Karsten Schöke pushed to branch upstream at Debian Med / python-skbio
Commits: b3a9d6a3 by Karsten Schöke at 2026-06-18T11:32:09+02:00 New upstream version 0.7.3 - - - - - 225 changed files: - + .github/workflows/array-api.yml - .github/workflows/ci.yml - .github/workflows/release.yml - .github/workflows/website.yml - .github/workflows/wheels.yml - .gitignore - .pre-commit-config.yaml - CHANGELOG.md - README.rst - checklist.py - ci/conda_requirements.txt → ci/requirements.txt - doc/source/_static/css/style.css - doc/source/_templates/TreeNode.rst - doc/source/autoinherit.py - doc/source/conf.py - pyproject.toml - setup.py - skbio/__init__.py - skbio/_config.py - skbio/alignment/__init__.py - skbio/alignment/_cutils.pyx - + skbio/alignment/_distance.py - skbio/alignment/_pair.py - skbio/alignment/_pairwise.py - skbio/alignment/_path.py - skbio/alignment/_score.py - skbio/alignment/_tabular_msa.py - skbio/alignment/_utils.py - + skbio/alignment/tests/data/tp53.nucl.aln - + skbio/alignment/tests/data/tp53.prot.aln - + skbio/alignment/tests/test_distance.py - skbio/alignment/tests/test_pair.py - skbio/alignment/tests/test_tabular_msa.py - skbio/binaries/__init__.py - skbio/binaries/_distance.py - skbio/binaries/_util.py - skbio/diversity/_block.py - skbio/diversity/_driver.py - skbio/diversity/_phylogenetic.pyx - skbio/diversity/alpha/tests/test_base.py - skbio/diversity/alpha/tests/test_chao1.py - skbio/diversity/alpha/tests/test_gini.py - skbio/diversity/beta/_unifrac.py - skbio/diversity/tests/test_driver.py - skbio/embedding/_protein.py - skbio/io/__init__.py - skbio/io/_exception.py - skbio/io/_fileobject.py - skbio/io/_iosources.py - skbio/io/descriptors.py - skbio/io/format/_sequence_feature_vocabulary.py - skbio/io/format/binary_dm.py - skbio/io/format/biom.py - skbio/io/format/blast6.py - skbio/io/format/blast7.py - skbio/io/format/clustal.py - skbio/io/format/embed.py - skbio/io/format/embl.py - skbio/io/format/emptyfile.py - skbio/io/format/fasta.py - skbio/io/format/fastq.py - skbio/io/format/genbank.py - skbio/io/format/gff3.py - skbio/io/format/lsmat.py - skbio/io/format/newick.py - skbio/io/format/ordination.py - skbio/io/format/phylip.py - + skbio/io/format/phylip_dm.py - skbio/io/format/qseq.py - skbio/io/format/sample_metadata.py - skbio/io/format/stockholm.py - skbio/io/format/taxdump.py - + skbio/io/format/tests/data/phylip_dm_good_simple_strict_square.dist - + skbio/io/format/tests/data/phylip_dm_good_simple_strict_square_reader.dist - + skbio/io/format/tests/data/phylip_dm_invalid_empty_line_after_header.dist - + skbio/io/format/tests/data/phylip_dm_invalid_empty_line_before_header.dist - + skbio/io/format/tests/data/phylip_dm_invalid_header_too_long.dist - + skbio/io/format/tests/data/phylip_dm_invalid_no_dists.dist - + skbio/io/format/tests/data/phylip_dm_invalid_no_header.dist - + skbio/io/format/tests/data/phylip_dm_invalid_too_few_columns_sq.dist - + skbio/io/format/tests/data/phylip_dm_invalid_too_few_rows.dist - + skbio/io/format/tests/data/phylip_dm_invalid_too_many_columns.dist - + skbio/io/format/tests/data/phylip_dm_invalid_too_many_rows.dist - + skbio/io/format/tests/data/phylip_dm_invalid_wrong_number_dists_lt.dist - + skbio/io/format/tests/data/phylip_dm_invalid_zero_header.dist - + skbio/io/format/tests/data/phylip_dm_simple_lt.dist - + skbio/io/format/tests/data/phylip_dm_simple_sq.dist - + skbio/io/format/tests/data/phylip_dm_sq_invalid_empty_line_after_header.dist - + skbio/io/format/tests/data/phylip_dm_sq_invalid_empty_line_before_header.dist - + skbio/io/format/tests/data/phylip_dm_valid_lt.dist - + skbio/io/format/tests/data/phylip_dm_valid_sq.dist - + skbio/io/format/tests/data/phylip_single_seq_relaxed - skbio/io/format/tests/test_binary_dm.py - skbio/io/format/tests/test_blast6.py - skbio/io/format/tests/test_fasta.py - skbio/io/format/tests/test_fastq.py - skbio/io/format/tests/test_lsmat.py - skbio/io/format/tests/test_phylip.py - + skbio/io/format/tests/test_phylip_dm.py - skbio/io/format/tests/test_sequence_feature_vocabulary.py - skbio/io/format/tests/test_stockholm.py - skbio/io/format/tests/test_taxdump.py - skbio/io/registry.py - + skbio/io/tests/test_descriptors.py - + skbio/io/tests/test_format_imports.py - skbio/io/tests/test_registry.py - skbio/io/util.py - skbio/metadata/_interval.py - skbio/metadata/_metadata.py - skbio/metadata/_mixin.py - skbio/metadata/tests/test_io.py - skbio/metadata/tests/test_metadata.py - skbio/metadata/tests/test_metadata_column.py - skbio/metadata/tests/test_missing.py - skbio/sequence/_genetic_code.py - skbio/sequence/_grammared_sequence.py - skbio/sequence/_nucleotide_mixin.py - skbio/sequence/_sequence.py - skbio/sequence/_substitution.py - skbio/sequence/distance.py - skbio/sequence/tests/test_distance.py - skbio/sequence/tests/test_grammared_sequence.py - skbio/sequence/tests/test_sequence.py - skbio/stats/_subsample.py - + skbio/stats/composition/__init__.py - + skbio/stats/composition/_ancom.py - + skbio/stats/composition/_ancombc.py - skbio/stats/composition.py → skbio/stats/composition/_base.py - + skbio/stats/composition/_dirmult.py - + skbio/stats/composition/_utils.py - + skbio/stats/composition/tests/data/pseq_feature_table_subset.csv.gz - + skbio/stats/composition/tests/data/pseq_meta_data_subset.csv.gz - + skbio/stats/composition/tests/data/pseq_subset_out_res_diff_abn.csv - + skbio/stats/composition/tests/test_ancom.py - + skbio/stats/composition/tests/test_ancombc.py - skbio/stats/tests/test_composition.py → skbio/stats/composition/tests/test_base.py - + skbio/stats/composition/tests/test_dirmult.py - + skbio/stats/composition/tests/test_utils.py - skbio/stats/distance/__init__.py - skbio/stats/distance/_anosim.py - skbio/stats/distance/_base.py - skbio/stats/distance/_cutils.pyx - skbio/stats/distance/_mantel.py - skbio/stats/distance/_permanova.py - skbio/stats/distance/_permdisp.py - skbio/stats/distance/_utils.py - skbio/stats/distance/tests/test_anosim.py - skbio/stats/distance/tests/test_base.py - skbio/stats/distance/tests/test_bioenv.py - skbio/stats/distance/tests/test_mantel.py - skbio/stats/distance/tests/test_permanova.py - skbio/stats/distance/tests/test_permdisp.py - skbio/stats/gradient.py - skbio/stats/ordination/__init__.py - skbio/stats/ordination/_correspondence_analysis.py - + skbio/stats/ordination/_mmvec.py - skbio/stats/ordination/_ordination_results.py - + skbio/stats/ordination/_principal_component_analysis.py - skbio/stats/ordination/_principal_coordinate_analysis.py - skbio/stats/ordination/_utils.py - + skbio/stats/ordination/tests/data/cf/README.md - + skbio/stats/ordination/tests/data/cf/metabolite_meta.tsv.sha256 - + skbio/stats/ordination/tests/data/cf/metabolites.tsv.sha256 - + skbio/stats/ordination/tests/data/cf/microbe_meta.tsv.sha256 - + skbio/stats/ordination/tests/data/cf/microbes.tsv.sha256 - + skbio/stats/ordination/tests/data/soils/README.md - + skbio/stats/ordination/tests/data/soils/metabolites.tsv - + skbio/stats/ordination/tests/data/soils/metabolites.tsv.sha256 - + skbio/stats/ordination/tests/data/soils/microbes.tsv - + skbio/stats/ordination/tests/data/soils/microbes.tsv.sha256 - skbio/stats/ordination/tests/test_correspondence_analysis.py - + skbio/stats/ordination/tests/test_mmvec.py - skbio/stats/ordination/tests/test_ordination_results.py - + skbio/stats/ordination/tests/test_principal_component_analysis.py - skbio/stats/ordination/tests/test_principal_coordinate_analysis.py - skbio/stats/power.py - − skbio/stats/tests/test_ndarray.py - skbio/stats/tests/test_power.py - skbio/table/_augment.py - skbio/table/_base.py - skbio/table/_tabular.py - skbio/table/tests/test_augment.py - skbio/table/tests/test_tabular.py - skbio/tree/__init__.py - skbio/tree/_c_me.pyx - skbio/tree/_c_nj.pyx - skbio/tree/_compare.py - skbio/tree/_me.py - skbio/tree/_nj.py - skbio/tree/_tree.py - + skbio/tree/tests/data/mp100.bme.nni.nwk - + skbio/tree/tests/data/mp100.bme.nwk - + skbio/tree/tests/data/mp100.gme.nni.nwk - + skbio/tree/tests/data/mp100.gme.nwk - + skbio/tree/tests/data/mp100.nj.nwk - + skbio/tree/tests/data/mp100.phy - + skbio/tree/tests/data/mp100.upgma.nwk - skbio/tree/tests/test_compare.py - skbio/tree/tests/test_me.py - skbio/tree/tests/test_nj.py - skbio/tree/tests/test_tree.py - skbio/tree/tests/test_upgma.py - skbio/util/__init__.py - skbio/util/_array.py - skbio/util/_decorator.py - skbio/util/_docstring.py - skbio/util/_optionals.py - skbio/util/_testing.py - skbio/util/_typing.py - skbio/util/tests/test_array.py - skbio/util/tests/test_decorator.py - skbio/util/tests/test_docstring.py - skbio/util/tests/test_optionals.py - skbio/util/tests/test_testing.py - skbio/workflow.py - web/about.rst - web/conf.py - web/contribute.rst - + web/devdoc/array_api.rst - web/devdoc/release.rst - web/devdoc/review.rst - web/index.rst - web/install.rst - web/roadmap.rst - web/versions.json The diff was not included because it is too large. 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