Karsten Schöke pushed to branch master at Debian Med / python-cogent
Commits: 3a23e570 by Karsten Schöke at 2026-05-15T18:35:02+02:00 New upstream version - - - - - ede21f07 by Karsten Schöke at 2026-05-15T18:35:03+02:00 New upstream version 2026.5.14a0+dfsg - - - - - 9af7b1c2 by Karsten Schöke at 2026-05-15T18:35:24+02:00 Update upstream source from tag 'upstream/2026.5.14a0+dfsg' Update to upstream version '2026.5.14a0+dfsg' with Debian dir 7013fe2256faf39b7c005d2d44d9689983d2edfb - - - - - c9fc360a by Karsten Schöke at 2026-05-15T18:35:25+02:00 Standards-Version: 4.7.4 (routine-update) - - - - - 833179ce by Karsten Schöke at 2026-05-24T12:04:55+02:00 Patches cleaned up following upstream update. - - - - - 83017b64 by Karsten Schöke at 2026-05-24T12:05:45+02:00 d/control: Update B-D - - - - - 1187dd51 by Karsten Schöke at 2026-05-24T12:07:05+02:00 d/rules: Update PYTHONPATH for docu build environment. - - - - - 616a64db by Karsten Schöke at 2026-05-24T12:08:47+02:00 prepare 2026.5.14a0+dfsg-1 release. - - - - - df9bff6c by Karsten Schöke at 2026-05-24T12:09:45+02:00 New upstream version 2026.5.19a0+dfsg - - - - - e74f16a6 by Karsten Schöke at 2026-05-24T12:10:14+02:00 Update upstream source from tag 'upstream/2026.5.19a0+dfsg' Update to upstream version '2026.5.19a0+dfsg' with Debian dir 58cc09f584b3c8f2c3936b753b32525d2bcb53e5 - - - - - f4fd9380 by Karsten Schöke at 2026-05-25T15:45:25+02:00 d/watch: convert to v5 Github template. - - - - - 712f5a45 by Karsten Schöke at 2026-05-25T15:55:59+02:00 NumPy Python headers integrated into the build environment. - - - - - e4195327 by Karsten Schöke at 2026-05-25T16:33:44+02:00 rebase patches. - - - - - 6e4b850b by Karsten Schöke at 2026-05-25T17:09:34+02:00 Tackle privacy breaches caused by MathML. - - - - - e41f3c1b by Karsten Schöke at 2026-05-26T09:53:55+02:00 Clean fonts that made their way to the documentation package - - - - - 59e6aa43 by Karsten Schöke at 2026-05-26T09:55:18+02:00 New upstream version 2026.5.25a0+dfsg - - - - - 4b8fe2c4 by Karsten Schöke at 2026-05-26T09:55:44+02:00 Update upstream source from tag 'upstream/2026.5.25a0+dfsg' Update to upstream version '2026.5.25a0+dfsg' with Debian dir 964a298dce74b7f441d3f71aed706ff27de8a871 - - - - - d3d2a907 by Karsten Schöke at 2026-05-26T13:28:46+02:00 Made tests runnable. - - - - - 6ca2259a by Karsten Schöke at 2026-05-26T13:29:55+02:00 Disabling the information due to the fonts actually contained within it. - - - - - fae860ac by Karsten Schöke at 2026-05-26T13:30:38+02:00 prepare 2026.5.25a0+dfsg-1 release - - - - - 87cd93b1 by Karsten Schöke at 2026-05-26T14:33:14+02:00 tests needs python3-loky. - - - - - bd477af9 by Karsten Schöke at 2026-05-26T15:19:01+02:00 Made `chmod` in `fixperms` more robust. - - - - - 2223cd54 by Karsten Schöke at 2026-05-26T16:26:10+02:00 pyproject.toml is not available in the package for tests. - - - - - fbae0122 by Karsten Schöke at 2026-05-26T19:32:07+02:00 only use autopkgtest-pkg-pybuild tests - - - - - 417 changed files: - + .coveragerc - .github/ISSUE_TEMPLATE/bug_report.md - .github/ISSUE_TEMPLATE/deprecation.md - .github/dependabot.yml - .github/workflows/codeql.yml - .github/workflows/linters.yml - .github/workflows/release.yml - .github/workflows/testing_develop.yml - .gitignore - .hgignore - .sourcery.yaml - README.md - changelog.d/README.md - changelog.md - − debian/README.test - debian/changelog - debian/control - − debian/docs - debian/patches/fix_interpreter.patch → debian/patches/Fix-broken-interpreter-lines.patch - + debian/patches/Work-around-failure-in-sphinx-doc-processing.patch - + debian/patches/fix-lazy-imports-for-Sphinx-autodoc-builds.patch - − debian/patches/ignore_tests_accessing_network.patch - − debian/patches/remove-jupyter-sphinx.patch - debian/patches/series - − debian/patches/skip-parallel-tests-on-single-cpu-systems.patch - − debian/patches/sphinx.patch - + debian/python-cogent-doc.lintian-overrides - − debian/python3-cogent3.install - debian/rules - − debian/tests/control - − debian/tests/run-unit-test - debian/watch - doc/api/alignment/alignment.rst - + doc/api/alignment/classes/cogent3.core.alignment.Aligned.rst - doc/api/alignment/classes/cogent3.core.alignment.Alignment.rst - − doc/api/alignment/classes/cogent3.core.alignment.ArrayAlignment.rst - doc/api/alignment/classes/cogent3.core.alignment.SequenceCollection.rst - doc/api/alphabet/alphabet.rst - doc/api/alphabet/classes/cogent3.core.alphabet.Alphabet.rst → doc/api/alphabet/classes/cogent3.core.alphabet.CharAlphabet.rst - + doc/api/alphabet/classes/cogent3.core.alphabet.KmerAlphabet.rst - + doc/api/alphabet/classes/cogent3.core.alphabet.PhredEncoding.rst - + doc/api/alphabet/classes/cogent3.core.alphabet.SenseCodonAlphabet.rst - + doc/api/alphabet/classes/cogent3.core.alphabet.bytes_to_array.rst - + doc/api/alphabet/classes/cogent3.core.alphabet.make_qual_converter.rst - + doc/api/alphabet/classes/cogent3.core.alphabet.make_text_to_array_converter.rst - doc/api/annotation/classes/cogent3.core.annotation.Feature.rst - doc/api/annotation_db/classes/cogent3.core.annotation_db.BasicAnnotationDb.rst - doc/api/annotation_db/classes/cogent3.core.annotation_db.GenbankAnnotationDb.rst - doc/api/annotation_db/classes/cogent3.core.annotation_db.GffAnnotationDb.rst - − doc/api/app/composable/define_app.rst - − doc/api/app/io/classes/cogent3.app.io.register_datastore_reader.rst - doc/api/genetic_code/classes/cogent3.core.genetic_code.GeneticCode.rst - doc/api/index.rst - doc/api/moltype/classes/cogent3.core.moltype.MolType.rst - doc/api/moltype/moltype.rst - − doc/api/new_alignment/classes/cogent3.core.new_alignment.Aligned.rst - − doc/api/new_alignment/classes/cogent3.core.new_alignment.AlignedDataView.rst - − doc/api/new_alignment/classes/cogent3.core.new_alignment.AlignedSeqsData.rst - − doc/api/new_alignment/classes/cogent3.core.new_alignment.Alignment.rst - − doc/api/new_alignment/classes/cogent3.core.new_alignment.SeqDataView.rst - − doc/api/new_alignment/classes/cogent3.core.new_alignment.SeqsData.rst - − doc/api/new_alignment/classes/cogent3.core.new_alignment.SequenceCollection.rst - − doc/api/new_alphabet/classes/cogent3.core.new_alphabet.CharAlphabet.rst - − doc/api/new_alphabet/classes/cogent3.core.new_alphabet.KmerAlphabet.rst - − doc/api/new_genetic_code/classes/cogent3.core.new_genetic_code.GeneticCode.rst - − doc/api/new_genetic_code/genetic_code.rst - − doc/api/new_moltype/classes/cogent3.core.new_moltype.MolType.rst - − doc/api/new_sequence/classes/cogent3.core.new_sequence.DnaSequence.rst - − doc/api/new_sequence/classes/cogent3.core.new_sequence.ProteinSequence.rst - − doc/api/new_sequence/classes/cogent3.core.new_sequence.RnaSequence.rst - − doc/api/new_sequence/classes/cogent3.core.new_sequence.SeqView.rst - − doc/api/new_sequence/sequence.rst - + doc/api/seq_storage/classes/cogent3.core.seq_storage.AlignedSeqsData.rst - + doc/api/seq_storage/classes/cogent3.core.seq_storage.SeqsData.rst - doc/api/new_moltype/moltype.rst → doc/api/seq_storage/seq_storage.rst - doc/api/sequence/classes/cogent3.core.sequence.DnaSequence.rst - doc/api/sequence/classes/cogent3.core.sequence.ProteinSequence.rst - doc/api/sequence/classes/cogent3.core.sequence.RnaSequence.rst - + doc/api/seqview/classes/cogent3.core.seqview.AlignedDataView.rst - + doc/api/seqview/classes/cogent3.core.seqview.SeqDataView.rst - + doc/api/seqview/classes/cogent3.core.seqview.SeqView.rst - doc/api/new_alignment/alignment.rst → doc/api/seqview/seqview.rst - doc/api/new_sequence/classes/cogent3.core.new_sequence.SliceRecord.rst → doc/api/slice_record/classes/cogent3.core.slice_record.SliceRecord.rst - doc/api/new_alphabet/alphabet.rst → doc/api/slice_record/slice_record.rst - + doc/api/table/classes/cogent3.core.table.Columns.rst - + doc/api/table/classes/cogent3.core.table.Table.rst - doc/api/table/classes/cogent3.parse.table.FilteringParser.rst - − doc/api/table/classes/cogent3.util.table.Columns.rst - − doc/api/table/classes/cogent3.util.table.Table.rst - doc/api/table/table.rst - doc/api/tree/classes/cogent3.core.tree.PhyloNode.rst - − doc/api/util/deserialise/classes/cogent3.util.deserialise.register_deserialiser.rst - − doc/api/util/deserialise/deserialise_object.rst - doc/app/app_cookbook/align-codon.rst - doc/app/app_cookbook/align-nucleotide.rst - doc/app/app_cookbook/align-protein.rst - doc/app/app_cookbook/index-writers.rst - doc/app/app_cookbook/load-aligned.rst - doc/app/app_cookbook/load-json.rst - doc/app/app_cookbook/load-tabular.rst - doc/app/app_cookbook/load-unaligned.rst - doc/app/app_cookbook/sample-concat.rst - doc/app/app_cookbook/sample-fixed-len.rst - doc/app/app_cookbook/sample-min-len.rst - doc/app/app_cookbook/sample-omit-bad.rst - doc/app/app_cookbook/sample-omit-degen.rst - doc/app/app_cookbook/sample-omit-duplicated.rst - doc/app/app_cookbook/sample-omit-gap.rst - doc/app/app_cookbook/sample-take-n-seqs.rst - doc/app/app_cookbook/sample-take-pos.rst - doc/app/app_cookbook/sample-take-seqs.rst - doc/app/app_cookbook/sample-trim-stops.rst - doc/app/app_cookbook/write-db.rst - doc/app/app_cookbook/write-json.rst - doc/app/app_cookbook/write-seqs.rst - doc/app/app_cookbook/write-tabular.rst - doc/app/app_overview/app-overview.rst - doc/app/app_overview/dstore.rst - doc/app/app_overview/not-completed.rst - + doc/app/app_overview/user_function.rst - doc/app/app_tutorials/evo-ancestral-states.rst - doc/app/app_tutorials/evo-dt-nuc-model.rst - doc/app/app_tutorials/evo-extract-model-stats.rst - doc/app/app_tutorials/evo-hypothesis.rst - doc/app/app_tutorials/evo-model-timehet.rst - doc/app/app_tutorials/evo-model-with-tree.rst - doc/app/app_tutorials/evo-model.rst - doc/app/app_tutorials/evo-natsel_neutral.rst - doc/app/app_tutorials/evo-natsel_sitehet.rst - doc/app/app_tutorials/evo-natsel_timehet.rst - doc/app/app_tutorials/evo-natsel_zhang.rst - doc/app/app_tutorials/evo-nstat-codon-model.rst - doc/app/app_tutorials/evo-tr-codon-model.rst - doc/app/app_tutorials/evo-tr-nuc-model.rst - doc/app/index-app.rst - − doc/app/index-custom.rst - doc/app/index.rst - − doc/app/user_function.rst - doc/conf.py - doc/cookbook/DNA_and_RNA_sequences.rst - doc/cookbook/alignments.rst - doc/cookbook/alphabet.rst - doc/cookbook/annotation_db.rst - doc/cookbook/building_alignments.rst - doc/cookbook/building_phylogenies.rst - doc/cookbook/calc_genetic_distance.rst - doc/cookbook/evo_modelling.rst - doc/cookbook/features.rst - doc/cookbook/genetic_code.rst - doc/cookbook/loading_sequences.rst - doc/cookbook/moltypes.rst - doc/cookbook/simple_trees.rst - doc/cookbook/tables.rst - doc/cookbook/useful_utilities.rst - doc/cookbook/what_codes.rst - doc/data/GN-tree.json - + doc/data/tp53-annotations.json - + doc/data/tp53.fa - − doc/data/tp53.json - doc/data/tree-with-support.json - doc/data_file_links.rst - doc/doctest_rsts.py - doc/draw/aln/plot_aln-coevolution.rst - doc/draw/aln/plot_aln-dotplot-1.rst - doc/draw/aln/plot_aln-dotplot-2.rst - doc/draw/aln/plot_aln-dotplot-3.rst - doc/draw/aln/plot_aln-info-plot.rst - + doc/draw/annotations/plot_annotation-db.rst - doc/draw/aln/plot_seq-features.rst → doc/draw/annotations/plot_seq-features.rst - doc/draw/index.rst - doc/draw/tree/plot_tree-angular.rst - doc/draw/tree/plot_tree-circular.rst - + doc/draw/tree/plot_tree-iplotx.rst - doc/draw/tree/plot_tree-radial.rst - doc/draw/tree/plot_tree-square.rst - doc/draw/tree/plot_tree-support.rst - doc/examples/align_codons_to_protein.rst - doc/examples/calculate_UPGMA_cluster.rst - doc/examples/calculate_neigbourjoining_tree.rst - doc/examples/calculate_pairwise_distances.rst - doc/examples/hmm_par_heterogeneity.rst - doc/examples/index.rst - − doc/examples/manipulating_tree_nodes.rst - doc/examples/neutral_test.rst - doc/examples/parametric_bootstrap.rst - doc/examples/phylo_by_ls.rst - doc/examples/rate_heterogeneity.rst - doc/examples/relative_rate.rst - doc/examples/scope_model_params_on_trees.rst - doc/examples/simple.rst - doc/examples/testing_multi_loci.rst - doc/index.rst - doc/pycogent.rst - noxfile.py - pyproject.toml - − requirements.txt - + ruff.toml - src/cogent3/__init__.py - + src/cogent3/_dataset/__init__.py - + src/cogent3/_dataset/brca1.fasta - + src/cogent3/_dataset/murphy.tree - + src/cogent3/_plugin.py - src/cogent3/_version.py - src/cogent3/align/align.py - src/cogent3/align/pairwise.py - src/cogent3/align/progressive.py - src/cogent3/align/pycompare.py - src/cogent3/align/traceback.py - src/cogent3/app/__init__.py - + src/cogent3/app/_citations.py - src/cogent3/app/align.py - src/cogent3/app/composable.py - src/cogent3/app/data_store.py - src/cogent3/app/dist.py - src/cogent3/app/evo.py - src/cogent3/app/io.py - src/cogent3/app/result.py - src/cogent3/app/sample.py - src/cogent3/app/sqlite_data_store.py - src/cogent3/app/translate.py - src/cogent3/app/tree.py - src/cogent3/app/typing.py - src/cogent3/cluster/UPGMA.py - src/cogent3/core/alignment.py - src/cogent3/core/alphabet.py - src/cogent3/core/annotation.py - src/cogent3/core/annotation_db.py - src/cogent3/core/genetic_code.py - src/cogent3/core/info.py - src/cogent3/core/location.py - src/cogent3/core/moltype.py - − src/cogent3/core/new_alignment.py - − src/cogent3/core/new_alphabet.py - − src/cogent3/core/new_genetic_code.py - − src/cogent3/core/new_moltype.py - − src/cogent3/core/new_sequence.py - src/cogent3/core/profile.py - + src/cogent3/core/seq_storage.py - src/cogent3/core/sequence.py - + src/cogent3/core/seqview.py - + src/cogent3/core/slice_record.py - src/cogent3/util/table.py → src/cogent3/core/table.py - src/cogent3/core/tree.py - src/cogent3/data/molecular_weight.py - src/cogent3/draw/__init__.py - + src/cogent3/draw/annotation.py - src/cogent3/draw/dendrogram.py - src/cogent3/draw/dotplot.py - src/cogent3/draw/drawable.py - src/cogent3/evolve/bootstrap.py - src/cogent3/evolve/coevolution.py - src/cogent3/evolve/distance.py - src/cogent3/evolve/fast_distance.py - src/cogent3/evolve/likelihood_function.py - src/cogent3/evolve/likelihood_tree.py - src/cogent3/evolve/models.py - src/cogent3/evolve/motif_prob_model.py - src/cogent3/evolve/ns_substitution_model.py - src/cogent3/evolve/pairwise_distance_numba.py - src/cogent3/evolve/parameter_controller.py - src/cogent3/evolve/substitution_model.py - − src/cogent3/format/alignment.py - src/cogent3/format/bedgraph.py - src/cogent3/format/clustal.py - src/cogent3/format/nexus.py - + src/cogent3/format/sequence.py - src/cogent3/format/table.py - src/cogent3/format/util.py - src/cogent3/maths/markov.py - src/cogent3/maths/measure.py - src/cogent3/maths/optimisers.py - src/cogent3/maths/stats/__init__.py - src/cogent3/maths/stats/contingency.py - − src/cogent3/maths/stats/distribution.py - src/cogent3/maths/stats/jackknife.py - src/cogent3/maths/stats/kendall.py - src/cogent3/maths/stats/number.py - src/cogent3/maths/stats/period.py - − src/cogent3/maths/stats/special.py - src/cogent3/maths/stats/test.py - src/cogent3/maths/util.py - src/cogent3/parse/__init__.py - src/cogent3/parse/cigar.py - src/cogent3/parse/cisbp.py - src/cogent3/parse/cogent3_json.py - src/cogent3/parse/dialign.py - src/cogent3/parse/ebi.py - src/cogent3/parse/fasta.py - + src/cogent3/parse/fastq.py - src/cogent3/parse/gbseq.py - src/cogent3/parse/gcg.py - src/cogent3/parse/genbank.py - src/cogent3/parse/gff.py - src/cogent3/parse/jaspar.py - src/cogent3/parse/locuslink.py - src/cogent3/parse/ncbi_taxonomy.py - src/cogent3/parse/newick.py - src/cogent3/parse/nexus.py - src/cogent3/parse/psl.py - src/cogent3/parse/rdb.py - src/cogent3/parse/record_finder.py - src/cogent3/parse/sequence.py - src/cogent3/parse/table.py - src/cogent3/parse/tinyseq.py - src/cogent3/parse/tree.py - − src/cogent3/parse/tree_xml.py - src/cogent3/phylo/consensus.py - src/cogent3/phylo/nj.py - src/cogent3/phylo/tree_collection.py - src/cogent3/phylo/tree_distance.py - src/cogent3/phylo/tree_space.py - + src/cogent3/py.typed - src/cogent3/recalculation/definition.py - src/cogent3/recalculation/scope.py - src/cogent3/util/deserialise.py - src/cogent3/util/dict_array.py - src/cogent3/util/io.py - src/cogent3/util/misc.py - src/cogent3/util/parallel.py - src/cogent3/util/progress_display.py - src/cogent3/util/transform.py - src/cogent3/util/warning.py - tests/benchmark.py - tests/data/fastq.txt - − tests/data/old_annotation_style.json - − tests/data/sample_locked.tinydb - − tests/data/sample_locked_w_log.tinydb - + tests/data/tree_json_new.json - + tests/data/tree_json_old.json - tests/test_align/test_align.py - tests/test_align/test_compare.py - tests/test_app/test_align.py - − tests/test_app/test_app_mpi.py - − tests/test_app/test_composable.py - tests/test_app/test_data_store.py - tests/test_app/test_dist.py - tests/test_app/test_evo.py - tests/test_app/test_init.py - tests/test_app/test_io.py - tests/test_app/test_plugins.py - tests/test_app/test_result.py - tests/test_app/test_sample.py - tests/test_app/test_sqlite_data_store.py - tests/test_app/test_translate.py - tests/test_app/test_tree.py - tests/test_app/test_typing.py - tests/test_cluster/test_UPGMA.py - tests/test_core/test_alignment.py - tests/test_core/test_new_aln_annotation.py → tests/test_core/test_aln_annotation.py - tests/test_core/test_alphabet.py - − tests/test_core/test_annotation.py - tests/test_core/test_annotation_db.py - − tests/test_core/test_core_standalone.py - tests/test_core/test_features.py - tests/test_core/test_genetic_code.py - tests/test_core/test_location.py - tests/test_core/test_maps.py - tests/test_core/test_moltype.py - − tests/test_core/test_new_alignment.py - − tests/test_core/test_new_alphabet.py - − tests/test_core/test_new_genetic_code.py - − tests/test_core/test_new_moltype.py - − tests/test_core/test_new_sequence.py - tests/test_core/test_profile.py - − tests/test_core/test_seq_aln_integration.py - tests/test_core/test_new_seq_annotation.py → tests/test_core/test_seq_annotation.py - tests/test_core/test_sequence.py - tests/test_util/test_table.py → tests/test_core/test_table.py - tests/test_core/test_tree.py - tests/test_data/test_molecular_weight.py - + tests/test_dataset.py - + tests/test_draw/test_annotations.py - tests/test_draw/test_dendrogram.py - tests/test_draw/test_dotplot.py - tests/test_draw/test_draw_integration.py - tests/test_draw/test_new_draw_integration.py - tests/test_evolve/test_best_likelihood.py - tests/test_evolve/test_coevolution.py - tests/test_evolve/test_distance.py - tests/test_evolve/test_likelihood_function.py - tests/test_evolve/test_motifchange.py - tests/test_evolve/test_newq.py - tests/test_evolve/test_ns_substitution_model.py - tests/test_evolve/test_parameter_controller.py - tests/test_evolve/test_scale_rules.py - tests/test_format/test_bedgraph.py - tests/test_format/test_clustal.py - tests/test_maths/test_stats/__init__.py - − tests/test_maths/test_stats/test_distribution.py - tests/test_maths/test_stats/test_ks.py - tests/test_maths/test_stats/test_number.py - − tests/test_maths/test_stats/test_special.py - tests/test_maths/test_stats/test_test.py - tests/test_maths/test_util.py - tests/test_parse/test_blast.py - tests/test_parse/test_cigar.py - tests/test_parse/test_clustal.py - tests/test_parse/test_ebi.py - tests/test_parse/test_fasta.py - + tests/test_parse/test_fastq.py - tests/test_parse/test_gbseq.py - tests/test_parse/test_genbank.py - tests/test_parse/test_ncbi_taxonomy.py - tests/test_parse/test_nexus.py - tests/test_parse/test_pwm_parsers.py - tests/test_parse/test_rdb.py - tests/test_parse/test_record_finder.py - tests/test_parse/test_tinyseq.py - tests/test_parse/test_tree.py - tests/test_phylo.py - + tests/test_top_level_imports.py - tests/test_util/test_deserialise.py - tests/test_util/test_dictarray.py - tests/test_util/test_io.py - tests/test_util/test_misc.py - − tests/test_util/test_parallel.py - − tests/test_util/test_warning.py The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/python-cogent/-/compare/7003257c79f910cf5d1418753c38375fda206d57...fbae0122756c5a4117d62c03235357fd20084f16 -- View it on GitLab: https://salsa.debian.org/med-team/python-cogent/-/compare/7003257c79f910cf5d1418753c38375fda206d57...fbae0122756c5a4117d62c03235357fd20084f16 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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