Michael R. Crusoe pushed to branch debian/experimental at Debian Med / python-skbio
Commits: 9e6b9d24 by Michael R. Crusoe at 2024-06-29T17:46:12+02:00 d/control: breaks the older packages of unifrac - - - - - fbdb5149 by Michael R. Crusoe at 2024-06-29T17:48:43+02:00 upload to unstable - - - - - d28f940f by Étienne Mollier at 2024-07-10T21:35:50+02:00 fix-test_shannon.patch: new: relax floating point comparison. Closes: #1074745 - - - - - 82bcfcee by Étienne Mollier at 2024-07-10T21:37:12+02:00 d/control: add myself to uploaders. - - - - - 756d9f21 by Étienne Mollier at 2024-07-10T21:37:35+02:00 d/control: declare compliance to standards version 4.7.0. - - - - - dacd70c8 by Étienne Mollier at 2024-07-10T21:38:29+02:00 ready to upload to unstable. - - - - - 88f5a990 by Alexandre Detiste at 2024-08-12T21:54:24+02:00 New upstream version 0.6.2 - - - - - 41ec8818 by Alexandre Detiste at 2024-08-12T21:54:29+02:00 Update upstream source from tag 'upstream/0.6.2' Update to upstream version '0.6.2' with Debian dir 96326d5ba805601785388e99b42433081d0c709a - - - - - 1233edd6 by Alexandre Detiste at 2024-08-12T21:56:54+02:00 add a new dependency on python3-statsmodels - - - - - 3962a222 by Alexandre Detiste at 2024-08-12T21:58:42+02:00 remove patch applied upstream - - - - - 79299979 by Alexandre Detiste at 2024-08-12T22:38:14+02:00 release - - - - - 910c5ab7 by Alexandre Detiste at 2024-09-13T10:21:58+02:00 remove dep on python3-lockfile, release - - - - - 9cc0604d by Michael R. Crusoe at 2024-09-28T10:08:24+02:00 Upgrade to cython 3.x. Closes: #1078527 - - - - - 86e8cf91 by Michael R. Crusoe at 2024-09-28T11:32:59+02:00 cleanup patch metadata to work nicely with gbp pq - - - - - 37e80fea by Michael R. Crusoe at 2024-09-28T11:35:05+02:00 Drop many unneeded patches - - - - - 7f71d802 by Michael R. Crusoe at 2024-09-28T12:29:05+02:00 Cherry-pick patch from upstream to fix cython segmentation error - - - - - 83fa3f57 by Michael R. Crusoe at 2024-09-28T12:29:05+02:00 Switch to pybuild-autopkgtest - - - - - b5f4b27e by Michael R. Crusoe at 2024-09-28T12:29:06+02:00 fixup autopkgtest - - - - - 850f7e49 by Michael R. Crusoe at 2024-09-28T12:29:07+02:00 routine-update: Ready to upload to unstable - - - - - 1cdaed1e by Michael R. Crusoe at 2024-11-18T09:59:20+00:00 Cherry-picked patch from upstream to fix test that failed under Python 3.13. Closes: #1087690 - - - - - 88786671 by Michael R. Crusoe at 2024-11-19T00:02:18+01:00 routine-update: Ready to upload to unstable - - - - - 2adc8e92 by Michael R. Crusoe at 2025-09-02T16:42:25+02:00 New upstream version 0.6.3 - - - - - 803d0d0b by Michael R. Crusoe at 2025-09-02T16:42:39+02:00 Update upstream source from tag 'upstream/0.6.3' Update to upstream version '0.6.3' with Debian dir 05841520975d4919d681cbd2c308c73093bd4a12 - - - - - 3b16ca72 by Michael R. Crusoe at 2025-09-02T16:43:15+02:00 New upstream release. - - - - - ce8427dc by Michael R. Crusoe at 2025-09-02T16:43:28+02:00 Standards-Version: 4.7.2 (routine-update) - - - - - b01ba0af by Michael R. Crusoe at 2025-09-02T16:44:14+02:00 d/control: reformat, remove unneeded versioned dependency information for scipy. - - - - - 3bb007d6 by Michael R. Crusoe at 2025-09-02T17:17:00+02:00 Refreshed patches, added additional -doc dependencies. Removed two patches applied upstream. - - - - - d05eb763 by Michael R. Crusoe at 2025-09-02T18:17:30+02:00 Add missing build dependency on python3-numpy-dev for command dh_numpy3. Changes-By: lintian-brush Fixes: lintian: missing-build-dependency-for-dh_-command See-also: https://lintian.debian.org/tags/missing-build-dependency-for-dh_-command.html - - - - - 8ba5473b by Michael R. Crusoe at 2025-09-02T18:17:56+02:00 Set upstream metadata fields: Registry. Changes-By: lintian-brush - - - - - b0183edf by Michael R. Crusoe at 2025-09-02T18:17:57+02:00 d/rules: set MPLCONFIGDIR while building the docs - - - - - 20db5a84 by Michael R. Crusoe at 2025-09-02T18:17:57+02:00 d/control: additional docs dependency: python3-sphinx-sitemap - - - - - 022908af by Michael R. Crusoe at 2025-09-02T18:17:57+02:00 d/rules: use the skbio.test wrapper for pytest. - - - - - d0228a36 by Michael R. Crusoe at 2025-09-02T18:58:35+02:00 Fixed some lintian overrides syntax - - - - - 5710bfe3 by Michael R. Crusoe at 2025-09-02T18:58:35+02:00 Added patch to disable use of Google analytics for the docs. - - - - - 37e759ba by Michael R. Crusoe at 2025-09-02T18:58:35+02:00 d/patches/no_privacy_breach_logo.patch: fix metadata - - - - - ffe4cda6 by Michael R. Crusoe at 2025-09-02T19:41:42+02:00 upload to unstable - - - - - 55931182 by Michael R. Crusoe at 2025-09-02T19:45:11+02:00 New upstream version - - - - - ce5714dd by Michael R. Crusoe at 2025-09-02T19:45:12+02:00 New upstream version 0.7.0 - - - - - 492eeefb by Michael R. Crusoe at 2025-09-02T19:45:26+02:00 Update upstream source from tag 'upstream/0.7.0' Update to upstream version '0.7.0' with Debian dir 9a83143bd8383fdd2ef93ba14395530b249bf6e4 - - - - - 95936574 by Michael R. Crusoe at 2025-09-02T21:03:56+02:00 Set upstream metadata field: Documentation. Changes-By: lintian-brush - - - - - f2054229 by Michael R. Crusoe at 2025-09-02T21:04:03+02:00 Refreshed patches. - - - - - d369ec44 by Michael R. Crusoe at 2025-09-02T21:37:23+02:00 this is a team release - - - - - 2a8e31cb by Michael R. Crusoe at 2025-09-02T22:02:12+02:00 more SSW cleanup - - - - - 38d28cdb by Michael R. Crusoe at 2025-09-02T22:02:12+02:00 d/control: use pybuild-plugin-pyproject - - - - - 244 changed files: - .codecov.yml - .coveragerc - .github/workflows/ci.yml - .github/workflows/release.yml - .github/workflows/website.yml - + .github/workflows/wheels.yml - .pre-commit-config.yaml - CHANGELOG.md - MANIFEST.in - README.rst - − aarch64.Dockerfile - − ci/aarch64.conda_requirements.txt - − ci/aarch64.requirements.txt - ci/conda_requirements.txt - ci/requirements.doc.txt - ci/requirements.test.txt - debian/changelog - debian/control - debian/copyright - − debian/patches/0002-use-libsww-as-library-not-embedded-src.patch - − debian/patches/cython3.patch - debian/patches/docs-no-version-switch - debian/patches/local_inventory - debian/patches/mathjax-path - − debian/patches/modify-test.patch - debian/patches/no_privacy_breach_logo.patch - − debian/patches/numpy-1.24.patch - − debian/patches/older-scipy.patch - + debian/patches/privacy - − debian/patches/python3.12-xfail-tests.patch - debian/patches/series - − debian/patches/use_packaged_simde - debian/python3-skbio.lintian-overrides - debian/rules - − debian/tests/control - − debian/tests/import-skbio - − debian/tests/testsuite - debian/upstream/metadata - + doc/editmap.py - + doc/metatag.py - + doc/source/_templates/TreeNode.rst - doc/source/_templates/autosummary/class.rst - + doc/source/_templates/namedtuple.rst - doc/source/alignment.rst - + doc/source/autoinherit.py - doc/source/conf.py - + doc/source/config.rst - doc/source/diversity.rst - doc/source/embedding.rst - doc/source/index.rst - doc/source/io.rst - doc/source/metadata.rst - doc/source/sequence.rst - doc/source/stats.rst - doc/source/table.rst - doc/source/tree.rst - doc/source/util.rst - doc/source/workflow.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/_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/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/_util.py - skbio/diversity/alpha/__init__.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_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/__init__.py - skbio/embedding/_embedding.py - skbio/io/__init__.py - skbio/io/_iosources.py - + skbio/io/descriptors.py - skbio/io/format/biom.py - skbio/io/format/blast6.py - skbio/io/format/blast7.py - skbio/io/format/embed.py - skbio/io/format/fasta.py - skbio/io/format/ordination.py - skbio/io/format/sample_metadata.py - skbio/io/format/taxdump.py - + skbio/io/format/tests/data/fasta_multi_seq_spaces - + skbio/io/format/tests/data/pdb_hits.txt - + skbio/io/format/tests/data/tiny_embedding_file.npz - skbio/io/format/tests/test_embed.py - skbio/io/format/tests/test_fasta.py - skbio/io/format/tests/test_ordination.py - skbio/io/format/tests/test_sample_metadata.py - skbio/io/registry.py - skbio/io/tests/test_iosources.py - skbio/io/tests/test_registry.py - skbio/io/tests/test_util.py - skbio/metadata/__init__.py - skbio/metadata/_intersection.pyx - skbio/metadata/_interval.py - skbio/metadata/_metadata.py - skbio/metadata/_mixin.py - skbio/metadata/tests/test_metadata.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/_protein.py - skbio/sequence/_rna.py - skbio/sequence/_sequence.py - skbio/sequence/_substitution.py - skbio/sequence/tests/test_alphabet.py - skbio/sequence/tests/test_sequence.py - skbio/sequence/tests/test_substitution.py - skbio/stats/_subsample.py - skbio/stats/composition.py - skbio/stats/distance/_anosim.py - skbio/stats/distance/_base.py - skbio/stats/distance/_bioenv.py - skbio/stats/distance/_mantel.py - skbio/stats/distance/_permanova.py - skbio/stats/distance/_permdisp.py - skbio/stats/distance/_utils.py - skbio/stats/distance/tests/data/pwmantel_exp_results_minimal.txt - skbio/stats/distance/tests/data/pwmantel_exp_results_minimal_with_labels.txt - skbio/stats/distance/tests/data/pwmantel_exp_results_reordered_distance_matrices.txt - skbio/stats/distance/tests/test_anosim.py - skbio/stats/distance/tests/test_base.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/evolve/_hommola.py - skbio/stats/evolve/tests/test_hommola.py - skbio/stats/gradient.py - skbio/stats/ordination/_canonical_correspondence_analysis.py - skbio/stats/ordination/_correspondence_analysis.py - skbio/stats/ordination/_ordination_results.py - skbio/stats/ordination/_principal_coordinate_analysis.py - skbio/stats/ordination/_redundancy_analysis.py - skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py - skbio/stats/ordination/tests/test_correspondence_analysis.py - skbio/stats/ordination/tests/test_ordination_results.py - skbio/stats/ordination/tests/test_principal_coordinate_analysis.py - skbio/stats/ordination/tests/test_redundancy_analysis.py - skbio/stats/power.py - skbio/stats/tests/test_composition.py - + skbio/stats/tests/test_ndarray.py - skbio/stats/tests/test_power.py - skbio/stats/tests/test_subsample.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/_majority_rule.py - + skbio/tree/_me.py - skbio/tree/_nj.py - skbio/tree/_tree.py - + skbio/tree/_upgma.py - + skbio/tree/_utils.py - + skbio/tree/tests/test_compare.py - skbio/tree/tests/test_majority_rule.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_warning.py - skbio/workflow.py - web/.exclude - web/conf.py - web/contribute.rst - web/devdoc/release.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/f5941fac12500b029eaaa696aeee54c55e75a396...38d28cdbf37489386931b0ece2d9cc92a230fd54 -- View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/compare/f5941fac12500b029eaaa696aeee54c55e75a396...38d28cdbf37489386931b0ece2d9cc92a230fd54 You're receiving this email because of your account on salsa.debian.org.
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