INCATools/ontology-access-kit: v0.7.0rc2

What's Changed

• Ensuring that pronto definition objects are stringified (730) by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/731
• Adding a notebook demonstrating statistics command. by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/724
• Fixed test by @hrshdhgd in https://github.com/INCATools/ontology-access-kit/pull/723
• Added diff markdown for AddNodeToSubset by @hrshdhgd in https://github.com/INCATools/ontology-access-kit/pull/736
• Ran formatter and minor code cleanup by @hrshdhgd in https://github.com/INCATools/ontology-access-kit/pull/737
• Adding definition validation functionality by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/738
• Adding option for non-redundant entialed relationships. by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/740
• Enriched mapping documentation by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/741
• Adding defusedxml dependency. Fixes #743 by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/744
• Refactored mappings to more generic relationships in diff markdown output by @hrshdhgd in https://github.com/INCATools/ontology-access-kit/pull/750
• Update obo compliance suite using latest robot by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/747
• Make ruff happy by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/757
• Adding additional docs on the OAK expression language by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/749
• Berkeley Hackathon: Enhancing semsim docs. by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/753
• Adding skos-xref-duplicate to obo compliance suite by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/752
• Update to support new semsimian IC map functionality by @caufieldjh in https://github.com/INCATools/ontology-access-kit/pull/755
• removing unneccessary quotes in expression language guide by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/762
• Adding has-part glyph to config. by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/765
• More efficient association-based IC calculation. by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/764
• Pass custom IC map to Semsimian through CLI by @caufieldjh in https://github.com/INCATools/ontology-access-kit/pull/759
• Adding MRCA example to expression docs by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/768
• Adding link to ontogenesis chapter on annotations. by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/771
• Python level access to query expression language by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/769
• New functionality: term usages by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/776
• Making prefix mapping less strict, fixes #702 by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/761
• rename edge to mapping by @twhetzel in https://github.com/INCATools/ontology-access-kit/pull/775
• Solves ClassCreation duplication & formats Mappings md table properly by @hrshdhgd in https://github.com/INCATools/ontology-access-kit/pull/780
• information content enhancements by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/781
• Added change handler for kgcl.RemoveNodeFromSubset by @hrshdhgd in https://github.com/INCATools/ontology-access-kit/pull/783
• Supporting skos mappings for simpleobo and pronto. by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/766
• structured_format.pattern-style permissible value creation eg for MIxS by @turbomam in https://github.com/INCATools/ontology-access-kit/pull/785
• Update sql_implementation.py to include sqlachemy output in debug logging. by @DnlRKorn in https://github.com/INCATools/ontology-access-kit/pull/782
• set_label will INSERT if label not already presented. Fixes #788 by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/789
• Implementing NodeDeletion which was earlier a comment. by @hrshdhgd in https://github.com/INCATools/ontology-access-kit/pull/791
• Fix test suite by @gouttegd in https://github.com/INCATools/ontology-access-kit/pull/796
• Bug in calculating all_by_all_pairwise_similarity by @hrshdhgd in https://github.com/INCATools/ontology-access-kit/pull/800
• Add test for all_by_all_pairwise_similarity() in semsimian using custom IC map by @justaddcoffee in https://github.com/INCATools/ontology-access-kit/pull/801
• Add cache management features by @gouttegd in https://github.com/INCATools/ontology-access-kit/pull/799
• Enhanced heatmap functionality by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/798
• Adding a .sample operator by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/797
• graph projections and subset validation by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/806
• Update cli.rst (fixed very minor documentation error) by @DnlRKorn in https://github.com/INCATools/ontology-access-kit/pull/804
• update docs by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/808
• Remove outdated warning, fix minor typos by @ialarmedalien in https://github.com/INCATools/ontology-access-kit/pull/814
• Moved Jupter notebooks to be part of sphinx docs by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/816
• Adding step to build pandoc for sphinx docs by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/817
• installing pandoc by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/818
• Adding more docs on how to use LLMs with OAK by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/819
• Adding crawl and chain commands by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/826
• association graphs by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/828
• Adding ability to specify obographviz config inside a crawl config by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/829
• Value Set examples and docs by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/830
• Add definition method to OLS implementation by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/831
• Add enrichment guide to OAK documentation by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/832
• Extend OntoportalImplementation with entities() and node() methods by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/833
• Allow choice of closure fields in amigo by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/835
• Additional utilities for handling boomer. by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/843
• Fix broken links to notebooks by @justaddcoffee in https://github.com/INCATools/ontology-access-kit/pull/837
• Pyproject.toml Update to python standard/UV Update For Oak by @DnlRKorn in https://github.com/INCATools/ontology-access-kit/pull/849
• Add --version option to runoak by @DnlRKorn in https://github.com/INCATools/ontology-access-kit/pull/859
• Adding Python 3.13 support, removing Python 3.9 support by @DnlRKorn in https://github.com/INCATools/ontology-access-kit/pull/864
• [codex] migrate funowl integration to py-horned-owl by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/868
• [codex] fix release build versioning by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/869
• [codex] fix owl input format detection by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/870

New Contributors

• @twhetzel made their first contribution in https://github.com/INCATools/ontology-access-kit/pull/775
• @turbomam made their first contribution in https://github.com/INCATools/ontology-access-kit/pull/785
• @DnlRKorn made their first contribution in https://github.com/INCATools/ontology-access-kit/pull/782
• @gouttegd made their first contribution in https://github.com/INCATools/ontology-access-kit/pull/796
• @ialarmedalien made their first contribution in https://github.com/INCATools/ontology-access-kit/pull/814

Full Changelog: https://github.com/INCATools/ontology-access-kit/compare/v0.6.0...v0.7.0rc2