[med-svn] [Git][med-team/python-skbio][master] 4 commits: New upstream version 0.7.4

Fri Oct 9 07:52:31 BST 2026

Karsten Schöke pushed to branch master at Debian Med / python-skbio

Commits:
63827b47 by Karsten Schöke at 2026-10-09T06:25:05+02:00
New upstream version 0.7.4
- - - - -
452e6d70 by Karsten Schöke at 2026-10-09T06:25:30+02:00
Update upstream source from tag 'upstream/0.7.4'

Update to upstream version '0.7.4'
with Debian dir 8ecc6f28a6062006fcb0f672cb73a6ae9925b22b

- - - - -
c79555c7 by Karsten Schöke at 2026-10-09T06:51:49+02:00
remove implemented upstream patches

 - fix-gzip-reader-mode.patch
 - Fix-missing-variable-declarations-in-Cython-code.patch

- - - - -
7f9644a6 by Karsten Schöke at 2026-10-09T08:14:06+02:00
Update changelog for 0.7.4-1 release

- - - - -

159 changed files:

- .codecov.yml
- − .coveragerc
- − .dockerignore
- .github/workflows/array-api.yml
- + .github/workflows/azure-start.yml
- + .github/workflows/azure-stop.yml
- .github/workflows/ci.yml
- + .github/workflows/gpu.yml
- + .github/workflows/numba.yml
- .github/workflows/release.yml
- .github/workflows/website.yml
- .github/workflows/wheels.yml
- .pre-commit-config.yaml
- CHANGELOG.md
- + CITATION.cff
- Makefile
- README.rst
- ci/requirements.txt
- debian/changelog
- − debian/patches/Fix-missing-variable-declarations-in-Cython-code.patch
- − debian/patches/fix-gzip-reader-mode.patch
- debian/patches/series
- doc/source/_static/css/style.css
- doc/source/conf.py
- doc/source/index.rst
- + doc/source/performance.rst
- pyproject.toml
- skbio/__init__.py
- skbio/_config.py
- skbio/alignment/__init__.py
- skbio/alignment/_cutils.pyx
- + skbio/alignment/_multi.py
- skbio/alignment/_pair.py
- skbio/alignment/_path.py
- skbio/alignment/_score.py
- skbio/alignment/_tabular_msa.py
- skbio/alignment/_utils.py
- + skbio/alignment/tests/test_multi.py
- skbio/alignment/tests/test_pair.py
- skbio/alignment/tests/test_pairwise.py
- skbio/alignment/tests/test_path.py
- skbio/alignment/tests/test_tabular_msa.py
- skbio/alignment/tests/test_utils.py
- skbio/binaries/_distance.py
- + skbio/binaries/tests/__init__.py
- skbio/diversity/_block.py
- skbio/diversity/_driver.py
- skbio/diversity/_phylogenetic.pyx
- skbio/diversity/_util.py
- skbio/diversity/alpha/_pd.py
- skbio/diversity/beta/_unifrac.py
- skbio/diversity/beta/tests/test_unifrac.py
- skbio/diversity/tests/test_driver.py
- skbio/io/_iosources.py
- skbio/io/format/fasta.py
- skbio/io/format/tests/test_base.py
- skbio/io/format/tests/test_clustal.py
- skbio/io/format/tests/test_fasta.py
- skbio/io/format/tests/test_fastq.py
- skbio/io/format/tests/test_sample_metadata.py
- skbio/io/tests/test_descriptors.py
- skbio/metadata/tests/test_mixin.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/_sequence.py
- skbio/sequence/_substitution.py
- skbio/sequence/distance.py
- skbio/sequence/tests/test_distance.py
- skbio/sequence/tests/test_genetic_code.py
- skbio/sequence/tests/test_grammared_sequence.py
- skbio/sequence/tests/test_nucleotide_sequences.py
- skbio/sequence/tests/test_sequence.py
- + skbio/sequence/tests/test_transition.py
- + skbio/sequence/transition.py
- skbio/stats/composition/__init__.py
- skbio/stats/composition/_ancom.py
- skbio/stats/composition/_ancombc.py
- skbio/stats/composition/_base.py
- skbio/stats/composition/_dirmult.py
- + skbio/stats/composition/_lme.py
- skbio/stats/composition/_utils.py
- + skbio/stats/composition/tests/__init__.py
- + skbio/stats/composition/tests/data/atlas_ancombc2_dunn.tsv
- + skbio/stats/composition/tests/data/atlas_ancombc2_global.tsv
- + skbio/stats/composition/tests/data/atlas_ancombc2_main.tsv
- + skbio/stats/composition/tests/data/atlas_ancombc2_pair.tsv
- + skbio/stats/composition/tests/data/atlas_ancombc2_trend.tsv
- + skbio/stats/composition/tests/data/atlas_ancombc_global.tsv
- + skbio/stats/composition/tests/data/atlas_ancombc_main.tsv
- + skbio/stats/composition/tests/data/atlas_feature_table.csv
- + skbio/stats/composition/tests/data/atlas_meta_data.csv
- − 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/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/_base.py
- skbio/stats/distance/_cutils.pyx
- + skbio/stats/distance/_gpu.py
- skbio/stats/distance/_mantel.py
- + skbio/stats/distance/_mantel_gpu.py
- skbio/stats/distance/_permanova.py
- + skbio/stats/distance/_permanova_gpu.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/gradient.py
- skbio/stats/ordination/__init__.py
- skbio/stats/ordination/_canonical_correspondence_analysis.py
- + skbio/stats/ordination/_center_distance_matrix_numba.py
- skbio/stats/ordination/_correspondence_analysis.py
- skbio/stats/ordination/_mmvec.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/test_correspondence_analysis.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/ordination/tests/test_redundancy_analysis.py
- skbio/stats/ordination/tests/test_util.py
- skbio/stats/power.py
- skbio/table/__init__.py
- skbio/table/_augment.py
- skbio/table/_tabular.py
- skbio/table/tests/test_tabular.py
- skbio/tests/test_config.py
- skbio/tree/_c_me.pyx
- 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_tree.py
- skbio/tree/tests/test_utils.py
- skbio/util/__init__.py
- skbio/util/_array.py
- skbio/util/_docstring.py
- skbio/util/_testing.py
- skbio/util/tests/test_array.py
- skbio/util/tests/test_decorator.py
- skbio/util/tests/test_docstring.py
- web/conf.py
- web/devdoc/array_api.rst
- web/devdoc/release.rst
- web/index.rst
- web/install.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/1ee2033fce459c64357f845e54d9dc2fd2517c9c...7f9644a6ccf80f1ec000fe433b9bb8ff539b6c63

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/compare/1ee2033fce459c64357f845e54d9dc2fd2517c9c...7f9644a6ccf80f1ec000fe433b9bb8ff539b6c63
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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20261009/390ffce6/attachment-0001.htm>