cellxgene-schema v2.0.0

[2.0.0] - 2021-09-15

Added

• All MUST requirements in schema version 2.0.0 are strictly enforced. For failures, an error message is displayed and validation fails.
• Some STRONGLY RECOMMENDED requirements in the schema version 2.0.0 are checked. Warnings are displayed when recommended best practices are not observed.
• Pinned versions of ontology and feature references (see ./cellxgene_schema/ontology_files/).
• Downloader and parser for ontology and feature references (see ./scripts/).
• Option to apply human-readable labels for ontology and feature references: cellxgene-schema validate --add-labels.
• Tests that mirror the requirements in schema version 2.0.0.

Changed

• cellxgene-schema validate validates schema version 2.0.0. The implementation is from scratch.
• Ontology validation and label retrieval depend on downloaded references instead of the EBI Ontology Service (see ./cellxgene_schema/ontology.py).
• Gene/feature validation and label retrieval depend on downloaded references (see ./cellxgene_schema/ontology.py).

Removed

• Subcommand cellxgene-schema apply.
• Support for schema versions 1.x.x.