[med-svn] [Git][med-team/paleomix][upstream] New upstream version 1.3.10

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch upstream at Debian Med / paleomix


Commits:
8063bf61 by Étienne Mollier at 2025-11-02T22:33:53+01:00
New upstream version 1.3.10
- - - - -


43 changed files:

- + .readthedocs.yaml
- CHANGES.md
- docs/conf.py
- docs/installation.rst
- paleomix/__init__.py
- paleomix/atomiccmd/pprint.py
- + paleomix/common/resources.py
- paleomix/common/rtools.py
- paleomix/main.py
- paleomix/nodes/formats.py
- paleomix/nodes/mapdamage.py
- paleomix/pipelines/bam/config.py
- paleomix/pipelines/bam/mkfile.py
- paleomix/pipelines/bam/pipeline.py
- paleomix/pipelines/phylo/example.py
- paleomix/pipelines/phylo/mkfile.py
- paleomix/pipelines/phylo/parts/msa.py
- paleomix/pipelines/zonkey/build_db.py
- paleomix/pipelines/zonkey/build_mito.py
- paleomix/pipelines/zonkey/common.py
- paleomix/pipelines/zonkey/parts/mitochondria.py
- paleomix/pipelines/zonkey/parts/nuclear.py
- paleomix/pipelines/zonkey/parts/report.py
- paleomix/pipelines/zonkey/parts/summary.py
- paleomix/pipelines/zonkey/pipeline.py
- paleomix/resources/__init__.py
- + paleomix/resources/examples/__init__.py
- paleomix/resources/reports/zonkey/report.css
- paleomix/tools/cleanup.py
- paleomix/tools/coverage.py
- paleomix/tools/depths.py
- paleomix/tools/dupcheck.py
- paleomix/tools/factory.py
- paleomix/tools/gtf_to_bed.py
- paleomix/tools/rmdup_collapsed.py
- + paleomix/tools/rscript.py
- paleomix/tools/vcf_filter.py
- paleomix/tools/vcf_to_fasta.py
- paleomix_environment.yaml
- setup.py
- tests/atomiccmd_test/command_test.py
- tests/tools_test/factory_test.py
- tox.ini


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/paleomix/-/commit/8063bf61112dff83e8046915715f15a442568ebf

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View it on GitLab: https://salsa.debian.org/med-team/paleomix/-/commit/8063bf61112dff83e8046915715f15a442568ebf
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