[med-svn] [Git][med-team/python-skbio][upstream] New upstream version 0.7.0

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch upstream 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
- - - - -


164 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.test.txt
- doc/source/_templates/TreeNode.rst
- 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/_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/_base.py
- skbio/diversity/alpha/_lladser.py
- skbio/diversity/alpha/_pd.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/_embedding.py
- skbio/io/__init__.py
- + skbio/io/descriptors.py
- skbio/io/format/biom.py
- skbio/io/format/embed.py
- skbio/io/format/ordination.py
- skbio/io/format/tests/test_ordination.py
- skbio/io/registry.py
- 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/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/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/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/tests/test_composition.py
- + skbio/stats/tests/test_ndarray.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_nj.pyx
- skbio/tree/_me.py
- skbio/tree/_nj.py
- skbio/tree/_tree.py
- skbio/tree/_upgma.py
- skbio/tree/_utils.py
- skbio/tree/tests/test_me.py
- skbio/tree/tests/test_nj.py
- skbio/tree/tests/test_tree.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_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/conf.py
- web/contribute.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/-/commit/ce5714dd0a85848ee46b65d9a6fa5b4e81e1d5db

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