Charles Plessy pushed to branch master at Debian Med / kalign
Commits: 92b24cbd by Charles Plessy at 2026-02-27T16:41:36+09:00 New upstream version - - - - - ce28fe71 by Charles Plessy at 2026-02-27T16:41:37+09:00 New upstream version 3.5.1 - - - - - 20deff66 by Charles Plessy at 2026-02-27T16:41:39+09:00 Update upstream source from tag 'upstream/3.5.1' Update to upstream version '3.5.1' with Debian dir cdac5fa5bca848ea6c76086cc04bef6720a42030 - - - - - 9d2dbe8d by Charles Plessy at 2026-02-27T16:41:39+09:00 Standards-Version: 4.7.3 (routine-update) - - - - - aebd0bf7 by Charles Plessy at 2026-02-27T16:41:41+09:00 Remove Priority field to comply with Debian Policy 4.7.3 (routine- update) - - - - - d32a6b43 by Charles Plessy at 2026-02-27T16:41:57+09:00 Set upstream metadata fields: Documentation. Changes-By: lintian-brush - - - - - b354582c by Charles Plessy at 2026-02-27T16:54:03+09:00 cme fix dpkg-control --save - - - - - 3536d0e8 by Charles Plessy at 2026-02-27T17:00:15+09:00 Relicensed to Apache 2.0 - - - - - ae470710 by Charles Plessy at 2026-02-27T17:00:50+09:00 Ready for upload and close upstream bug. - - - - - 150 changed files: - + .claude/commands/release.md - + .containerignore - + .github/workflows/benchmark.yml - .github/workflows/cmake.yml - .github/workflows/codeql-analysis.yml - + .github/workflows/python.yml - + .github/workflows/wheels.yml - .gitignore - + CITATION.cff - + CLAUDE.md - CMakeLists.txt - + CONTRIBUTING.md - COPYING - ChangeLog - + Containerfile - + Containerfile.downstream - + README-python.md - README.md - + benchmarks/__init__.py - + benchmarks/__main__.py - + benchmarks/analysis.py - + benchmarks/app.py - + benchmarks/combined_improvements.py - + benchmarks/datasets.py - + benchmarks/downstream/__init__.py - + benchmarks/downstream/__main__.py - + benchmarks/downstream/alignment_accuracy.py - + benchmarks/downstream/calibration.py - + benchmarks/downstream/figures.py - + benchmarks/downstream/hmmer_detection.py - + benchmarks/downstream/phylo_accuracy.py - + benchmarks/downstream/positive_selection.py - + benchmarks/downstream/provenance.py - + benchmarks/downstream/simulation.py - + benchmarks/downstream/utils.py - + benchmarks/external_balibase.py - + benchmarks/full_comparison.py - + benchmarks/make_summary_figure.py - + benchmarks/mumsa_plots.py - + benchmarks/mumsa_precision.py - + benchmarks/runner.py - + benchmarks/scoring.py - + benchmarks/vsm_ensemble_experiment.py - + build.zig - debian/changelog - debian/control - debian/copyright - debian/upstream/metadata - lib/CMakeLists.txt - lib/include/kalign/kalign.h - + lib/src/aln_apair_dist.c - + lib/src/aln_apair_dist.h - lib/src/aln_controller.c - lib/src/aln_mem.c - lib/src/aln_param.c - lib/src/aln_param.h - lib/src/aln_profileprofile.c - + lib/src/aln_refine.c - + lib/src/aln_refine.h - lib/src/aln_run.c - lib/src/aln_run.h - lib/src/aln_seqprofile.c - lib/src/aln_seqseq.c - lib/src/aln_setup.c - lib/src/aln_setup.h - lib/src/aln_struct.h - lib/src/aln_wrap.c - lib/src/aln_wrap.h - lib/src/alphabet.c - lib/src/alphabet.h - + lib/src/anchor_consistency.c - + lib/src/anchor_consistency.h - lib/src/bisectingKmeans.c - lib/src/bisectingKmeans.h - lib/src/bpm.c - lib/src/bpm.h - + lib/src/consensus_msa.c - + lib/src/consensus_msa.h - + lib/src/ensemble.c - + lib/src/ensemble.h - lib/src/euclidean_dist.c - lib/src/euclidean_dist.h - lib/src/msa_alloc.c - lib/src/msa_check.c - lib/src/msa_cmp.c - lib/src/msa_cmp.h - lib/src/msa_io.c - lib/src/msa_op.c - lib/src/msa_struct.h - lib/src/pick_anchor.c - + lib/src/poar.c - + lib/src/poar.h - lib/src/sequence_distance.c - lib/src/sequence_distance.h - + lib/src/sp_score.c - + lib/src/sp_score.h - lib/src/task.c - lib/src/task.h - lib/src/test.c - lib/src/tldevel.c - lib/src/tldevel.h - lib/src/tlmisc.c - lib/src/weave_alignment.c - lib/src/weave_alignment.h - + pyproject.toml - + python-kalign/__init__.py - + python-kalign/_core.cpp - + python-kalign/cli.py - + python-kalign/io.py - + python-kalign/py.typed - + python-kalign/utils.py - scripts/balibase_test.org - scripts/benchmark.org - scripts/bralibase.org - src/CMakeLists.txt - src/parameters.c - src/parameters.h - src/run_kalign.c - src/run_reformat.c - tests/CMakeLists.txt - tests/dssim.c - tests/dssim_test.c - + tests/kalign_api_test.c - + tests/kalign_ensemble_test.c - tests/kalign_lib_test.c - tests/large_benchmark.c - + tests/python/conftest.py - + tests/python/pytest.ini - + tests/python/test_basic_alignment.py - + tests/python/test_cli.py - + tests/python/test_compare.py - + tests/python/test_data/dna_sequences.fasta - + tests/python/test_data/invalid_sequences.fasta - + tests/python/test_data/protein_sequences.fasta - + tests/python/test_data/rna_sequences.fasta - + tests/python/test_downstream_foundation.py - + tests/python/test_downstream_integration.py - + tests/python/test_ecosystem_integration.py - + tests/python/test_ecosystem_real.py - + tests/python/test_edge_cases.py - + tests/python/test_error_handling.py - + tests/python/test_file_operations.py - + tests/python/test_input_validation.py - + tests/python/test_integration.py - + tests/python/test_modes.py - + tests/python/test_parameters.py - + tests/python/test_performance.py - + tests/python/test_sequence_types.py - + tests/zig_test.c - + uv.lock The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/kalign/-/compare/8b8bb89b976a9c7011570a1149fce3b6f22aef86...ae4707100dec9ac79546c124906d3732d86c9815 -- View it on GitLab: https://salsa.debian.org/med-team/kalign/-/compare/8b8bb89b976a9c7011570a1149fce3b6f22aef86...ae4707100dec9ac79546c124906d3732d86c9815 You're receiving this email because of your account on salsa.debian.org.
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