Karsten Schöke pushed to branch master at Debian Med / python-skbio
Commits: ce5714dd by Michael R. Crusoe at 2025-09-02T19:45:12+02:00 New upstream version 0.7.0 - - - - - 9cf977e4 by Karsten Schöke at 2026-06-18T11:31:36+02:00 d/watch: Convert to version 5 - - - - - b3a9d6a3 by Karsten Schöke at 2026-06-18T11:32:09+02:00 New upstream version 0.7.3 - - - - - fed29940 by Karsten Schöke at 2026-06-18T11:32:24+02:00 Update upstream source from tag 'upstream/0.7.3' Update to upstream version '0.7.3' with Debian dir 12402b583e5916df7d813f32aaac71d49690d1ab - - - - - f44c6ec9 by Karsten Schöke at 2026-06-18T11:32:48+02:00 Packaging update (routine-update) - - - - - 981c28bd by Karsten Schöke at 2026-06-18T11:32:48+02:00 Standards-Version: 4.7.4 (routine-update) - - - - - 01dfe984 by Karsten Schöke at 2026-06-27T19:59:48+02:00 remove obsolete patches. - - - - - 27b89f4b by Karsten Schöke at 2026-06-27T20:01:49+02:00 set expliziet mathjax_path - - - - - 66d84c42 by Karsten Schöke at 2026-06-27T20:03:38+02:00 remove google analytics_id - - - - - 142d63fa by Karsten Schöke at 2026-06-27T20:04:38+02:00 Fix missing variable declarations in Cython code - - - - - 6ca2892b by Karsten Schöke at 2026-06-27T20:05:01+02:00 rebuild patches. - - - - - 013b930f by Karsten Schöke at 2026-06-27T20:05:22+02:00 dd gbp.conf file - - - - - 6a0e3aa1 by Karsten Schöke at 2026-06-27T20:06:10+02:00 Package modernized. - - - - - d20491f3 by Karsten Schöke at 2026-06-27T20:08:24+02:00 Removed files no longer present upstream. - - - - - 02df233a by Karsten Schöke at 2026-06-27T20:10:26+02:00 Update B-D and wrap-and-sort - - - - - c2b0dc58 by Karsten Schöke at 2026-06-27T20:11:43+02:00 Update lintian-overrides - - - - - c831772c by Karsten Schöke at 2026-06-27T20:14:59+02:00 prepare 0.7.3-1 release. - - - - - 6a08795a by Karsten Schöke at 2026-06-27T21:42:16+02:00 d/rules: disable doctest - - - - - 1192b41b by Karsten Schöke at 2026-08-10T15:16:33+02:00 Merge remote-tracking branch 'origin/master' - - - - - 714b6031 by Karsten Schöke at 2026-08-10T18:53:15+02:00 d/rules: Removing tests from the binary package - - - - - 1b9811be by Karsten Schöke at 2026-08-11T07:45:38+02:00 FontAwesome fonts are required by pydata-sphinx-theme for its icons - - - - - 1af58529 by Karsten Schöke at 2026-08-11T07:58:08+02:00 Use setuptools package discovery for all scikit-bio modules - - - - - 91b02138 by Karsten Schöke at 2026-08-11T07:58:39+02:00 d/control: Update B-D. - - - - - 5d3ca731 by Karsten Schöke at 2026-08-11T08:24:16+02:00 prepare release - - - - - fc25086e by Karsten Schöke at 2026-08-11T10:15:05+02:00 Changes made by cme - - - - - 1d091a17 by Karsten Schöke at 2026-08-11T10:15:09+02:00 Remove trailing whitespace in debian/rules (routine-update) - - - - - 93507ed4 by Karsten Schöke at 2026-08-11T09:15:16+01:00 Trim trailing whitespace. Changes-By: lintian-brush Fixes: lintian: source: trailing-whitespace [debian/rules:EOF] See-also: https://lintian.debian.org/tags/trailing-whitespace.html - - - - - d84c85e1 by Karsten Schöke at 2026-08-11T09:15:19+01:00 Remove redundant relation in debian/control. Changes-By: lintian-brush Fixes: lintian: source: redundant-control-relation (in source paragraph) Build-Depends python3-array-api-compat <!nodoc> See-also: https://lintian.debian.org/tags/redundant-control-relation.html - - - - - fa803ef7 by Karsten Schöke at 2026-08-11T10:17:19+02:00 Set upstream metadata fields: Documentation. Changes-By: lintian-brush - - - - - a6c52bf9 by Karsten Schöke at 2026-08-15T16:39:47+02:00 insert pybuild.testfiles to discover Autopkgtests - - - - - f0417d31 by Karsten Schöke at 2026-08-15T16:52:57+02:00 Update changelog for 0.7.3-1 release - - - - - 312 changed files: - .codecov.yml - .coveragerc - + .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 - MANIFEST.in - README.rst - − aarch64.Dockerfile - checklist.py - − ci/aarch64.conda_requirements.txt - − ci/aarch64.requirements.txt - ci/requirements.test.txt - ci/conda_requirements.txt → ci/requirements.txt - + debian/README.autopkgtest - debian/changelog - debian/control - debian/copyright - + debian/gbp.conf - − debian/patches/0002-use-libsww-as-library-not-embedded-src.patch - + debian/patches/Fix-missing-variable-declarations-in-Cython-code.patch - + debian/patches/Use-setuptools-package-discovery-for-all-scikit-bio-modul.patch - − debian/patches/local_inventory - − debian/patches/mathjax-path - − debian/patches/no_privacy_breach_logo.patch - debian/patches/privacy → debian/patches/remove-google-analytics_id.patch - debian/patches/series - + debian/patches/set-expliziet-mathjax_path.patch - − debian/patches/use_packaged_simde - + debian/pybuild.testfiles - + debian/python-skbio-doc.lintian-overrides - − debian/python3-skbio.lintian-overrides - debian/rules - debian/upstream/metadata - doc/source/_static/css/style.css - doc/source/_templates/TreeNode.rst - doc/source/autoinherit.py - doc/source/conf.py - + doc/source/config.rst - doc/source/index.rst - − licenses/simde.txt - − licenses/ssw.txt - pyproject.toml - setup.py - − simde-sse2.h - skbio/__init__.py - skbio/_base.py - + skbio/_config.py - skbio/alignment/__init__.py - + skbio/alignment/_cutils.pyx - + skbio/alignment/_distance.py - − skbio/alignment/_lib/ssw.c - − skbio/alignment/_lib/ssw.h - + skbio/alignment/_pair.py - skbio/alignment/_pairwise.py - skbio/alignment/_path.py - + skbio/alignment/_score.py - − skbio/alignment/_ssw_wrapper.pyx - skbio/alignment/_tabular_msa.py - + skbio/alignment/_utils.py - + skbio/alignment/tests/data/16s.frn - + skbio/alignment/tests/data/il6.nucl.aln - + skbio/alignment/tests/data/insulin.faa - + 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_pairwise.py - skbio/alignment/tests/test_path.py - + skbio/alignment/tests/test_score.py - − skbio/alignment/tests/test_ssw.py - skbio/alignment/tests/test_tabular_msa.py - + skbio/alignment/tests/test_utils.py - + skbio/binaries/__init__.py - + skbio/binaries/_distance.py - + skbio/binaries/_ordination.py - + skbio/binaries/_util.py - + skbio/binaries/tests/test_util.py - skbio/diversity/__init__.py - skbio/diversity/_block.py - skbio/diversity/_driver.py - skbio/diversity/_phylogenetic.pyx - skbio/diversity/_util.py - skbio/diversity/alpha/_base.py - skbio/diversity/alpha/_lladser.py - skbio/diversity/alpha/_pd.py - skbio/diversity/alpha/tests/test_base.py - skbio/diversity/alpha/tests/test_chao1.py - skbio/diversity/alpha/tests/test_gini.py - skbio/diversity/alpha/tests/test_lladser.py - skbio/diversity/alpha/tests/test_pd.py - skbio/diversity/beta/__init__.py - skbio/diversity/beta/_unifrac.py - skbio/diversity/beta/tests/test_unifrac.py - skbio/diversity/tests/test_block.py - skbio/diversity/tests/test_driver.py - skbio/diversity/tests/test_util.py - skbio/embedding/_embedding.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_ordination.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/__init__.py - skbio/sequence/_alphabet.py - skbio/sequence/_dna.py - skbio/sequence/_genetic_code.py - skbio/sequence/_grammared_sequence.py - skbio/sequence/_nucleotide_mixin.py - skbio/sequence/_protein.py - skbio/sequence/_rna.py - skbio/sequence/_sequence.py - skbio/sequence/_substitution.py - skbio/sequence/distance.py - skbio/sequence/tests/test_alphabet.py - skbio/sequence/tests/test_distance.py - skbio/sequence/tests/test_grammared_sequence.py - skbio/sequence/tests/test_sequence.py - skbio/sequence/tests/test_substitution.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/tests/test_composition.py → skbio/stats/composition/tests/test_ancom.py - + skbio/stats/composition/tests/test_ancombc.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/_bioenv.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/distance/tests/test_util.py - skbio/stats/gradient.py - skbio/stats/ordination/__init__.py - skbio/stats/ordination/_canonical_correspondence_analysis.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/_redundancy_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_canonical_correspondence_analysis.py - 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_power.py - skbio/table/__init__.py - + skbio/table/_augment.py - skbio/table/_base.py - + skbio/table/_tabular.py - + skbio/table/tests/test_augment.py - skbio/table/tests/test_base.py - + skbio/table/tests/test_tabular.py - + skbio/tests/test_config.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/_upgma.py - skbio/tree/_utils.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/tree/tests/test_utils.py - skbio/util/__init__.py - + skbio/util/_array.py - skbio/util/_decorator.py - skbio/util/_docstring.py - skbio/util/_exception.py - skbio/alignment/_lib/__init__.py → skbio/util/_gpu.py - skbio/util/_misc.py - + skbio/util/_optionals.py - skbio/util/_plotting.py - + skbio/util/_random.py - skbio/util/_testing.py - + skbio/util/_typing.py - skbio/util/_warning.py - + skbio/util/tests/test_array.py - skbio/util/tests/test_decorator.py - skbio/util/tests/test_docstring.py - skbio/util/tests/test_misc.py - + skbio/util/tests/test_optionals.py - skbio/util/tests/test_plotting.py - + skbio/util/tests/test_random.py - skbio/util/tests/test_testing.py - skbio/util/tests/test_warning.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/learn.rst - + web/roadmap.rst - web/versions.json The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/compare/dc6e109cb6e03184da2e4d94f7ebfac1e28dd019...f0417d31dca95090b3437cab2693bed6f9702cf4 -- View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/compare/dc6e109cb6e03184da2e4d94f7ebfac1e28dd019...f0417d31dca95090b3437cab2693bed6f9702cf4 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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