[med-svn] [Git][med-team/macsyfinder][upstream] New upstream version 2.1.5

Sun Aug 24 12:30:51 BST 2025

Michael R. Crusoe pushed to branch upstream at Debian Med / macsyfinder

Commits:
6d984f32 by Michael R. Crusoe at 2025-08-23T14:09:25+01:00
New upstream version 2.1.5
- - - - -

174 changed files:

- .github/PULL_REQUEST_TEMPLATE.md
- .github/workflows/ruff.yml
- .github/workflows/testing.yml
- .gitignore
- .gitlab-ci.yml
- .gitlab/issue_templates/Enhancement → .gitlab/issue_templates/Enhancement.md
- .readthedocs.yaml
- CONTRIBUTORS.md
- COPYRIGHT
- Docker/Macsyfinder/Dockerfile.2.1.4
- macsypy/error.py → Docker/Macsyfinder/Dockerfile.2.1.5
- Docker/Macsyfinder/macsyfinder-entrypoint.sh
- Docker/coverage/Dockerfile
- MANIFEST.in
- README.md
- codemeta.json
- + doc/source/_static/github-banner.svg
- − doc/source/_static/macsyfinder_classes.pdf
- − doc/source/_static/macsyfinder_classes.svg
- doc/source/_templates/layout.html
- doc/source/conf.py
- − doc/source/developer_guide/api/cluster.rst
- − doc/source/developer_guide/api/config.rst
- − doc/source/developer_guide/api/database.rst
- − doc/source/developer_guide/api/definition_parser.rst
- − doc/source/developer_guide/api/error.rst
- − doc/source/developer_guide/api/gene.rst
- − doc/source/developer_guide/api/hit.rst
- doc/source/developer_guide/api/index.rst
- + doc/source/developer_guide/api/io.rst
- − doc/source/developer_guide/api/model.rst
- − doc/source/developer_guide/api/model_conf_parser.rst
- − doc/source/developer_guide/api/package.rst
- − doc/source/developer_guide/api/profile.rst
- − doc/source/developer_guide/api/registries.rst
- − doc/source/developer_guide/api/report.rst
- doc/source/developer_guide/api/scripts.rst
- − doc/source/developer_guide/api/search_genes.rst
- − doc/source/developer_guide/api/serialization.rst
- − doc/source/developer_guide/api/solution.rst
- − doc/source/developer_guide/api/system.rst
- − doc/source/developer_guide/api/utils.rst
- doc/source/developer_guide/index.rst
- doc/source/developer_guide/installation.rst
- doc/source/developer_guide/overview.rst
- doc/source/index.rst
- doc/source/modeler_guide/FAQ_modeler.rst
- doc/source/modeler_guide/gallery.rst
- doc/source/modeler_guide/helper_tools.rst
- doc/source/modeler_guide/index.rst
- doc/source/modeler_guide/installation.rst
- doc/source/modeler_guide/modeling.rst
- doc/source/modeler_guide/models_V1ToV2.rst
- doc/source/modeler_guide/package.rst
- doc/source/modeler_guide/publish_package.rst
- doc/source/user_guide/FAQ.rst
- doc/source/user_guide/big_data.rst
- doc/source/user_guide/functioning.rst
- doc/source/user_guide/gembase_convention.rst
- doc/source/user_guide/index.rst
- doc/source/user_guide/input.rst
- doc/source/user_guide/installation.rst
- doc/source/user_guide/model_definition.rst
- doc/source/user_guide/new_v2.rst
- doc/source/user_guide/outputs.rst
- doc/source/user_guide/quickstart.rst
- − macsypy/__init__.py
- − macsypy/cluster.py
- − macsypy/config.py
- − macsypy/data/pre-push
- − macsypy/database.py
- − macsypy/definition_parser.py
- − macsypy/gene.py
- − macsypy/hit.py
- − macsypy/metadata.py
- − macsypy/model.py
- − macsypy/model_conf_parser.py
- − macsypy/package.py
- − macsypy/profile.py
- − macsypy/registries.py
- − macsypy/report.py
- − macsypy/scripts/macsydata.py
- − macsypy/scripts/macsyprofile.py
- − macsypy/search_genes.py
- − macsypy/serialization.py
- − macsypy/solution.py
- − macsypy/system.py
- − macsypy/utils.py
- nextflow.config
- parallel_macsyfinder.nf
- pyproject.toml
- − setup.cfg
- setup.py
- + src/macsyfinder/__init__.py
- macsypy/licenses.py → src/macsyfinder/io.py
- macsypy/scripts/__init__.py → src/macsyfinder/scripts/__init__.py
- macsypy/scripts/macsy_gembase_split.py → src/macsyfinder/scripts/macsy_gembase_split.py
- macsypy/scripts/macsy_merge_results.py → src/macsyfinder/scripts/macsy_merge_results.py
- macsypy/scripts/macsyconfig.py → src/macsyfinder/scripts/macsyconfig.py
- tests/test_ProfileFactory.py → src/macsyfinder/scripts/macsydata.py
- tests/test_ModelBank.py → src/macsyfinder/scripts/macsyprofile.py
- macsypy/scripts/macsyfinder.py → src/macsyfinder/scripts/msf.py
- tests/__init__.py
- − tests/data/conf_files/macsy_models.conf
- − tests/data/conf_files/macsy_test_bad_conf.conf
- − tests/data/conf_files/macsy_test_conf.conf
- − tests/data/conf_files/macsy_virtualenv_test.conf
- − tests/data/conf_files/macsyfinder-old.conf
- − tests/data/conf_files/model_conf.xml
- − tests/data/conf_files/model_conf_wo_filtering.xml
- − tests/data/conf_files/model_conf_wo_weights.xml
- − tests/data/conf_files/project.conf
- tests/data/functional_test_unordered/all_systems.tsv
- + tests/data/hmm/old_profile.hmm
- + tests/data/hmm/one_profile.hmm
- + tests/data/hmm/several_profiles.hmm
- tests/data/conf_files/macsyfinder_default.conf → tests/data/macsyfinder_default.conf
- − tests/data/minimal_pack/README.md
- − tests/data/minimal_pack/definitions/model_example.xml
- − tests/data/minimal_pack/metadata.yml
- − tests/data/minimal_pack/model_conf.xml
- − tests/data/pack_metadata/bad_metadata.yml
- − tests/data/pack_metadata/good_metadata.yml
- − tests/data/pack_metadata/metadata_no_cite.yml
- − tests/data/pack_metadata/metadata_no_copyright.yml
- − tests/data/pack_metadata/metadata_no_desc.yml
- − tests/data/pack_metadata/metadata_no_doc.yml
- − tests/data/pack_metadata/metadata_no_email.yml
- − tests/data/pack_metadata/metadata_no_license.yml
- − tests/data/pack_metadata/metadata_no_maintainer.yml
- − tests/data/pack_metadata/metadata_no_name.yml
- − tests/data/pack_metadata/metadata_no_vers.yml
- − tests/data/pack_metadata/metadata_poor_quality.yml
- − tests/data/results_macsyprofile.tsv
- − tests/data/results_macsyprofile_best_score.tsv
- − tests/data/results_macsyprofile_coverage.tsv
- − tests/data/results_macsyprofile_evalue.tsv
- − tests/data/results_macsyprofile_no_hits.tsv
- − tests/data/results_macsyprofile_pattern.tsv
- − tests/run_tests.py
- − tests/test_Config.py
- − tests/test_DefinitionParser.py
- − tests/test_Exchangeable.py
- − tests/test_GeneBank.py
- − tests/test_Indexes.py
- − tests/test_LikelySystem.py
- − tests/test_MacsyDefaults.py
- − tests/test_MatchMaker.py
- − tests/test_Model.py
- − tests/test_Profile.py
- − tests/test_RejectedCandiate.py
- − tests/test_RepliconDB.py
- − tests/test_Report.py
- − tests/test_System.py
- − tests/test_cluster.py
- tests/test_functional_test.py
- − tests/test_gene.py
- − tests/test_hit.py
- + tests/test_io.py
- tests/test_macsy_gembase_split.py
- tests/test_macsy_merge_results.py
- tests/test_macsyconfig.py
- − tests/test_macsydata.py
- tests/test_macsyfinder.py
- − tests/test_macsyprofile.py
- − tests/test_metadata.py
- − tests/test_model_conf_parser.py
- − tests/test_package.py
- − tests/test_registries.py
- tests/test_macsypy.py → tests/test_scripts.py
- − tests/test_search_genes.py
- − tests/test_serialization.py
- − tests/test_solution.py
- − tests/test_utils.py

The diff was not included because it is too large.

View it on GitLab: https://salsa.debian.org/med-team/macsyfinder/-/commit/6d984f325c9580af3b57279ec1e98a506090f228

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