[med-svn] [Git][med-team/macs][upstream] New upstream version 3.0.5

[Michael R. Crusoe (@crusoe)]

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


Commits:
3cbb6858 by Michael R. Crusoe at 2026-10-04T10:47:54+02:00
New upstream version 3.0.5
- - - - -


61 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
- 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/-/commit/3cbb685841f358b4461d990f9aad7d33e2aa566a

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View it on GitLab: https://salsa.debian.org/med-team/macs/-/commit/3cbb685841f358b4461d990f9aad7d33e2aa566a
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