[med-svn] [Git][med-team/gubbins][upstream] New upstream version 3.4

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch upstream at Debian Med / gubbins


Commits:
8ed57cf9 by Étienne Mollier at 2024-11-30T18:36:38+01:00
New upstream version 3.4
- - - - -


30 changed files:

- .github/workflows/build.yml
- R/scripts/plot_gubbins.R
- README.md
- VERSION
- configure.ac
- docs/gubbins_manual.md
- python/gubbins/common.py
- python/gubbins/tests/test_python_scripts.py
- python/gubbins/tests/test_utils.py
- python/gubbins/treebuilders.py
- python/gubbins/utils.py
- + python/scripts/extract_recombinant_sequences.py
- python/scripts/generate_ska_alignment.py
- python/setup.py
- src/Newickform.c
- src/Newickform.h
- src/block_tab_file.c
- src/branch_sequences.c
- src/branch_sequences.h
- src/csv_of_snp_sites.c
- src/gubbins.c
- src/gubbins.h
- src/main.c
- src/parse_phylip.c
- src/parse_phylip.h
- src/snp_searching.c
- src/tree_statistics.c
- tests/check_branch_sequences.c
- tests/check_gubbins.c
- tests/data/multiple_recombinations.expected.tre


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/gubbins/-/commit/8ed57cf96e71e00ace67702e586053f35286b036

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