[med-svn] [Git][med-team/python-skbio][debian/experimental] 44 commits: d/control: breaks the older packages of unifrac

Tue Sep 2 21:09:09 BST 2025

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

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fbdb5149 by Michael R. Crusoe at 2024-06-29T17:48:43+02:00
upload to unstable

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d28f940f by Étienne Mollier at 2024-07-10T21:35:50+02:00
fix-test_shannon.patch: new: relax floating point comparison.

Closes: #1074745

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82bcfcee by Étienne Mollier at 2024-07-10T21:37:12+02:00
d/control: add myself to uploaders.

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756d9f21 by Étienne Mollier at 2024-07-10T21:37:35+02:00
d/control: declare compliance to standards version 4.7.0.

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dacd70c8 by Étienne Mollier at 2024-07-10T21:38:29+02:00
ready to upload to unstable.

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88f5a990 by Alexandre Detiste at 2024-08-12T21:54:24+02:00
New upstream version 0.6.2
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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
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1233edd6 by Alexandre Detiste at 2024-08-12T21:56:54+02:00
add a new dependency on python3-statsmodels

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3962a222 by Alexandre Detiste at 2024-08-12T21:58:42+02:00
remove patch applied upstream

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79299979 by Alexandre Detiste at 2024-08-12T22:38:14+02:00
release

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910c5ab7 by Alexandre Detiste at 2024-09-13T10:21:58+02:00
remove dep on python3-lockfile, release

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9cc0604d by Michael R. Crusoe at 2024-09-28T10:08:24+02:00
Upgrade to cython 3.x. Closes: #1078527

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86e8cf91 by Michael R. Crusoe at 2024-09-28T11:32:59+02:00
cleanup patch metadata to work nicely with gbp pq

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37e80fea by Michael R. Crusoe at 2024-09-28T11:35:05+02:00
Drop many unneeded patches

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7f71d802 by Michael R. Crusoe at 2024-09-28T12:29:05+02:00
Cherry-pick patch from upstream to fix cython segmentation error

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83fa3f57 by Michael R. Crusoe at 2024-09-28T12:29:05+02:00
Switch to pybuild-autopkgtest

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b5f4b27e by Michael R. Crusoe at 2024-09-28T12:29:06+02:00
fixup autopkgtest

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850f7e49 by Michael R. Crusoe at 2024-09-28T12:29:07+02:00
routine-update: Ready to upload to unstable

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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

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88786671 by Michael R. Crusoe at 2024-11-19T00:02:18+01:00
routine-update: Ready to upload to unstable

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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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55931182 by Michael R. Crusoe at 2025-09-02T19:45:11+02:00
New upstream version

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ce5714dd by Michael R. Crusoe at 2025-09-02T19:45:12+02:00
New upstream version 0.7.0
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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
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95936574 by Michael R. Crusoe at 2025-09-02T21:03:56+02:00
Set upstream metadata field: Documentation.

Changes-By: lintian-brush

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f2054229 by Michael R. Crusoe at 2025-09-02T21:04:03+02:00
Refreshed patches.

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d369ec44 by Michael R. Crusoe at 2025-09-02T21:37:23+02:00
this is a team release

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2a8e31cb by Michael R. Crusoe at 2025-09-02T22:02:12+02:00
more SSW cleanup

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38d28cdb by Michael R. Crusoe at 2025-09-02T22:02:12+02:00
d/control: use pybuild-plugin-pyproject

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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

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