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Release v2.0.4#455

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ielis merged 23 commits intomastermonarch-initiative/phenol:masterfrom release-v2.0.4monarch-initiative/phenol:release-v2.0.4Copy head branch name to clipboardNov 20, 2023

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Commits on Aug 1, 2023

• Next development iteration 2.0.4-SNAPSHOT.

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Commits on Oct 31, 2023

• Setup benchmark stubs.

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• Refactor CsrOntologyGraph to CsrPolyOntologyGraph.

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Commits on Nov 1, 2023

• Implement CsrMonoOntologyGraph. Fix bug in CsrPolyOntologyGraph that supports to iterate over the iterable only once. Improve OntologyGraph testing.

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• Expose mono CSR builder through OntologyGraphBuilders.

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• Setup benchmark for poly vs. mono. Use mono by default in MinimalOntologyLoader and OntologyLoader.

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• Use hash map instead of binary search. Extend benchmarks.

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• Add bench results

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Commits on Nov 3, 2023

• Set max line length to 120.

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• Improve documentation and logging.

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Commits on Nov 4, 2023

• Update documentation on TermAnnotation.

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Commits on Nov 6, 2023

• Implement sub ontology in mono graph.

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Commits on Nov 12, 2023

• Implement sub ontology in poly graph.

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Commits on Nov 13, 2023

• Add comprehensive tests of the subgraph. Fix CSR data bug. Remove methods & tests for unsetting bits.

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• Simplify CsrPolyOntologyGraph.

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• Add subOntology tests, update meta info.

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• Improve subontology test.

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• Merge pull request #451 from monarch-initiative/petty-fixes

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• Update the dependencies, remove unnecessary guava module and code.

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Commits on Nov 20, 2023

• Merge pull request #448 from monarch-initiative/mono-graph

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• Merge pull request #453 from monarch-initiative/sub-ontology-graph

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• Merge pull request #454 from monarch-initiative/#449-update-dependencies

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• Set version to 2.0.4, update changelog.

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