[med-svn] [Git][med-team/augur][upstream] New upstream version 22.3.0

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch upstream at Debian Med / augur


Commits:
cf0dadad by Étienne Mollier at 2023-08-20T17:56:51+02:00
New upstream version 22.3.0
- - - - -


28 changed files:

- .github/workflows/ci.yaml
- CHANGES.md
- augur/__version__.py
- augur/ancestral.py
- augur/filter/include_exclude_rules.py
- augur/refine.py
- 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/-/commit/cf0dadad6b6fa6f7fb419cc003b419852a5c61ec

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View it on GitLab: https://salsa.debian.org/med-team/augur/-/commit/cf0dadad6b6fa6f7fb419cc003b419852a5c61ec
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