[med-svn] [Git][med-team/macs][master] 13 commits: d/control: limit to 64-bit little-endian systems.

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch master at Debian Med / macs


Commits:
df34893c by Michael R. Crusoe at 2026-10-04T10:47:01+02:00
d/control: limit to 64-bit little-endian systems.

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7264819e by Michael R. Crusoe at 2026-10-04T10:47:48+02:00
New upstream version

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3cbb6858 by Michael R. Crusoe at 2026-10-04T10:47:54+02:00
New upstream version 3.0.5
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91557ba3 by Michael R. Crusoe at 2026-10-04T11:02:46+02:00
Update upstream source from tag 'upstream/3.0.5'

Update to upstream version '3.0.5'
with Debian dir d3b7eb9f75fb6f40ad7cdf83dc3fcc9638c079f2
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92956590 by Michael R. Crusoe at 2026-10-04T11:02:53+02:00
Changes made by cme

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3ca3e4a2 by Michael R. Crusoe at 2026-10-04T10:03:03+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

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773fbf8b by Michael R. Crusoe at 2026-10-04T10:03:06+01:00
Use GitHub template in watch file instead of explicit Source/Matching-Pattern.

Changes-By: lintian-brush

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e971725b by Michael R. Crusoe at 2026-10-04T10:03:19+01:00
Set upstream metadata fields: Repository, Repository-Browse.

Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html

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1ef5c3a7 by Michael R. Crusoe at 2026-10-04T11:03:23+02:00
debputy lint --auto-fix (routine-update)

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b5b2475f by Michael R. Crusoe at 2026-10-04T11:09:20+02:00
d/control: python3-cykhash is no longer needed; make dependency on scipy, pandas, and anndata Python packages more explicit.

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2d6c60fc by Michael R. Crusoe at 2026-10-04T11:17:25+02:00
Added patch to improve reproducibility by turning off the Cython line tracing feature.

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a8bd24f9 by Michael R. Crusoe at 2026-10-04T11:34:27+02:00
Added spelling typo fix patch.

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ba501cf8 by Michael R. Crusoe at 2026-10-04T11:59:06+02:00
added two entries to the list of subcommands to build manual pages for

callvar hmmratac (both added in version 3.0.0).

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69 changed files:

- − .dockerignore
- .github/workflows/build-and-test-MACS3-macos.yml
- .github/workflows/build-and-test-MACS3-non-x64.yml
- .github/workflows/build-and-test-MACS3-website.yml
- .github/workflows/build-and-test-MACS3-x64.yml
- + .github/workflows/macs-version-benchmark.yml
- + .github/workflows/macs3-release-benchmark.yml
- .github/workflows/publish-to-gh-with-sphinx.yml
- .gitignore
- CODE_OF_CONDUCT.md
- CONTRIBUTING.md
- ChangeLog
- MACS3/Commands/hmmratac_cmd.py
- MACS3/Commands/pileup_cmd.py
- + MACS3/Commands/pileup_v2_cmd.py
- MACS3/Signal/BedGraph.py
- MACS3/Signal/CallPeakUnit.py
- MACS3/Signal/FixWidthTrack.py
- MACS3/Signal/HMMR_EM.py
- MACS3/Signal/PairedEndTrack.py
- MACS3/Signal/PeakModel.py
- MACS3/Signal/PileupV2.py
- MACS3/Signal/ScoreTrack.py
- MACS3/Signal/SignalProcessing.py
- MACS3/Utilities/Constants.py
- README.md
- bin/macs3
- debian/changelog
- debian/control
- + debian/patches/reproducibility
- debian/patches/series
- + debian/patches/spelling
- debian/rules
- debian/upstream/metadata
- debian/watch
- docs/source/conf.py
- docs/source/docs/INSTALL.md
- docs/source/docs/bdgcmp.md
- docs/source/docs/bdgpeakcall.md
- docs/source/docs/callpeak.md
- docs/source/docs/cutoffanalysis.md
- + docs/source/docs/version_benchmark.md
- docs/source/index.md
- + notebooks/500-PBMC-test/anndata_implemetation_dev.ipynb
- + notebooks/500-PBMC-test/macs3-scATAC-pbmc-500-anndata.ipynb
- notebooks/500-PBMC-test/macs3-scATAC-pbmc-500.ipynb
- pyproject.toml
- requirements.txt
- + scripts/benchmark_pileup_mlx.py
- + scripts/benchmark_scoretrack_torch.py
- + scripts/build_docs.py
- + scripts/run_macs3_release_benchmark.sh
- + scripts/run_macs_version_survey.sh
- + scripts/summarize_macs3_release_benchmark.py
- + scripts/summarize_macs_version_survey.py
- setup.py
- test/cmdlinetest
- test/standard_results_callpeak_narrow/run_callpeak_narrow1_peaks.narrowPeak
- test/standard_results_callpeak_narrow/run_callpeak_narrow1_summits.bed
- test/standard_results_callpeak_pe_narrow/run_callpeak_bampe_narrow_peaks.narrowPeak
- test/standard_results_callpeak_pe_narrow/run_callpeak_bampe_narrow_summits.bed
- test/standard_results_callpeak_pe_narrow/run_callpeak_bedpe_narrow_peaks.narrowPeak
- test/standard_results_callpeak_pe_narrow/run_callpeak_bedpe_narrow_summits.bed
- test/test_BedGraph.py
- test/test_CallPeakUnit.py
- test/test_PairedEndTrack.py
- test/test_Pileup.py
- test/test_ScoreTrack.py
- test/test_SignalProcessing.py


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/macs/-/compare/12434340c200ca4d2445003e1bed3356b6b745c4...ba501cf8251c3a426d821508c5f60d7477cb8aa2

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View it on GitLab: https://salsa.debian.org/med-team/macs/-/compare/12434340c200ca4d2445003e1bed3356b6b745c4...ba501cf8251c3a426d821508c5f60d7477cb8aa2
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