[med-svn] [Git][med-team/gubbins][master] 8 commits: New upstream version 2.4.1

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / gubbins


Commits:
fed4523a by Andreas Tille at 2022-02-13T14:31:17+01:00
New upstream version 2.4.1
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f0f1dfc3 by Andreas Tille at 2022-02-13T15:11:56+01:00
New upstream version 2.4.1
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c3ba1c52 by Andreas Tille at 2023-02-07T10:04:38+01:00
New upstream version 3.3
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186f119a by Andreas Tille at 2023-02-07T10:04:38+01:00
routine-update: New upstream version

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1f5b8bec by Andreas Tille at 2023-02-07T10:04:48+01:00
Update upstream source from tag 'upstream/3.3'

Update to upstream version '3.3'
with Debian dir f4e2540bdfa05cc2925bfd77c5f9951958af7271
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aee636a0 by Andreas Tille at 2023-02-07T10:04:48+01:00
routine-update: Standards-Version: 4.6.2

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46d8db0d by Andreas Tille at 2023-02-07T10:04:59+01:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository-Browse..

Changes-By: lintian-brush

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3b9891c9 by Andreas Tille at 2023-02-07T17:11:20+01:00
Refresh patches

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30 changed files:

- + .github/workflows/build.yml
- − .travis.yml
- CHANGELOG.md
- − Dockerfile
- − GubbinsManual_latest.docx
- Makefile.am
- + R/scripts/treeWAS_run.R
- README.md
- VERSION
- + codecov.yml
- configure.ac
- debian/changelog
- debian/control
- debian/patches/do_not_handle_python_by_upstream_build_system.patch
- debian/patches/gubbins_exe_in_usr_lib.patch
- debian/patches/iqtree2.patch
- − debian/patches/port-to-pytest.patch
- debian/patches/series
- − debian/patches/spelling-error-in-binary.patch
- debian/upstream/metadata
- + docs/gubbins_manual.md
- + docs/gubbins_tutorial.md
- + docs/pmen3_output.png
- + environment.yml
- example_data/PMEN1/PMEN1.branch_base_reconstruction.embl
- example_data/PMEN1/PMEN1.filtered_polymorphic_sites.fasta
- example_data/PMEN1/PMEN1.filtered_polymorphic_sites.phylip
- example_data/PMEN1/PMEN1.final_tree.tre
- + example_data/PMEN1/PMEN1.log
- + example_data/PMEN1/PMEN1.node_labelled.final_tree.tre


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/gubbins/-/compare/b67b2ee4557630cd4a0557a5caebf74a2d37f59c...3b9891c9f74e842cd7d927d3525ac0679a23a39b

-- 
View it on GitLab: https://salsa.debian.org/med-team/gubbins/-/compare/b67b2ee4557630cd4a0557a5caebf74a2d37f59c...3b9891c9f74e842cd7d927d3525ac0679a23a39b
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