[med-svn] [Git][med-team/kalign][upstream] New upstream version 3.5.1

[Charles Plessy (@plessy)]

Charles Plessy pushed to branch upstream at Debian Med / kalign


Commits:
ce28fe71 by Charles Plessy at 2026-02-27T16:41:37+09:00
New upstream version 3.5.1
- - - - -


146 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
- 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/-/commit/ce28fe71f132ea819e72747073ba4068879b2719

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