[med-svn] [Git][med-team/cnvkit][master] 7 commits: New upstream version 0.9.14

Fri Oct 9 13:04:24 BST 2026

Santiago Vila pushed to branch master at Debian Med / cnvkit

Commits:
e8f59147 by Santiago Vila at 2026-10-09T10:00:00+02:00
New upstream version 0.9.14
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e6f05960 by Santiago Vila at 2026-10-09T10:00:00+02:00
Update upstream source from tag 'upstream/0.9.14'

Update to upstream version '0.9.14'
with Debian dir 5ef7b1a64688363554f83b4b8934f4fe4e99e4b5
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b794863f by Santiago Vila at 2026-10-09T13:30:00+02:00
Refresh patches.

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88d36a0b by Santiago Vila at 2026-10-09T13:35:00+02:00
Always run all tests again.

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b5b05066 by Santiago Vila at 2026-10-09T13:40:00+02:00
Add build-dependencies on python3-bioframe and python3-statsmodels.

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07aa75b2 by Santiago Vila at 2026-10-09T13:45:00+02:00
Add devtools to debian/pybuild.testfiles.

Otherwise test/test_check_version.py fails. Not that it's an essential test
in a Debian environment, but this way we don't have to fiddle with debian/rules.

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595581bc by Santiago Vila at 2026-10-09T13:50:00+02:00
Upload for unstable as 0.9.14-1

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180 changed files:

- .devcontainer/Dockerfile
- .devcontainer/devcontainer.json
- .dockerignore
- + .github/FUNDING.yml
- − .github/workflows/claude-code-review.yml
- .github/workflows/claude.yml
- + .github/workflows/docker-build.yml
- .github/workflows/integration-tests.yaml
- .github/workflows/tests-tox.yaml
- + .github/workflows/version-guard.yaml
- .gitignore
- + .pre-commit-config.yaml
- CITATION
- CLAUDE.md
- + CONTRIBUTING.md
- Dockerfile
- + Makefile
- README.rst
- cnvlib/__init__.py
- cnvlib/_version.py
- cnvlib/access.py
- cnvlib/antitarget.py
- cnvlib/autobin.py
- cnvlib/batch.py
- cnvlib/bintest.py
- cnvlib/call.py
- cnvlib/cli/cnv_annotate.py
- cnvlib/cli/cnv_expression_correlate.py
- + cnvlib/cli/cnv_gene_info.py
- cnvlib/cli/cnv_updater.py
- cnvlib/cli/genome_instability_index.py
- cnvlib/cli/guess_baits.py
- cnvlib/cli/reference2targets.py
- cnvlib/cluster.py
- cnvlib/cmdutil.py
- cnvlib/cnary.py
- cnvlib/cnvkit.py
- cnvlib/commands.py
- cnvlib/core.py
- cnvlib/coverage.py
- cnvlib/descriptives.py
- cnvlib/diagram.py
- cnvlib/export.py
- cnvlib/fix.py
- cnvlib/heatmap.py
- cnvlib/import_rna.py
- cnvlib/importers.py
- cnvlib/metrics.py
- cnvlib/parallel.py
- cnvlib/params.py
- cnvlib/plots.py
- + cnvlib/purity.py
- cnvlib/reference.py
- cnvlib/reports.py
- cnvlib/rna.py
- cnvlib/samutil.py
- cnvlib/scatter.py
- cnvlib/segfilters.py
- cnvlib/segmentation/__init__.py
- cnvlib/segmentation/cbs.py
- − cnvlib/segmentation/flasso.py
- cnvlib/segmentation/haar.py
- cnvlib/segmentation/hmm.py
- cnvlib/segmentation/none.py
- cnvlib/segmetrics.py
- cnvlib/smoothing.py
- cnvlib/target.py
- cnvlib/vary.py
- conda-env.yml
- debian/changelog
- debian/control
- − debian/patches/0004-test-update-a-call-to-smooth-bootstrap-int-now.patch
- debian/patches/controldir → debian/patches/controldir.patch
- debian/patches/ignore-warnings-in-tests.patch
- debian/patches/python3compat.patch
- debian/patches/series
- debian/pybuild.testfiles
- debian/rules
- + devtools/check_version.py
- devtools/conda-recipe/meta.yaml
- doc/baf.rst
- doc/bias.rst
- doc/calling.rst
- doc/cnvlib.rst
- doc/conf.py
- + doc/development.rst
- + doc/docker.rst
- doc/fileformats.rst
- doc/heterogeneity.rst
- doc/importexport.rst
- doc/index.rst
- doc/nonhybrid.rst
- doc/pipeline.rst
- doc/plots.rst
- doc/quickstart.rst
- doc/reports.rst
- doc/rna.rst
- doc/scripts.rst
- doc/sex.rst
- doc/skgenome.rst
- doc/tumor.rst
- doc/whoelse.rst
- environment-dev.yml
- − galaxy/cnvkit_tool.xml
- pyproject.toml
- requirements/core.txt
- requirements/min.txt
- requirements/tests.txt
- skgenome/__init__.py
- + skgenome/_pysam.py
- + skgenome/chromnames.py
- skgenome/chromsort.py
- skgenome/cli/skg_convert.py
- skgenome/combiners.py
- + skgenome/cut.py
- skgenome/gary.py
- + skgenome/genomebuild.py
- skgenome/intersect.py
- skgenome/merge.py
- skgenome/rangelabel.py
- skgenome/subdivide.py
- skgenome/subtract.py
- skgenome/tabio/__init__.py
- skgenome/tabio/bedio.py
- skgenome/tabio/genepred.py
- skgenome/tabio/gff.py
- skgenome/tabio/picard.py
- skgenome/tabio/seg.py
- skgenome/tabio/seqdict.py
- skgenome/tabio/tab.py
- skgenome/tabio/textcoord.py
- skgenome/tabio/util.py
- skgenome/tabio/vcfio.py
- skgenome/tabio/vcfsimple.py
- test/Makefile
- test/clustering.makefile
- test/conftest.py
- + test/formats/format-no-sample.vcf
- + test/formats/gt-nocall.vcf
- + test/formats/gt-partial.vcf
- test/formats/na12878-chrM-Y-trunc.bam
- + test/formats/na12878-chrM-Y-trunc.cram
- + test/formats/na12878-chrM-Y-trunc.cram.crai
- + test/formats/regression/p2-9_2.call.cns
- + test/formats/regression/p2-9_2.cnr
- + test/formats/regression/p2-9_2.cns
- + test/formats/rna-gene-resource.tsv
- + test/formats/rna-sample-A.counts.txt
- + test/formats/rna-sample-B.counts.txt
- + test/formats/rna-sample-C.counts.txt
- + test/formats/strelka.vcf
- + test/formats/vcf-het-no-altcount.vcf
- + test/test_analysis.py
- + test/test_batch.py
- + test/test_call.py
- + test/test_check_version.py
- + test/test_chromnames.py
- test/test_cnvlib.py
- test/test_commands.py
- + test/test_export.py
- test/test_genome.py
- + test/test_genomebuild.py
- + test/test_guess_baits.py
- + test/test_haar.py
- + test/test_hmm.py
- test/test_io.py
- test/test_parallel.py
- + test/test_plots.py
- + test/test_preprocessing.py
- + test/test_properties.py
- test/test_r.py
- + test/test_reference.py
- + test/test_regression.py
- test/test_rna.py
- + test/test_samutil.py
- + test/test_segfilters.py
- + test/test_segmentation.py
- + test/test_vary.py
- tox.ini
- − wdl/cnvkit.wdl

The diff was not included because it is too large.

View it on GitLab: https://salsa.debian.org/med-team/cnvkit/-/compare/47e7bab523e7effc51dd3244a02aa6184cfece2d...595581bc12bbdef56c698b681f59a1b6e8eb36ca

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View it on GitLab: https://salsa.debian.org/med-team/cnvkit/-/compare/47e7bab523e7effc51dd3244a02aa6184cfece2d...595581bc12bbdef56c698b681f59a1b6e8eb36ca
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