1.5.5

What's Changed

• Add jsonlines to the spec. by @cbizon in #340
• Patch for issues 348 by @RichardBruskiewich in #349
• Patch to resolve issue 360 remove !!set and other odd markup in yaml output of graph-summary output by @RichardBruskiewich in #361
• Issue 359 error exit codes by @RichardBruskiewich @sierra-moxon in #362
• update bmt to get new biolink-model, fix linkml changes, add test coverage to click in order to pass sonarcloud coverage requirements by @sierra-moxon in #367
• list delimiters (issue 345) by @EvanDietzMorris in #370
• Switch from neo4jrestclient to neo4j for Neo4j 4.3 compatibility by @kevinschaper @RichardBruskiewich @sierra-moxon in #343
• Issue 338 enhanced kgx transform logging by @RichardBruskiewich @sierra-moxon in #365

New Contributors

• @cbizon made their first contribution in #340
• @EvanDietzMorris made their first contribution in #370

Full Changelog: 1.5.4...1.5.5

1.5.4

update to use new version of bmt, thus new version (2.2.5) of biolink-model.

1.5.3

• remove pystache requirement

1.5.1

• Keep track of edge properties in owl source

1.5.0

• Support mixins in ancestors hierarchy
• Invalidate mixins as categories
• Maintenance and bug fixes

Biolink 2.* update

• This version replaces the previously hard-coded config.yaml Biolink Model release number with use of the current Biolink Model Toolkit default model release value.
• Users of the KGX 'validate' functionality can also reset the Biolink Model (SemVer) release number at the CLI, and programmatically, with the Validator.set_biolink_model() class method.
• KGX made Biolink Model 2.0++ aware with respect to new provenance slots - knowledge_source and its descendant slot definitions. These slot properties need to be explicitly specified in the Transformer.transform input_args dictionary.
• Some support for heuristic auto-generation of candidate format-compliant CURIES Biolink Model 2.0++ Information Resource ("InfoRes") CURIES. The new code also provides a regular expression and meta-data based rewrite of knowledge source names into such CURIES.
• Some additional clarification in the 'readTheDocs' documentation including for 1.3.0 streaming release features.

1.3.0

• Add streaming option to validation

1.2.0

• Update BMT to 0.7.2
• Update LinkML to 1.0.0
• Pin some major release versions in requirements.txt

1.1.0

• Migrate to LinkML from BiolinkML

1.0.0

• Fix bug with caching records in RdfSource
• Add shortcuts for arguments in all CLI operations
• Fix usage in CLI