[med-svn] [Git][med-team/augur][master] 4 commits: routine-update: New upstream version

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / augur


Commits:
b794449e by Étienne Mollier at 2023-08-20T17:56:50+02:00
routine-update: New upstream version

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cf0dadad by Étienne Mollier at 2023-08-20T17:56:51+02:00
New upstream version 22.3.0
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00632630 by Étienne Mollier at 2023-08-20T17:57:49+02:00
Update upstream source from tag 'upstream/22.3.0'

Update to upstream version '22.3.0'
with Debian dir 4096858bf1cf64500e9455d5ef3b13ae2b032527
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b3ac3e3e by Étienne Mollier at 2023-08-20T18:20:02+02:00
ready to upload to unstable.

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29 changed files:

- .github/workflows/ci.yaml
- CHANGES.md
- augur/__version__.py
- augur/ancestral.py
- augur/filter/include_exclude_rules.py
- augur/refine.py
- debian/changelog
- tests/builds/zika/results/nt_muts.json
- − tests/functional/ancestral.t
- − tests/functional/ancestral/aligned.fasta
- + tests/functional/ancestral/cram/_setup.sh
- + tests/functional/ancestral/cram/default-nucleotide-reconstruction.t
- + tests/functional/ancestral/cram/infer-ambiguous-nucleotides.t
- + tests/functional/ancestral/cram/infer-amino-acid-sequences-with-missing-arguments.t
- + tests/functional/ancestral/cram/infer-amino-acid-sequences-with-root-sequence.t
- + tests/functional/ancestral/cram/infer-amino-acid-sequences.t
- + tests/functional/ancestral/cram/keep-ambiguous-nucleotides.t
- + tests/functional/ancestral/data/aa_sequences_2K.fasta
- + tests/functional/ancestral/data/aa_sequences_CA.fasta
- + tests/functional/ancestral/data/aa_sequences_ENV.fasta
- + tests/functional/ancestral/data/aa_sequences_MP.fasta
- + tests/functional/ancestral/data/aa_sequences_NS1.fasta
- + tests/functional/ancestral/data/aa_sequences_NS2A.fasta
- + tests/functional/ancestral/data/aa_sequences_NS2B.fasta
- + tests/functional/ancestral/data/aa_sequences_NS3.fasta
- + tests/functional/ancestral/data/aa_sequences_NS4A.fasta
- + tests/functional/ancestral/data/aa_sequences_NS4B.fasta
- + tests/functional/ancestral/data/aa_sequences_NS5.fasta
- + tests/functional/ancestral/data/aa_sequences_PRO.fasta


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/augur/-/compare/aac580f9f9c6c5346ea5a27dcb3b1b41d4becda5...b3ac3e3e0e1c03d328b0018585af3e6e8acfe278

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View it on GitLab: https://salsa.debian.org/med-team/augur/-/compare/aac580f9f9c6c5346ea5a27dcb3b1b41d4becda5...b3ac3e3e0e1c03d328b0018585af3e6e8acfe278
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