-cp,xtract}.1: SEE ALSO rchive(1).
* rchive.1: New; portions copied or moved from xtract.1.
* xtract.1:
- Belatedly split -input into a Data Source section.
- Drop Local Record Indexing (-archive/-index/-flag/-gzip/-hash) and
-extras, taken over by rchive.1.
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af28cc0a by Aaron M. Ucko at 2018-12-05T21:04:00Z
Merge tag 'upstream/7.60.20171115+ds'
Upstream version 7.60.20171115(+ds).
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838466b3 by Aaron M. Ucko at 2018-12-05T21:04:00Z
debian/man/{rchive,xtract}.1: Update for new release.
* rchive.1: Drop -accent, -ascii, -compress, and -spaces; add -unique
and -advanced.
* xtract.1: Add -repair.
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920d0a53 by Aaron M. Ucko at 2018-12-05T21:04:00Z
debian/examples: Add repack-pubmed.
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c66fda6b by Aaron M. Ucko at 2018-12-05T21:04:00Z
Merge tag 'upstream/7.70.20171212+ds'
Upstream version 7.70.20171212(+ds).
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2c1a8218 by Aaron M. Ucko at 2018-12-05T21:04:22Z
Account for new dep on github.com/surgebase (dataence)/porter2.
* debian/control: Build-depend on golang-github-dataence-porter2-dev.
* debian/rules: Pull github.com/surgebase/porter2 (aka
github.com/dataence/porter2) into the path.
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f72497ee by Aaron M. Ucko at 2018-12-05T21:04:28Z
debian/examples: Add {index,invert,merge,promote}-pubmed.
Also trim a trailing blank line that cropped up at some point.
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260babe4 by Aaron M. Ucko at 2018-12-05T21:04:28Z
debian/man: Update for new release (7.70.20171212[+ds-1]).
* rchive.1: Remove -extras and -advanced (no longer mentioned in -help)
and corresponding sections Processing Commands and Miscellaneous.
* xtract.1: Add -stems.
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6dfa8bfc by Aaron M. Ucko at 2018-12-05T21:04:28Z
Merge tag 'upstream/7.70.20180111+ds'
Upstream version 7.70.20180111(+ds).
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4973d1ac by Aaron M. Ucko at 2018-12-05T21:04:28Z
debian/examples: Add {archive,log,master}-pubmed, refresh-versioned.
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0ae9dbbc by Aaron M. Ucko at 2018-12-05T21:04:28Z
debian/man/xtract.1: Update for new release (7.70.20180111[+ds-1]).
* -stems has moved from Phrase Processing to Processing Flags and no
longer takes an argument.
* Add -stops (Processing Flags) and -matches (String Constraints).
* -indices (Phrase Processing) no longer claims to be experimental.
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e90ee8e1 by Aaron M. Ucko at 2018-12-05T21:04:28Z
Merge tag 'upstream/7.80.20180112+ds'
Upstream version 7.80.20180112(+ds).
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6e47ac37 by Aaron M. Ucko at 2018-12-05T21:04:28Z
Merge tag 'upstream/7.80.20180126+ds'
Upstream version 7.80.20180126(+ds).
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0db5e25d by Aaron M. Ucko at 2018-12-05T21:04:28Z
debian/rules: Install run-ncbi-converter; correct Perl shebangs.
* Install run-ncbi-converter (accidentally left off earlier).
* Flip Perl scripts back to running via /usr/bin/perl (from /usr/bin/env perl).
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bc9ee90f by Aaron M. Ucko at 2018-12-05T21:04:28Z
debian/examples: Add local-phrase-search (a WIP at this point).
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a854cefa by Aaron M. Ucko at 2018-12-05T21:04:28Z
Merge tag 'upstream/7.90.20180126+ds'
Upstream version 7.90.20180126(+ds).
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105eadce by Aaron M. Ucko at 2018-12-05T21:04:28Z
debian/man/rchive.1: Update for new release (7.90.20180126[+ds-1]).
Add -fetch (under Local Record Indexing).
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d26d5cf6 by Aaron M. Ucko at 2018-12-05T21:04:28Z
Merge tag 'upstream/7.90.20180216+ds'
Upstream version 7.90.20180216(+ds).
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1753c31c by Aaron M. Ucko at 2018-12-05T21:04:28Z
debian/rules: common.go is gone (reincorporated).
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6c0ed693 by Aaron M. Ucko at 2018-12-05T21:04:28Z
debian/man/efetch.1: Update for new release (7.90.20180216[+ds-1]).
Add -raw under Miscellaneous; split -complexity, -extend, and
-extrafeat out into a new Sequence Flags section.
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08fb6231 by Aaron M. Ucko at 2018-12-05T21:04:28Z
debian/examples: master-pubmed is now process-pubmed.
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da4ce7fe by Aaron M. Ucko at 2018-12-05T21:04:28Z
Merge tag 'upstream/8.00.20180220+ds'
Upstream version 8.00.20180220(+ds).
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ead3f798 by Aaron M. Ucko at 2018-12-05T21:04:28Z
Use at least Go 1.10 for strings.Builder.
* debian/control: Bump minimum Go version to 1.10.
* debian/rules: Enforce use of Go version 1.10 or newer, even if the
default is older.
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def77453 by Aaron M. Ucko at 2018-12-05T21:04:28Z
Move local storage/indexing scripts to /usr/bin (#901028).
* 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.
* debian/rules: Install local storage/indexing scripts to /usr/bin.
(Closes: #901028.)
Man pages will follow in a separate round-up commit.
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6dc2419e by Aaron M. Ucko at 2018-12-05T21:04:28Z
debian/man: Update for new release (8.00.20180220[+ds]).
* Document new additions to /usr/bin (many previously installed as
undocumented examples, in some cases with a different naming scheme):
archive-pubmed, download-pubmed, download-sequence, fetch-pubmed,
index-pubmed, local-phrase-search, and
pm-{erase,index,invert,log,merge,prepare,promote,refresh,repack,stash,uids}.
* rchive.1: Add a new Local Record Index section, with the new options
-invert, -merge, -promote, -query, -count, -counts, -stems, and -stops;
rename Local Record Indexing to Local Record Cache; document stems as
another possible -flag argument.
* xtract.1: Add -e2index, under Miscellaneous.
* Add SEE ALSO links to new additions as appropriate; ensure all affected
man pages use \- instead of - in SEE ALSO (others not yet swept).
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725120ed by Aaron M. Ucko at 2018-12-05T21:04:28Z
Merge tag 'upstream/8.00.20180301+ds'
Upstream version 8.00.20180301(+ds).
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86574dc2 by Aaron M. Ucko at 2018-12-05T21:04:28Z
debian/man/{rchive,xtract}.1: Update for 8.00.20180301[+ds] release.
* rchive.1: Broaden description of -strict.
* xtract.1: Add -revcomp, in a new Sequence Processing subsection;
broaden descriptions of -strict and -accent.
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ba98b5b7 by Aaron M. Ucko at 2018-12-05T21:04:29Z
Merge tag 'upstream/8.10.20180305+ds'
Upstream version 8.10.20180305(+ds).
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65f5713d by Aaron M. Ucko at 2018-12-05T21:04:29Z
debian/rules: Reinstate compilation against common.go.
This reverts commit adc3ed15a3f9a17ae48996d7295d43fb25c157b5.
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5f39b811 by Aaron M. Ucko at 2018-12-05T21:04:29Z
Merge tag 'upstream/8.20.20180312+ds'
Upstream version 8.20.20180312(+ds).
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19985694 by Aaron M. Ucko at 2018-12-05T21:04:29Z
debian/man: Update for new release (8.20.20180312[+ds]).
* Document new pm-clean script, and mention it in SEE ALSO as appropriate.
* xtract.1: Remove -spaces and -repair; reword descriptions of -accent
and -ascii per -help.
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76f6189a by Aaron M. Ucko at 2018-12-05T21:04:29Z
Merge tag 'upstream/8.20.20180323+ds'
Upstream version 8.20.20180323(+ds).
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dfa82365 by Aaron M. Ucko at 2018-12-05T21:04:29Z
debian/rules: Install new stream-pubmed script (via AS_IS_SCRIPTS).
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7b954d1a by Aaron M. Ucko at 2018-12-05T21:04:29Z
debian/man: Update for new release (8.20.20180323[+ds]).
* Document new stream-pubmed script; mention it in SEE ALSO as appropriate.
* xtract.1: Document new -unicode, -script, and -mathml options (all
under Reformatting, and moreover under -format according to -help).
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79bf651a by Aaron M. Ucko at 2018-12-05T21:04:29Z
Merge tag 'upstream/8.30.20180402+ds'
Upstream version 8.30.20180402(+ds).
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0b51c39f by Aaron M. Ucko at 2018-12-05T21:04:29Z
debian/man/rchive.1: Add -deleted (under Local Record Index).
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24cf97be by Aaron M. Ucko at 2018-12-05T21:04:29Z
Merge tag 'upstream/8.30.20180405+ds'
Upstream version 8.30.20180405(+ds).
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812c45c9 by Aaron M. Ucko at 2018-12-05T21:04:29Z
debian/man/xtract.1: Add -plg (under Output Customization).
Note that -rst additionally resets -plg.
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2059a045 by Aaron M. Ucko at 2018-12-05T21:04:29Z
Merge tag 'upstream/8.40.20180406+ds'
Upstream version 8.40.20180406(+ds).
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de13070c by Aaron M. Ucko at 2018-12-05T21:04:29Z
Merge tag 'upstream/8.40.20180412+ds'
Upstream version 8.40.20180412(+ds).
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34b4aa42 by Aaron M. Ucko at 2018-12-05T21:04:29Z
debian/man/xtract.1: Remove -matches (folded into -pattern).
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0ecb7f40 by Aaron M. Ucko at 2018-12-05T21:04:29Z
Merge tag 'upstream/8.50.20180413+ds'
Upstream version 8.50.20180413(+ds).
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d37ff2c4 by Aaron M. Ucko at 2018-12-05T21:04:29Z
debian/man: Update for new release (8.50.20180413[+ds]).
* pm-prepare.1: Advice appears for Linux too now; stop mentioning OS list.
* xtract.1: Rename -phrase to -require; add a complementary -exclude
option (also under Phrase Filtering).
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a99a1102 by Aaron M. Ucko at 2018-12-05T21:04:29Z
Merge tag 'upstream/8.50.20180418+ds'
Upstream version 8.50.20180418(+ds).
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d26f380c by Aaron M. Ucko at 2018-12-05T21:04:29Z
Merge tag 'upstream/8.60.20180425+ds'
Upstream version 8.60.20180425(+ds).
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7dea8f64 by Aaron M. Ucko at 2018-12-05T21:04:29Z
debian/man: Update for new release (8.60.20180425[+ds]).
* Document new pm-verify script; mention it in SEE ALSO as appropriate.
* rchive.1: Tweak descriptions of -archive, -merge, and -promote per -help.
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30ff0441 by Aaron M. Ucko at 2018-12-05T21:04:29Z
Merge tag 'upstream/8.60.20180426+ds'
Upstream version 8.60.20180426(+ds).
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86b61bc0 by Aaron M. Ucko at 2018-12-05T21:04:30Z
Merge tag 'upstream/8.70.20180511+ds'
Upstream version 8.70.20180511(+ds).
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ddeaf203 by Aaron M. Ucko at 2018-12-05T21:04:30Z
debian/man: Update for new release (8.70.20180511[+ds]).
* Remove page for pm-index (effectively folded into pm-invert); update
pm-invert.1 and various pages' SEE ALSO links accordingly.
* rchive.1: Remove -deleted, -(flag )stems, and -stops.
* xtract.1: Add -elg (covered by -rst) and -wrp (both in Format Customization)
and -select (in Conditional Execution) replacing -require and -exclude;
remove -stems; move -e2index to Phrase Processing from Miscellaneous (where
it wound up by default due to having previously been mentioned only(!) in
rchive's -help output).
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303bb7fa by Aaron M. Ucko at 2018-12-05T21:04:30Z
Merge tag 'upstream/8.70.20180524+ds'
Upstream version 8.70.20180524(+ds).
- - - - -
10fd9fa3 by Aaron M. Ucko at 2018-12-05T21:04:30Z
debian/rules: +intersect-uid-lists (via AS_IS_SCRIPTS).
- - - - -
4b55b740 by Aaron M. Ucko at 2018-12-05T21:04:30Z
debian/man: Update for new release (8.70.20180524[+ds]).
* Document new intersect-uid-lists script.
* local-phrase-search.1: Drop -stems (retired) and -phrase (now an
undocumented synonym for -query); reword -query's description.
- - - - -
573c9dd6 by Aaron M. Ucko at 2018-12-05T21:04:30Z
Merge tag 'upstream/8.80.20180529+ds'
Upstream version 8.80.20180529(+ds).
- - - - -
68b52004 by Aaron M. Ucko at 2018-12-05T21:04:30Z
debian/man: Update for new release (8.80.20180529[+ds]).
* rchive.1: Document new -path option (under Local Record Index), so
that -query and -count(s) just need to take the actual query.
* xtract.1: Reorder Format Customization options so that those -rst
resets are contiguous; rename Phrase Processing to Text Processing,
and tweak -terms's description accordingly.
- - - - -
9cdff99b by Aaron M. Ucko at 2018-12-05T21:04:30Z
Merge tag 'upstream/8.80.20180531+ds'
Upstream version 8.80.20180531(+ds).
- - - - -
76568ea5 by Aaron M. Ucko at 2018-12-05T21:04:30Z
debian/man/xtract.1: + -clauses (under Text Processing).
Leave -e2index even though it's disappeared from -help, since rchive's
-help still mentions it.
- - - - -
c779f015 by Aaron M. Ucko at 2018-12-05T21:04:30Z
Merge tag 'upstream/8.90.20180604+ds'
Upstream version 8.90.20180604(+ds).
- - - - -
1cffbe3e by Aaron M. Ucko at 2018-12-05T21:04:30Z
debian/man/xtract.1: Add new -transform/-translate option pair.
-transform is under Data Source; -translate is under String Processing.
- - - - -
1948e5cd by Aaron M. Ucko at 2018-12-05T21:04:30Z
Merge tag 'upstream/8.90.20180605+ds'
Upstream version 8.90.20180605(+ds).
- - - - -
9d275179 by Aaron M. Ucko at 2018-12-05T21:04:30Z
Merge tag 'upstream/9.00.20180606+ds'
Upstream version 9.00.20180606(+ds).
- - - - -
76ae79b4 by Aaron M. Ucko at 2018-12-05T21:04:30Z
Merge tag 'upstream/9.10.20180618+ds'
Upstream version 9.10.20180618(+ds).
- - - - -
e81523b6 by Aaron M. Ucko at 2018-12-05T21:04:30Z
debian/man/xtract.1: Update for new release (9.10.20180618[+ds]).
Add -year (under String Processing) and Unrestricted (element option);
move Recursive up to match -help output.
- - - - -
857b761f by Aaron M. Ucko at 2018-12-05T21:04:30Z
Merge tag 'upstream/9.20.20180622+ds'
Upstream version 9.20.20180622(+ds).
- - - - -
29837aaf by Aaron M. Ucko at 2018-12-05T21:04:30Z
debian/man/xtract.1: Mention -format clean, per -help.
Leave description blank for now, since -help doesn't specify and it's
not clear from the code.
- - - - -
620b51d0 by Aaron M. Ucko at 2018-12-05T21:04:30Z
Merge tag 'upstream/9.20.20180702+ds'
Upstream version 9.20.20180702(+ds).
- - - - -
d6d8e85d by Aaron M. Ucko at 2018-12-05T21:04:30Z
debian/man: Update for new release (9.20.20180702[+ds]).
* {archive,index}-pubmed.1: Remove references to pm-clean, no longer
used here.
* pm-clean.1: Remove reciprocal SEE ALSO references and also the one
to pm-stash (previously the next step).
- - - - -
2f9d545f by Aaron M. Ucko at 2018-12-05T21:04:30Z
Merge tag 'upstream/9.30.20180705+ds'
Upstream version 9.30.20180705(+ds).
- - - - -
74998d3c by Aaron M. Ucko at 2018-12-05T21:04:30Z
debian/man: Update for new release (9.30.20180705[+ds]).
* (Re)document new pm-current script and reinstated pm-index script.
* Mention both in SEE ALSO as appropriate.
- - - - -
acc38bcd by Aaron M. Ucko at 2018-12-05T21:04:30Z
Merge tag 'upstream/9.30.20180706+ds'
Upstream version 9.30.20180706(+ds).
- - - - -
b7ae528c by Aaron M. Ucko at 2018-12-05T21:04:31Z
Merge tag 'upstream/9.40.20180716+ds'
Upstream version 9.40.20180716(+ds).
- - - - -
2bf214fb by Aaron M. Ucko at 2018-12-05T21:04:31Z
Merge tag 'upstream/9.40.20180718+ds'
Upstream version 9.40.20180718(+ds).
- - - - -
f9a49375 by Aaron M. Ucko at 2018-12-05T21:04:31Z
Merge tag 'upstream/9.50.20180727+ds'
Upstream version 9.50.20180727(+ds).
- - - - -
92d96e23 by Aaron M. Ucko at 2018-12-05T21:05:01Z
Reflect new dependency on github.com/fatih/color.
* debian/control: Build-depend on golang-github-fatih-color-dev.
* debian/rules: Pull github.com/fatih/color into the path,
along with its dependencies github.com/mattn/go-{colorable,isatty}.
- - - - -
66cb7295 by Aaron M. Ucko at 2018-12-05T21:05:04Z
debian/man: Update for new release (9.50.20180727[+ds]).
* {archive,index}-pubmed.1: Document support for an auxiliary
-temp/-work(ing) directory to hold intermediate subtrees.
* {local-phrase-search,rchive}.1: Document new -exact mode.
- - - - -
b7462155 by Aaron M. Ucko at 2018-12-05T21:05:04Z
Merge tag 'upstream/9.50.20180731+ds'
Upstream version 9.50.20180731(+ds).
- - - - -
62ba25a4 by Aaron M. Ucko at 2018-12-05T21:05:04Z
Merge tag 'upstream/9.60.20180809+ds'
Upstream version 9.60.20180809(+ds).
- - - - -
d94af591 by Aaron M. Ucko at 2018-12-05T21:05:04Z
debian/rules: Install eblast script and protein-neighbors example.
Install new eblast wrapper (corresponding to new -blast mode) and
protein-neighbors example (not counted as a script due to lacking a
proper #! line).
- - - - -
10dd0d82 by Aaron M. Ucko at 2018-12-05T21:05:04Z
debian/man: Update for new release (9.60.20180809[+ds]).
* Document new eblast wrapper (and corresponding edirect -blast mode).
* Add SEE ALSO links as appropriate.
- - - - -
a9f4753a by Aaron M. Ucko at 2018-12-05T21:05:04Z
Merge tag 'upstream/9.70.20180816+ds'
Upstream version 9.70.20180816(+ds).
- - - - -
55e97295 by Aaron M. Ucko at 2018-12-05T21:05:04Z
Merge tag 'upstream/9.70.20180824+ds'
Upstream version 9.70.20180824(+ds).
- - - - -
cfe35a8d by Aaron M. Ucko at 2018-12-05T21:05:04Z
debian/man: Update for new release (9.70.20180824[+ds]).
* {local-phrase-search,rchive}.1: Document new -search mode; resync
mode descriptions with rchive's -help output.
- - - - -
8f7e2e90 by Aaron M. Ucko at 2018-12-05T21:05:04Z
Merge tag 'upstream/9.80.20180904+ds'
Upstream version 9.80.20180904(+ds).
- - - - -
d0c1862c by Aaron M. Ucko at 2018-12-05T21:05:04Z
Reflect new dependency on github.com/klauspost/cpuid.
* debian/control: Build-depend on golang-github-klauspost-cpuid-dev.
* debian/rules: Pull github.com/klauspost/cpuid into the path.
- - - - -
d655a3c6 by Aaron M. Ucko at 2018-12-05T21:05:04Z
debian/man/xtract.1: Document new -position even/odd options.
- - - - -
e9c51807 by Aaron M. Ucko at 2018-12-05T21:05:04Z
Merge tag 'upstream/9.80.20180907+ds'
Upstream version 9.80.20180907(+ds).
- - - - -
368b7776 by Aaron M. Ucko at 2018-12-05T21:05:05Z
Merge tag 'upstream/9.90.20180917+ds'
Upstream version 9.90.20180917(+ds).
- - - - -
e57a6d85 by Aaron M. Ucko at 2018-12-05T21:05:05Z
Merge tag 'upstream/9.90.20180925+ds'
Upstream version 9.90.20180925(+ds).
- - - - -
9cd5bfb8 by Aaron M. Ucko at 2018-12-05T21:05:05Z
debian/rules: Install demixifier (new), via PERL_SCRIPTS.
- - - - -
c818fc32 by Aaron M. Ucko at 2018-12-05T21:05:05Z
debian/man: Update for new release (9.90.20180925[+ds]).
* demixifier.1: Document new program.
* efilter.1: Document new -country sequence filter.
* Update SEE ALSO as appropriate.
- - - - -
b432eaee by Aaron M. Ucko at 2018-12-05T21:05:05Z
Merge tag 'upstream/10.0.20180927+ds'
Upstream version 10.0.20180927(+ds).
- - - - -
96299c87 by Aaron M. Ucko at 2018-12-05T21:05:05Z
debian/man/pm-current.1: Document new syntax (explicit input dir).
Name the arguments target and archive to match the variable names.
- - - - -
ee3a6c8f by Aaron M. Ucko at 2018-12-05T21:05:05Z
Merge tag 'upstream/10.0.20181004+ds'
Upstream version 10.0.20181004(+ds).
- - - - -
551b0fd0 by Aaron M. Ucko at 2018-12-05T21:05:05Z
Accommodate new transmute script, subsuming demixifier.
* debian/control: Suggest libjson-any-perl and libxml-simple-perl.
* debian/rules: Update PERL_SCRIPTS accordingly.
- - - - -
7634b8ff by Aaron M. Ucko at 2018-12-05T21:05:05Z
debian/man: Update for new release (10.0.20181004[+ds]).
* transmute.1: Document new program (subsuming demixifier).
* xtract.1: Document new exhaustive exploration construct and new
object name -element operation.
* Update SEE ALSO for demixifier -> transmute name change.
- - - - -
19843dc4 by Aaron M. Ucko at 2018-12-05T21:05:05Z
Merge tag 'upstream/10.1.20181009+ds'
Upstream version 10.1.20181009(+ds).
- - - - -
1765ee37 by Aaron M. Ucko at 2018-12-05T21:05:05Z
debian/man: Update for new release (10.1.20181009[+ds]).
* pm-stash.1: Reflect switch to taking two directories and removal of input.
* rchive.1: Resync description of -mixed with -help output.
* transmute.1: Remove -jats (swiftly retired).
* xtract.1: Add -aft (under Format Customization); resync -mixed description.
- - - - -
eccd1fd9 by Aaron M. Ucko at 2018-12-05T21:05:05Z
Merge tag 'upstream/10.1.20181012+ds'
Upstream version 10.1.20181012(+ds).
- - - - -
8f6cb79a by Aaron M. Ucko at 2018-12-05T21:05:05Z
Upgrade new Perl suggestions to dependencies (of edirect.pl).
debian/control: Move libjson-any-perl and libxml-simple-perl from
Suggests to Depends now that they're needed for edirect.pl, not just
transmute.
- - - - -
b981fc20 by Aaron M. Ucko at 2018-12-05T21:05:05Z
debian/man/nquire.1: Document new -ftp mode.
- - - - -
12a4a33b by Aaron M. Ucko at 2018-12-05T21:05:05Z
Merge tag 'upstream/10.2.20181015+ds'
Upstream version 10.2.20181015(+ds).
- - - - -
ae716559 by Aaron M. Ucko at 2018-12-05T21:05:05Z
debian/man: Update for new release (10.2.20181015[+ds]).
* efetch.1: New -json flag.
* elink.1: Give more -name examples, per -help.
- - - - -
08d37fa9 by Aaron M. Ucko at 2018-12-05T21:05:05Z
Merge tag 'upstream/10.2.20181018+ds'
Upstream version 10.2.20181018(+ds).
- - - - -
ebf39fd1 by Aaron M. Ucko at 2018-12-05T21:05:05Z
Drop dependency on libjson-any-perl, no longer needed.
edirect.pl and transmute have switched from JSON::Any to JSON::PP,
which is in Perl's standard library.
- - - - -
9afc9eca by Aaron M. Ucko at 2018-12-05T21:05:05Z
Merge tag 'upstream/10.3.20181024+ds'
Upstream version 10.3.20181024(+ds).
- - - - -
78ddafd7 by Aaron M. Ucko at 2018-12-05T21:05:05Z
Merge tag 'upstream/10.3.20181102+ds'
Upstream version 10.3.20181102(+ds).
- - - - -
c7ac6095 by Aaron M. Ucko at 2018-12-05T21:05:06Z
Build against gh.c/shirou/gopsutil, in lieu of gh.c/pbnjay/memory.
* debian/control: Add a build dependency on golang-github-shirou-gopsutil-dev.
* debian/rules: Pull github.com/shirou/gopsutil (along with its dependency
golang.org/x/sys/unix) and our ersatz gh.c/pbnjay/memory into the path.
* 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.
- - - - -
78267498 by Aaron M. Ucko at 2018-12-05T21:05:06Z
debian/man: Update for new release (10.3.20181102[+ds]).
* local-phrase-search.1: Add phrase-search as a synonym (at least as
far as documented flags are concerned).
* pm-current.1: Note pre-clearing of *.xml.gz files under target.
* pm-stash.1: Revert usage changes.
- - - - -
5a3ba6cd by Aaron M. Ucko at 2018-12-05T21:05:06Z
Merge tag 'upstream/10.4.20181106+ds'
Upstream version 10.4.20181106(+ds).
- - - - -
211f7d04 by Aaron M. Ucko at 2018-12-05T21:05:06Z
Install test-pubmed-index as an example.
- - - - -
cd07c816 by Aaron M. Ucko at 2018-12-05T21:05:06Z
debian/man/xtract.1: Rename -aft to -deq (for 10.4.20181106[+ds]).
- - - - -
5fbb8f37 by Aaron M. Ucko at 2018-12-05T21:05:06Z
Merge tag 'upstream/10.4.20181114+ds'
Upstream version 10.4.20181114(+ds).
- - - - -
30632d6e by Aaron M. Ucko at 2018-12-05T21:05:06Z
Install protein-neighbors as a script rather than an example.
Take the opportunity to clean up another(!) trailing blank line from
debian/examples.
- - - - -
5ed53e64 by Aaron M. Ucko at 2018-12-05T21:05:06Z
debian/man: Update for new release (10.4.20181114[+ds]).
* efilter.1: Note support for raw organism names, not just keywords.
* protein-neighbors.1: New; add appropriate SEE ALSO links.
* rchive.1: Note new -join flag (under Local Record Index).
- - - - -
9c150e7c by Aaron M. Ucko at 2018-12-05T21:05:06Z
Merge tag 'upstream/10.5.20181121+ds'
Upstream version 10.5.20181121(+ds).
- - - - -
74e7fda4 by Aaron M. Ucko at 2018-12-05T21:05:06Z
Merge tag 'upstream/10.5.20181130+ds'
Upstream version 10.5.20181130(+ds).
- - - - -
7a28c989 by Aaron M. Ucko at 2018-12-05T21:05:06Z
debian/man: Update for new release (10.5.20181130[+ds]).
* nquire.1: Document new -examples and -version flags.
* rchive.1: -invert no longer takes a field name (instead covering all
of them); -search is gone (redundant with -query).
* transmute.1: Undocument -pubmed (no longer advertised); document
-decode, -encode, and -x(ml)2j(son).
- - - - -
81d9ffd1 by Aaron M. Ucko at 2018-12-05T21:05:06Z
Merge tag 'upstream/10.5.20181204+ds'
Upstream version 10.5.20181204(+ds).
- - - - -
692b3a1a by Aaron M. Ucko at 2018-12-05T21:05:06Z
debian/control: Repoint Vcs-{Browser,Git} at salsa.debian.org.
- - - - -
5096d603 by Aaron M. Ucko at 2018-12-05T22:41:41Z
debian/control: Rules-Requires-Root: no (confirmed safe).
- - - - -
31481224 by Aaron M. Ucko at 2018-12-05T22:43:33Z
debian/control: Standards-Version: 4.2.1 (compliant at this point).
- - - - -
40e8a250 by Aaron M. Ucko at 2018-12-06T02:21:29Z
Finalize ncbi-entrez-direct 10.5.20181204+ds-1 for unstable.
- - - - -
30 changed files:
- .gitignore
- + archive-pubmed
- asp-ls
- + build.sh
- + common.go
- debian/.gitignore
- debian/changelog
- debian/control
- debian/examples
- + debian/man/archive-pubmed.1
- + debian/man/download-pubmed.1
- + debian/man/download-sequence.1
- + debian/man/eblast.1
- debian/man/edirect.1
- debian/man/efetch.1
- debian/man/efilter.1
- debian/man/elink.1
- debian/man/entrez-phrase-search.1
- + debian/man/fetch-pubmed.1
- debian/man/ftp-cp.1
- debian/man/ftp-ls.1
- + debian/man/index-pubmed.1
- + debian/man/intersect-uid-lists.1
- + debian/man/local-phrase-search.1
- debian/man/nquire.1
- + debian/man/phrase-search.1
- + debian/man/pm-clean.1
- + debian/man/pm-current.1
- + debian/man/pm-erase.1
- + debian/man/pm-index.1
The diff was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/compare/d4dd398c8391ae6b3f858d4a8a3b640f0bfa7768...40e8a2506fb1eac59f833634eb8f9e836e337694
--
View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/compare/d4dd398c8391ae6b3f858d4a8a3b640f0bfa7768...40e8a2506fb1eac59f833634eb8f9e836e337694
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