[med-svn] [Git][med-team/snakemake][master] 29 commits: New upstream version 5.14.0

Sat Apr 25 19:10:51 BST 2020

Rebecca N. Palmer pushed to branch master at Debian Med / snakemake

Commits:
ce27b1da by Andreas Tille at 2020-04-09T10:41:01+02:00
New upstream version 5.14.0
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484cdb23 by Andreas Tille at 2020-04-09T10:41:01+02:00
routine-update: New upstream version

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8d134ae3 by Andreas Tille at 2020-04-09T10:41:17+02:00
Update upstream source from tag 'upstream/5.14.0'

Update to upstream version '5.14.0'
with Debian dir 559c55c33e4d63d8cdd14b7208f344f4b1907ba0
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6692c23a by Andreas Tille at 2020-04-09T10:52:34+02:00
Refresh patches

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36701c13 by Andreas Tille at 2020-04-09T10:53:08+02:00
R-U: Trailing whitespace in debian/changelog

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5ede8016 by Andreas Tille at 2020-04-09T10:53:09+02:00
routine-update: Add salsa-ci file

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c1b4cc8c by Andreas Tille at 2020-04-09T10:53:09+02:00
routine-update: Rules-Requires-Root: no

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f671d67b by Andreas Tille at 2020-04-09T10:53:17+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
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ddcda055 by Rebecca N. Palmer at 2020-04-09T14:27:49+01:00
Use Python 3 in subprocess calls.

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c8284853 by Rebecca N. Palmer at 2020-04-09T14:58:47+01:00
Merge branch 'master' into debian_for_upstream_5.14.0_which_requires_conda

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56367974 by Rebecca N. Palmer at 2020-04-09T17:15:09+01:00
move python3 fixes to a single patch

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e9fcd301 by Rebecca N. Palmer at 2020-04-09T17:18:45+01:00
Disable buggy test (upstream 322) and tests needing conda or docker.

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925c7493 by Rebecca N. Palmer at 2020-04-09T17:20:29+01:00
Delete unused patches.

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1cf3a516 by Rebecca N. Palmer at 2020-04-09T17:21:38+01:00
Use boto3 (like upstream) not boto.

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e5b407fe by Rebecca N. Palmer at 2020-04-09T18:12:13+01:00
Reproducibility: don't ship (timestamped) test logs.

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a767af98 by Rebecca N. Palmer at 2020-04-09T18:14:04+01:00
Add self to Uploaders.

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f156c10e by Rebecca N. Palmer at 2020-04-09T22:13:55+01:00
Update d/copyright.

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e5cc7980 by Rebecca N. Palmer at 2020-04-09T22:15:05+01:00
Remove Files-Excluded: the excluded directory no longer exists upstream.

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bf14fd40 by Rebecca N. Palmer at 2020-04-10T13:05:16+01:00
Update d/copyright.

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12901587 by Rebecca N. Palmer at 2020-04-10T13:07:02+01:00
Enable verbose test output.

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8fa5ce30 by Rebecca N. Palmer at 2020-04-10T13:07:47+01:00
Update dependencies, add minimal-Depends test.

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2dc6d5bd by Rebecca N. Palmer at 2020-04-10T22:36:40+01:00
Update d/copyright.

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e7d154fa by Rebecca N. Palmer at 2020-04-11T11:24:08+01:00
Privacy: use local dagre-d3, add missing Javascript dependencies,
don't appear to show live status when we don't.

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148f0055 by Rebecca N. Palmer at 2020-04-24T16:42:38+01:00
Use https for links where available.

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fa393738 by Rebecca N. Palmer at 2020-04-24T16:44:27+01:00
Fix rather than disable broken test_cluster_sync

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7d50f8d3 by Rebecca N. Palmer at 2020-04-24T17:07:11+01:00
edit patch descriptions, include upstream status

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ae057049 by Rebecca N. Palmer at 2020-04-25T15:53:53+01:00
fix link_security.patch (needs both upstream commits,
and overlaps with local_javascript.patch)

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d5c191a1 by Rebecca N. Palmer at 2020-04-25T17:35:43+01:00
Remove inconveniently licensed (CC-BY-SA) snippets.

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ff24eb24 by Rebecca N. Palmer at 2020-04-25T19:01:32+01:00
Install examples.

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30 changed files:

- .gitattributes
- .github/workflows/main.yml
- CHANGELOG.rst
- debian/README.source
- debian/changelog
- debian/control
- debian/copyright
- − debian/patches/0003-Use-debian-s-mathjax-package.patch
- − debian/patches/0004-drop_test_symlink_time_handling.patch
- − debian/patches/0005-drop_test_symlink_temp.patch
- − debian/patches/0007-noop-rate-limiter.patch
- debian/patches/0009-skip-test-without-google-cloud-sdk.patch
- − debian/patches/0010-skip-test-without-rmarkdown.patch
- − debian/patches/0011-fix-privacy-breach.patch
- − debian/patches/boto3_is_just_boto
- + debian/patches/bug322_cluster_sync.patch
- + debian/patches/link_security.patch
- + debian/patches/local_javascript.patch
- debian/patches/python3 → debian/patches/python3.patch
- + debian/patches/remove_ccbysa_snippets.patch
- debian/patches/series
- debian/patches/workaround_sphinx_issue.patch
- debian/rules
- + debian/salsa-ci.yml
- + debian/snakemake.examples
- debian/snakemake.install
- − debian/svg/get-svgs
- − debian/svg/install_with-bioconda-brightgreen.svg
- − debian/svg/johanneskoester_follow.svg
- − debian/svg/master.svg

The diff was not included because it is too large.

View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/13a15261cc8ba2b641dcfaf1410a298f60d5f496...ff24eb24855ae1cf2e52bd66f4a0d41d66858d01

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View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/13a15261cc8ba2b641dcfaf1410a298f60d5f496...ff24eb24855ae1cf2e52bd66f4a0d41d66858d01
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