Michael R. Crusoe pushed to branch master at Debian Med / cnvkit
Commits: f9489e8a by Michael R. Crusoe at 2026-05-14T10:28:27+02:00 New upstream version - - - - - 3d4bf86e by Michael R. Crusoe at 2026-05-14T10:28:29+02:00 New upstream version 0.9.13 - - - - - 7cddcecf by Michael R. Crusoe at 2026-05-14T10:31:17+02:00 Update upstream source from tag 'upstream/0.9.13' Update to upstream version '0.9.13' with Debian dir cabdc5317086ce2d7006fc66b466e64d58a4e4e2 - - - - - 1d0bd3dd by Michael R. Crusoe at 2026-05-14T10:31:17+02:00 Standards-Version: 4.7.4 (routine-update) - - - - - 96a7c77e by Michael R. Crusoe at 2026-05-14T10:34:31+02:00 debputy lint --auto-fix (routine-update) - - - - - 88b00077 by Michael R. Crusoe at 2026-05-14T10:42:24+02:00 Refreshed patches. - - - - - 860418ad by Michael R. Crusoe at 2026-05-14T10:50:02+02:00 d/control: needs pomegranate v1.x+. - - - - - e8abd64f by Michael R. Crusoe at 2026-05-18T17:49:28+02:00 d/control: only build for the default version of Python, to match pomegranate/pytorch. - - - - - 495f7f83 by Michael R. Crusoe at 2026-05-18T17:49:59+02:00 d/install: there is not a scripts directory anymore. - - - - - 049186a6 by Michael R. Crusoe at 2026-05-18T17:55:08+02:00 Cherry-picked patch from upstream to fix the tests. - - - - - 95177901 by Michael R. Crusoe at 2026-05-18T17:23:12+01:00 Update watch file format version to 5. Changes-By: lintian-brush Fixes: lintian: older-debian-watch-file-standard See-also: https://lintian.debian.org/tags/older-debian-watch-file-standard.html - - - - - f6218b16 by Michael R. Crusoe at 2026-05-18T17:23:12+01:00 Use GitHub template in watch file instead of explicit Source/Matching-Pattern. Changes-By: lintian-brush - - - - - 5087fd36 by Michael R. Crusoe at 2026-05-18T18:36:54+02:00 upload to unstable. - - - - - 114 changed files: - + .devcontainer/Dockerfile - + .devcontainer/devcontainer.json - + .dockerignore - + .github/workflows/claude-code-review.yml - + .github/workflows/claude.yml - + .github/workflows/integration-tests.yaml - .github/workflows/tests-tox.yaml - .gitignore - .readthedocs.yaml - + CLAUDE.md - Dockerfile - 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/__init__.py - scripts/cnv_annotate.py → cnvlib/cli/cnv_annotate.py - scripts/cnv_expression_correlate.py → cnvlib/cli/cnv_expression_correlate.py - + cnvlib/cli/cnv_updater.py - scripts/genome_instability_index.py → cnvlib/cli/genome_instability_index.py - scripts/guess_baits.py → cnvlib/cli/guess_baits.py - scripts/reference2targets.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/reference.py - cnvlib/reports.py - cnvlib/rna.py - cnvlib/samutil.py - cnvlib/scatter.py - cnvlib/segfilters.py - cnvlib/segmentation/__init__.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/install - − debian/patches/0004-Remove-np.asfarray-np.float_-usage-to-support-numpy-.patch - + debian/patches/0004-test-update-a-call-to-smooth-bootstrap-int-now.patch - − debian/patches/0005-Another-numpy-2.x-fix.patch - debian/patches/controldir - debian/patches/ignore-warnings-in-tests.patch - debian/patches/python3compat.patch - debian/patches/series - debian/watch - devtools/conda-recipe/meta.yaml - doc/conf.py - doc/index.rst - + environment-dev.yml - pyproject.toml - requirements/core.txt - requirements/dev.txt - requirements/min.txt - requirements/tests.txt - − requirements/typing.txt - − scripts/cnv_updater.py - skgenome/chromsort.py - + skgenome/cli/__init__.py - scripts/skg_convert.py → skgenome/cli/skg_convert.py - skgenome/combiners.py - skgenome/gary.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/formats/na12878-M-Y-trunc-nochr.bed.gz - + test/formats/na12878-M-Y-trunc-nochr.bed.gz.tbi - + test/formats/na12878-chrM-Y-trunc.bed.gz - + test/formats/na12878-chrM-Y-trunc.bed.gz.tbi - test/test_commands.py - test/test_genome.py - test/test_io.py - + test/test_parallel.py - + test/test_rna.py - tox.ini The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/cnvkit/-/compare/6dbbee2eab88f64211ea5d4e404337df5b81f484...5087fd365ed45a949acb2bed709dc0b48e3fc1c1 -- View it on GitLab: https://salsa.debian.org/med-team/cnvkit/-/compare/6dbbee2eab88f64211ea5d4e404337df5b81f484...5087fd365ed45a949acb2bed709dc0b48e3fc1c1 You're receiving this email because of your account on salsa.debian.org. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help
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