[med-svn] [Git][med-team/qiime][upstream] New upstream version 2025.10.1

Mon Dec 1 12:24:56 GMT 2025

Andreas Tille pushed to branch upstream at Debian Med / qiime

Commits:
64a08ecb by Andreas Tille at 2025-12-01T13:08:04+01:00
New upstream version 2025.10.1
- - - - -

186 changed files:

- + .copier-answers.yml
- .gitattributes
- − .github/CONTRIBUTING.md
- − .github/SUPPORT.md
- − .github/rubric.png
- .github/workflows/ci-dev.yaml
- + .github/workflows/update-copyright-headers.yaml
- .gitignore
- LICENSE
- − MANIFEST.in
- Makefile
- README.md
- − ci/recipe/meta.yaml
- + conda-recipe/meta.yaml
- + pyproject.toml
- qiime2/__init__.py
- − qiime2/_version.py
- qiime2/core/__init__.py
- + qiime2/core/annotate.py
- qiime2/core/archive/__init__.py
- qiime2/core/archive/archiver.py
- qiime2/core/archive/format/__init__.py
- qiime2/core/archive/format/tests/__init__.py
- qiime2/core/archive/format/tests/test_util.py
- qiime2/core/archive/format/tests/test_v0.py
- qiime2/core/archive/format/util.py
- qiime2/core/archive/format/v0.py
- qiime2/core/archive/format/v1.py
- qiime2/core/archive/format/v2.py
- qiime2/core/archive/format/v3.py
- qiime2/core/archive/format/v4.py
- qiime2/core/archive/format/v5.py
- qiime2/core/archive/format/v6.py
- + qiime2/core/archive/format/v7_0.py
- + qiime2/core/archive/format/v7_1.py
- qiime2/core/archive/provenance.py
- qiime2/core/archive/provenance_lib/__init__.py
- qiime2/core/archive/provenance_lib/_checksum_validator.py
- qiime2/core/archive/provenance_lib/archive_parser.py
- qiime2/core/archive/provenance_lib/parse.py
- qiime2/core/archive/provenance_lib/replay.py
- qiime2/core/archive/provenance_lib/tests/__init__.py
- + qiime2/core/archive/provenance_lib/tests/data/mixed-archive-versions/e8010137-d27e-4d97-ba21-123bb917a5b4/VERSION
- + qiime2/core/archive/provenance_lib/tests/data/mixed-archive-versions/e8010137-d27e-4d97-ba21-123bb917a5b4/checksums.sha512
- + qiime2/core/archive/provenance_lib/tests/data/mixed-archive-versions/e8010137-d27e-4d97-ba21-123bb917a5b4/data/ints.txt
- + qiime2/core/archive/provenance_lib/tests/data/mixed-archive-versions/e8010137-d27e-4d97-ba21-123bb917a5b4/metadata.yaml
- + qiime2/core/archive/provenance_lib/tests/data/mixed-archive-versions/e8010137-d27e-4d97-ba21-123bb917a5b4/provenance/VERSION
- + qiime2/core/archive/provenance_lib/tests/data/mixed-archive-versions/e8010137-d27e-4d97-ba21-123bb917a5b4/provenance/action/action.yaml
- + qiime2/core/archive/provenance_lib/tests/data/mixed-archive-versions/e8010137-d27e-4d97-ba21-123bb917a5b4/provenance/artifacts/f8e289f7-636b-481d-add3-a38ea3975708/VERSION
- + qiime2/core/archive/provenance_lib/tests/data/mixed-archive-versions/e8010137-d27e-4d97-ba21-123bb917a5b4/provenance/artifacts/f8e289f7-636b-481d-add3-a38ea3975708/action/action.yaml
- + qiime2/core/archive/provenance_lib/tests/data/mixed-archive-versions/e8010137-d27e-4d97-ba21-123bb917a5b4/provenance/artifacts/f8e289f7-636b-481d-add3-a38ea3975708/citations.bib
- + qiime2/core/archive/provenance_lib/tests/data/mixed-archive-versions/e8010137-d27e-4d97-ba21-123bb917a5b4/provenance/artifacts/f8e289f7-636b-481d-add3-a38ea3975708/metadata.yaml
- + qiime2/core/archive/provenance_lib/tests/data/mixed-archive-versions/e8010137-d27e-4d97-ba21-123bb917a5b4/provenance/citations.bib
- + qiime2/core/archive/provenance_lib/tests/data/mixed-archive-versions/e8010137-d27e-4d97-ba21-123bb917a5b4/provenance/conda-env.yaml
- + qiime2/core/archive/provenance_lib/tests/data/mixed-archive-versions/e8010137-d27e-4d97-ba21-123bb917a5b4/provenance/metadata.yaml
- qiime2/core/archive/provenance_lib/tests/test_archive_parser.py
- qiime2/core/archive/provenance_lib/tests/test_checksum_validator.py
- qiime2/core/archive/provenance_lib/tests/test_parse.py
- qiime2/core/archive/provenance_lib/tests/test_replay.py
- qiime2/core/archive/provenance_lib/tests/test_usage_drivers.py
- qiime2/core/archive/provenance_lib/tests/test_util.py
- qiime2/core/archive/provenance_lib/tests/test_version_parser.py
- qiime2/core/archive/provenance_lib/tests/test_yaml_constructors.py
- qiime2/core/archive/provenance_lib/tests/testing_utilities.py
- qiime2/core/archive/provenance_lib/usage_drivers.py
- qiime2/core/archive/provenance_lib/util.py
- qiime2/core/archive/tests/__init__.py
- qiime2/core/archive/tests/test_archiver.py
- qiime2/core/archive/tests/test_citations.py
- qiime2/core/archive/tests/test_provenance.py
- qiime2/core/cache.py
- qiime2/core/cite.py
- qiime2/core/enan.py
- qiime2/core/exceptions.py
- qiime2/core/format.py
- qiime2/core/missing.py
- qiime2/core/path.py
- qiime2/core/testing/__init__.py
- qiime2/core/testing/examples.py
- qiime2/core/testing/format.py
- qiime2/core/testing/mapped.py
- qiime2/core/testing/method.py
- qiime2/core/testing/pipeline.py
- qiime2/core/testing/plugin.py
- qiime2/core/testing/tests/__init__.py
- qiime2/core/testing/tests/test_mapped_actions.py
- qiime2/core/testing/transformer.py
- qiime2/core/testing/type.py
- qiime2/core/testing/util.py
- qiime2/core/testing/validator.py
- qiime2/core/testing/visualizer.py
- qiime2/core/tests/__init__.py
- + qiime2/core/tests/test_annotate.py
- qiime2/core/tests/test_cache.py
- qiime2/core/tests/test_enan.py
- qiime2/core/tests/test_missing.py
- qiime2/core/tests/test_path.py
- qiime2/core/tests/test_pipeline_resumption.py
- qiime2/core/tests/test_util.py
- qiime2/core/tests/test_validate.py
- qiime2/core/transform.py
- qiime2/core/type/__init__.py
- qiime2/core/type/collection.py
- qiime2/core/type/grammar.py
- qiime2/core/type/meta.py
- qiime2/core/type/parse.py
- qiime2/core/type/primitive.py
- qiime2/core/type/semantic.py
- qiime2/core/type/signature.py
- qiime2/core/type/template.py
- qiime2/core/type/tests/__init__.py
- qiime2/core/type/tests/test_collection.py
- qiime2/core/type/tests/test_grammar.py
- qiime2/core/type/tests/test_meta.py
- qiime2/core/type/tests/test_parse.py
- qiime2/core/type/tests/test_primitive.py
- qiime2/core/type/tests/test_semantic.py
- qiime2/core/type/tests/test_util.py
- qiime2/core/type/util.py
- qiime2/core/type/visualization.py
- qiime2/core/util.py
- qiime2/core/validate.py
- qiime2/jupyter/__init__.py
- qiime2/jupyter/handlers.py
- qiime2/jupyter/hooks.py
- qiime2/jupyter/template.py
- qiime2/metadata/__init__.py
- qiime2/metadata/base.py
- qiime2/metadata/io.py
- qiime2/metadata/metadata.py
- qiime2/metadata/tests/__init__.py
- qiime2/metadata/tests/test_io.py
- qiime2/metadata/tests/test_metadata.py
- qiime2/metadata/tests/test_metadata_column.py
- qiime2/plugin/__init__.py
- qiime2/plugin/model/__init__.py
- qiime2/plugin/model/base.py
- qiime2/plugin/model/directory_format.py
- qiime2/plugin/model/file_format.py
- qiime2/plugin/model/tests/__init__.py
- qiime2/plugin/model/tests/test_directory_format.py
- qiime2/plugin/model/tests/test_file_format.py
- qiime2/plugin/plugin.py
- qiime2/plugin/testing.py
- qiime2/plugin/tests/__init__.py
- qiime2/plugin/tests/test_plugin.py
- qiime2/plugin/tests/test_tests.py
- qiime2/plugin/util.py
- qiime2/plugins.py
- qiime2/sdk/__init__.py
- qiime2/sdk/action.py
- qiime2/sdk/actiongraph.py
- + qiime2/sdk/context/__init__.py
- + qiime2/sdk/context/asynchronous.py
- qiime2/sdk/context.py → qiime2/sdk/context/base.py
- + qiime2/sdk/context/parallel.py
- + qiime2/sdk/iresult.py
- qiime2/sdk/parallel_config.py
- qiime2/sdk/plugin_manager.py
- qiime2/sdk/proxy.py
- qiime2/sdk/result.py
- qiime2/sdk/results.py
- qiime2/sdk/tests/__init__.py
- qiime2/sdk/tests/test_action.py
- qiime2/sdk/tests/test_actiongraph.py
- qiime2/sdk/tests/test_artifact.py
- qiime2/sdk/tests/test_config.py
- qiime2/sdk/tests/test_method.py
- qiime2/sdk/tests/test_pipeline.py
- qiime2/sdk/tests/test_plugin_manager.py
- qiime2/sdk/tests/test_result.py
- qiime2/sdk/tests/test_results.py
- qiime2/sdk/tests/test_usage.py
- qiime2/sdk/tests/test_util.py
- qiime2/sdk/tests/test_visualization.py
- qiime2/sdk/tests/test_visualizer.py
- qiime2/sdk/usage.py
- qiime2/sdk/util.py
- qiime2/tests/__init__.py
- qiime2/tests/mystery_stew.py
- qiime2/tests/test_artifact_api.py
- qiime2/tests/test_util.py
- qiime2/util.py
- − setup.cfg
- − setup.py
- − versioneer.py

The diff was not included because it is too large.

View it on GitLab: https://salsa.debian.org/med-team/qiime/-/commit/64a08ecb38480d6cf66a52f7298f8f0e1f200311

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