[med-svn] [Git][med-team/paleomix][master] 9 commits: New upstream version 1.3.10

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / paleomix


Commits:
8063bf61 by Étienne Mollier at 2025-11-02T22:33:53+01:00
New upstream version 1.3.10
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1f3abfe7 by Étienne Mollier at 2025-11-02T22:33:55+01:00
Update upstream source from tag 'upstream/1.3.10'

Update to upstream version '1.3.10'
with Debian dir dd7913bb3766ea332b8bd80c3515291776ab1c0f
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344d8986 by Étienne Mollier at 2025-11-02T22:35:54+01:00
d/copyright: update copyright years.

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18c690e8 by Étienne Mollier at 2025-11-02T22:36:30+01:00
python3.11.patch: delete: issue fixed upstream.

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f1c5e940 by Étienne Mollier at 2025-11-02T22:37:15+01:00
shlex.patch: delete: issue fixed upstream.

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e659e2b6 by Étienne Mollier at 2025-11-02T22:37:54+01:00
d/control: drop redundant Rules-Requires-Root: no.

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d27e5faa by Étienne Mollier at 2025-11-02T22:38:16+01:00
d/control: declare compliance to standards version 4.7.2.

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23ffcf3b by Étienne Mollier at 2025-11-02T22:42:14+01:00
d/watch: convert to v5 Github template.

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ec2b0902 by Étienne Mollier at 2025-11-02T22:43:05+01:00
d/changelog: ready for upload to unstable.

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50 changed files:

- + .readthedocs.yaml
- CHANGES.md
- debian/changelog
- debian/control
- debian/copyright
- − debian/patches/python3.11.patch
- debian/patches/series
- − debian/patches/shlex.patch
- debian/watch
- 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/-/compare/ccbb6a565f6d38cd57730cd8638e9b872ae8aad4...ec2b0902d3f58d683ae762bcf2b1037e46dd79bd

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View it on GitLab: https://salsa.debian.org/med-team/paleomix/-/compare/ccbb6a565f6d38cd57730cd8638e9b872ae8aad4...ec2b0902d3f58d683ae762bcf2b1037e46dd79bd
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