[med-svn] [Git][med-team/python-skbio][master] 15 commits: New upstream version 0.6.3

Tue Sep 2 18:44:32 BST 2025

Michael R. Crusoe pushed to branch master at Debian Med / python-skbio

Commits:
2adc8e92 by Michael R. Crusoe at 2025-09-02T16:42:25+02:00
New upstream version 0.6.3
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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
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3b16ca72 by Michael R. Crusoe at 2025-09-02T16:43:15+02:00
New upstream release.

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ce8427dc by Michael R. Crusoe at 2025-09-02T16:43:28+02:00
Standards-Version: 4.7.2 (routine-update)

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b01ba0af by Michael R. Crusoe at 2025-09-02T16:44:14+02:00
d/control: reformat, remove unneeded versioned dependency information for scipy.

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3bb007d6 by Michael R. Crusoe at 2025-09-02T17:17:00+02:00
Refreshed patches, added additional -doc dependencies. Removed two patches applied upstream.

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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

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8ba5473b by Michael R. Crusoe at 2025-09-02T18:17:56+02:00
Set upstream metadata fields: Registry.

Changes-By: lintian-brush

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b0183edf by Michael R. Crusoe at 2025-09-02T18:17:57+02:00
d/rules: set MPLCONFIGDIR while building the docs

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20db5a84 by Michael R. Crusoe at 2025-09-02T18:17:57+02:00
d/control: additional docs dependency: python3-sphinx-sitemap

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022908af by Michael R. Crusoe at 2025-09-02T18:17:57+02:00
d/rules: use the skbio.test wrapper for pytest.

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d0228a36 by Michael R. Crusoe at 2025-09-02T18:58:35+02:00
Fixed some lintian overrides syntax

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5710bfe3 by Michael R. Crusoe at 2025-09-02T18:58:35+02:00
Added patch to disable use of Google analytics for the docs.

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37e759ba by Michael R. Crusoe at 2025-09-02T18:58:35+02:00
d/patches/no_privacy_breach_logo.patch: fix metadata

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ffe4cda6 by Michael R. Crusoe at 2025-09-02T19:41:42+02:00
upload to unstable

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151 changed files:

- .coveragerc
- .github/workflows/ci.yml
- .github/workflows/release.yml
- .github/workflows/website.yml
- .pre-commit-config.yaml
- CHANGELOG.md
- README.rst
- ci/aarch64.conda_requirements.txt
- ci/conda_requirements.txt
- ci/requirements.doc.txt
- debian/changelog
- debian/control
- debian/patches/0002-use-libsww-as-library-not-embedded-src.patch
- − debian/patches/0007-Fix-cython-segmentation-error-2090.patch
- − debian/patches/45127698e270024bacb670cdd0bd2e4850104b6f.patch
- debian/patches/docs-no-version-switch
- debian/patches/local_inventory
- debian/patches/mathjax-path
- debian/patches/no_privacy_breach_logo.patch
- + debian/patches/privacy
- debian/patches/series
- debian/python3-skbio.lintian-overrides
- debian/rules
- 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/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
- pyproject.toml
- setup.py
- simde-sse2.h
- skbio/__init__.py
- skbio/alignment/_pairwise.py
- skbio/alignment/_tabular_msa.py
- skbio/diversity/__init__.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_lladser.py
- skbio/diversity/beta/_unifrac.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/format/blast6.py
- skbio/io/format/blast7.py
- skbio/io/format/embed.py
- skbio/io/format/fasta.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/registry.py
- skbio/io/tests/test_iosources.py
- skbio/io/tests/test_registry.py
- skbio/metadata/__init__.py
- skbio/metadata/_intersection.pyx
- skbio/metadata/_interval.py
- skbio/metadata/_metadata.py
- skbio/sequence/__init__.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/tests/test_sequence.py
- skbio/stats/_subsample.py
- skbio/stats/composition.py
- skbio/stats/distance/_anosim.py
- skbio/stats/distance/_base.py
- skbio/stats/distance/_mantel.py
- skbio/stats/distance/_permanova.py
- skbio/stats/distance/_permdisp.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/evolve/_hommola.py
- skbio/stats/evolve/tests/test_hommola.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_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_power.py
- skbio/stats/tests/test_subsample.py
- skbio/table/_base.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/util/__init__.py
- skbio/util/_decorator.py
- + skbio/util/_docstring.py
- skbio/util/_misc.py
- skbio/util/_testing.py
- skbio/util/_warning.py
- skbio/util/tests/test_decorator.py
- + skbio/util/tests/test_docstring.py
- skbio/util/tests/test_misc.py
- + skbio/util/tests/test_warning.py
- web/.exclude
- web/conf.py
- web/devdoc/release.rst
- web/index.rst
- web/install.rst
- web/learn.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/88786671311b6e14988e34cccfffdf39eda2465f...ffe4cda60081e362ba75b8e50f6ec0ac88e47d88

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