Release 5.2.1

What's Changed

• fix: pin anndata to <0.11 by @Bento007 in #1097

Full Changelog: v5.2.0...v5.2.1

Release 5.2.0

What's Changed

• chore: bump COG version for schema 5.2 by @nayib-jose-gloria in #1004
• feat: use isoform lengths median to determine gene feature_length + write feature_length for 'spike-in' features in var by @nayib-jose-gloria in #1005
• feat: add feature_type to var df during add labels step by @nayib-jose-gloria in #1006
• feat: update suspension_type mapping by @nayib-jose-gloria in #1007
• feat: update development stage ontology term ID validation rules by @nayib-jose-gloria in #1009
• chore: create GH Page with "latest-schema.html" redirect to latest schema version doc by @nayib-jose-gloria in #1026
• AUTO: update migrate.py by @github-actions in #1011

Full Changelog: v5.1.1...v5.2.0

Release 5.1.1

What's Changed

• feat: remove canonical enforcement from CLI by @nayib-jose-gloria in #974
• chore: bump dependencies by @nayib-jose-gloria in #982

Full Changelog: v5.1.0...v5.1.1

v5.1.0

What's Changed

Schema

• editorial by @brianraymor in #880
• editorial by @brianraymor in #883
• Refreshed ontologies by @brianraymor in #892
• clarified the Slide-seqV2 requirement by @brianraymor in #850
• restored 3.1.0 obsm requirements by @brianraymor in #860
• updated image requirements by @brianraymor in #868
• Updated requirements for assay_ontology_term_id by @brianraymor in #872

Feat

• feat: remove intermediate pypi publish from schema version bump by @danieljhegeman in #841
• feat: datasets demo with visibility by @MillenniumFalconMechanic in #835

Schema 5.1.0

• feat(schema 5.1.0): update validation for obsm X_ embeddings by @nayib-jose-gloria in #856
• feat(schema 5.1.0): validate uns[spatial] by @MillenniumFalconMechanic in #858
• feat: cellxgene-schema CLI must add validation for obsm['spatial'] by @nayib-jose-gloria in #863
• feat(schema 5.1.0): validate obs[array_col], obs[array_row] and obs[in_tissue] by @MillenniumFalconMechanic in #861
• feat(schema 5.1.0): validate obs[cell_type_ontology_term_id] by @MillenniumFalconMechanic in #864
• feat: update validation for obs['is_primary_data'] to enforce False if uns['spatial']['is_single'] is False by @nayib-jose-gloria in #865
• feat: update X matrix validation to validate Visium assays by @nayib-jose-gloria in #876
• feat(schema 5.1.0): unique spatial assay ontology term id by @MillenniumFalconMechanic in #885
• fix: rename ontology_files and ONTOLOGY_DIR references to gencode_files and GENCODE_DIR by @nayib-jose-gloria in #847
• fix(schema 5.1.0): throw error if obsm is not type np.ndarray by @Bento007 in #859
• fix(5.1.0): type check for spatial and nested values by @Bento007 in #875
• fix: check type of uns["spatial"][library_id] is dict by @Bento007 in #886
• fix(schema 5.1.0): validate ['library_id']['images'][image] of type u… by @MillenniumFalconMechanic in #882
• fix: load SparseDatasets into memory by @Bento007 in #898
• fix: update migration_template for linting and generate_script.py to add GENCODE_MAPPER by @nayib-jose-gloria in #914

Chore

• chore(deps): bump cython from 0.29.34 to 3.0.10 in /cellxgene_schema_cli by @dependabot in #924

Full Changelog: v5.0.2...v5.1.0

v5.0.2

What's Changed

• Replaced all ontology term metadata parsing / term ancestry validation logic in validator / write-labels with cellxgene-ontology-guide dependency. No functional changes expected
• Set cellxgene-schema CLI scipy requirement to <1.13.0 to patch incompatibility with anndata <= 0.10.6
• Set package requirements to >= python 3.10
• Deprecates 'convert' command, marked for deprecation in v3.1.0

Full Changelog: v5.0.1...v5.0.2

v5.0.1

What's Changed

• feat: allow numbers as uns values by @danieljhegeman in #822

Full Changelog: v5.0.0...v5.0.1

v5.0.0

What's Changed

• Updated schema validator to validate datasets per changes/requirements defined here

Full Changelog: v4.0.0...v5.0.0

Release 4.0.0

What's Changed

• Updated schema validator to validate datasets per changes/requirements defined here
• Updated migrate command to convert schema 3 compliant datasets to schema 4 compliant datasets

Full Changelog: v3.1.3...v4.0.0

Release 3.1.3

• feat(write_labels): store all sparse X and raw.X in canonical form

Release 3.1.2

• Patch fix to no longer require schema_version to be populated in the uns of an h5ad when validating using cellxgene-schema validate.