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 -- View it on GitLab: https://salsa.debian.org/med-team/macsyfinder/-/commit/6d984f325c9580af3b57279ec1e98a506090f228 You're receiving this email because of your account on salsa.debian.org.
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