[med-svn] [Git][med-team/bedtools][master] 14 commits: routine-update: New upstream version

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / bedtools


Commits:
50e76de3 by Étienne Mollier at 2023-06-23T22:12:45+02:00
routine-update: New upstream version

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de42b012 by Étienne Mollier at 2023-06-23T22:12:47+02:00
New upstream version 2.31.0+dfsg
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b045ade9 by Étienne Mollier at 2023-06-23T22:13:12+02:00
Update upstream source from tag 'upstream/2.31.0+dfsg'

Update to upstream version '2.31.0+dfsg'
with Debian dir a5f8b71ca488edf4146df385591d9f977eb0f379
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a7381107 by Étienne Mollier at 2023-06-23T22:13:12+02:00
routine-update: Standards-Version: 4.6.2

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821afd62 by Étienne Mollier at 2023-06-23T22:14:07+02:00
remove_barski_binding_site.png.patch: unfuzz.

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ca88564d by Étienne Mollier at 2023-06-23T22:17:52+02:00
2to3.patch: refresh.

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04322fad by Étienne Mollier at 2023-06-23T22:19:47+02:00
2to3.patch: declare forwarding not-needed.

Upstream looks to assume python is python3 nowadays.

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df5ad2bd by Étienne Mollier at 2023-06-23T22:20:50+02:00
hardening patch: unfuzz.

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a7b07acb by Étienne Mollier at 2023-06-23T22:21:08+02:00
htsutil patch: unfuzz.

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0555677f by Étienne Mollier at 2023-06-23T22:24:46+02:00
gcc-13.patch: add; fix ftbfs with gcc-13.

Closes: #1037588
Thanks: David Seifert

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9a4d3bff by Étienne Mollier at 2023-06-23T22:51:57+02:00
2to3.patch: remove my unneeded "fix".

Gbp-Dch: ignore

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9411a762 by Étienne Mollier at 2023-06-23T22:52:22+02:00
d/control: bedtools-test depend on python3.

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f9286654 by Étienne Mollier at 2023-06-23T22:56:20+02:00
2to3.patch: remove remaining occurrences of python.

There are still some tests and some documentation referring to the
unversionned python, which in Debian is by default python2.

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ad36a93f by Étienne Mollier at 2023-06-23T23:18:39+02:00
ready to upload to unstable.

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30 changed files:

- .gitignore
- Makefile
- README.md
- debian/changelog
- debian/control
- debian/patches/2to3.patch
- + debian/patches/gcc-13.patch
- debian/patches/hardening
- debian/patches/htsutil
- debian/patches/remove_barski_binding_site.png.patch
- debian/patches/series
- docs/conf.py
- docs/content/bedtools-suite.rst
- docs/content/general-usage.rst
- docs/content/history.rst
- + docs/content/images/tool-glyphs/multiinter-glyph.png
- + docs/content/images/tool-glyphs/summary.png
- docs/content/installation.rst
- docs/content/overview.rst
- docs/content/tools/bamtobed.rst
- docs/content/tools/bamtofastq.rst
- docs/content/tools/closest.rst
- docs/content/tools/genomecov.rst
- docs/content/tools/groupby.rst
- docs/content/tools/maskfasta.rst
- docs/content/tools/multiinter.rst
- docs/content/tools/overlap.rst
- docs/content/tools/shift.rst
- + docs/content/tools/summary.rst
- docs/index.rst


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/bedtools/-/compare/4219183268d78af75628673989254cea91ef006b...ad36a93f547695e9e3fd55c94cfcbfe7b081b932

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View it on GitLab: https://salsa.debian.org/med-team/bedtools/-/compare/4219183268d78af75628673989254cea91ef006b...ad36a93f547695e9e3fd55c94cfcbfe7b081b932
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