Schema: 7.0.0

What's Changed

• fix: don't convert dense matrices to COO in feature_is_filtered validation by @nayib-jose-gloria in #1398
• approved schema by @brianraymor in #1399
• Created 7.0.0 draft by @brianraymor in #1400
• updated gene references by @brianraymor in #1401
• added cellosaurus ontology by @brianraymor in #1403
• Updated tissue_ontology_term_id and tissue_type by @brianraymor in #1404
• editorial by @brianraymor in #1406
• updated cell type by @brianraymor in #1408
• updated development stage by @brianraymor in #1409
• updated donor by @brianraymor in #1410
• updated ethnicity by @brianraymor in #1411
• updated sex by @brianraymor in #1412
• updated suspension_type by @brianraymor in #1413
• editorial by @brianraymor in #1414
• feat: bump gencode versions for schema 7.0.0 by @nayib-jose-gloria in #1421
• chore: CCIE-4984 conform to open sourcing guidelines by @wontonst in #1417
• fix: rename opensource files by @Bento007 in #1426
• fix: resolve parquet duplication of rows by @Bento007 in #1424
• fix: atac seq duplicate check by @Bento007 in #1427
• feat: update tissue_type and tissue_ontology_term_id, minus cell line changes by @joyceyan in #1430
• restore disease and tissue by @brianraymor in #1431
• fix: invalid gene check by @joyceyan in #1432
• feat: update development_stage_ontology_term_id and development_stage for 7.0 by @joyceyan in #1428
• fix: stricter control on sorting by @Bento007 in #1433
• fix: add na as valid for uberon organisms by @joyceyan in #1434
• feat: update cell_type and cell_type_ontology_term_id for 7.0 by @joyceyan in #1438
• feat: cellosaurus terms for tissue_ontology_term_id by @joyceyan in #1443
• fix: improve error handling for subprocess commands in atac_seq.py by @Bento007 in #1446
• feat: sex ontology term id changes for 7.0 by @joyceyan in #1444
• feat: fix cell type ontology term id by @joyceyan in #1445
• fix: dedupe error 13 by @Bento007 in #1447
• fix: pin duckdb version in requirements.txt by @Bento007 in #1450
• fix: decouple schema version from package version by @nayib-jose-gloria in #1453
• VC-3520 feat: schema 7.0 changes to suspension_type by @kliu-czi in #1454
• Jhilton/7ont updates 1402 by @jahilton in #1456
• Updated changelog by @brianraymor in #1457
• feat: update self-reported ethnicity for schema 7.0.0 by @Bento007 in #1452
• feat: add donor_id handling and validation rules for cell_line in schema and tests by @Bento007 in #1455
• editorial by @brianraymor in #1458
• Updated HANCESTRO reference by @brianraymor in #1459
• fix: VC 3520 by @kliu-czi in #1460
• feat: add forbidden values for donor_id and validation test for tissu… by @Bento007 in #1461
• Created 7.1.0 draft by @brianraymor in #1465
• feat: update schema version to 7.0.0 and bump COG to 1.9.0 by @Bento007 in #1466
• fix: ontology_bump skip to support '||' separator. by @Bento007 in #1467
• added genetic perturbations by @brianraymor in #1468

New Contributors

• @wontonst made their first contribution in #1417
• @kliu-czi made their first contribution in #1454

Full Changelog: v6.0.0...v7.0.0

v6.2.2

Full Changelog: v6.2.1...v6.2.2

Schema: 6.2.1

Full Changelog: v6.1.0...v6.2.1

Schema: 6.1.0

Full Changelog: v6.0.3...v6.1.0

Schema 6.0.3

Full Changelog: v6.0.0...v6.0.3

Schema 6.0.0

What's Changed

• chore: bump latest schema link to point to schema 5.3.0 by @nayib-jose-gloria in #1333
• approved schema by @brianraymor in #1334
• Created 6.0.0 draft by @brianraymor in #1335
• updates for one organism per dataset by @brianraymor in #1336
• Updated feature_name by @brianraymor in #1337
• Is filtered by @brianraymor in #1338
• Allow multiple values for disease by @brianraymor in #1339
• Updated delimiter for ethnicity by @brianraymor in #1340
• Updated X table by @brianraymor in #1341
• revert is_filtered to 5.3.0 by @brianraymor in #1342
• Updated is_filtered by @brianraymor in #1343
• feat: validate that no two rows in obs are identical by row counts by @joyceyan in #1346
• fix: package setup with validation_internals by @joyceyan in #1350
• feat: update validation of feature_is_filtered by @joyceyan in #1349
• fix: clean up intermediate sort files for ATAC by @Bento007 in #1354
• feat: support multiple terms with disease ontology term id + alter delimiter for multi terms by @joyceyan in #1356
• feat: fix validation of is_primary_data to handle numpy bools by @joyceyan in #1355
• fix: only check duplicate rows of raw matrix, not normalized matrix by @joyceyan in #1358
• feat: support only one organism by @joyceyan in #1357
• feat: remove deduplication of genes by @joyceyan in #1359
• fix: catch indexerror by @joyceyan in #1360
• feat: update migration script for moving organism from obs to uns by @joyceyan in #1361
• chore: Update LICENSE.txt by @Bento007 in #1362
• chore: update copy of disease error msg by @joyceyan in #1363
• fix: organism validation for atac_seq 6.0 by @joyceyan in #1366
• fix: take smaller step when sorting. by @Bento007 in #1353
• updated pinned ontologies by @brianraymor in #1368
• fix: 6.0 one organism implementation by @joyceyan in #1369
• fix: deprecate organism column in addition to organism_ontology_term_id by @joyceyan in #1373
• fix: unique organisms from feature ids by @joyceyan in #1374
• fix: forbid organism from being provided in uns by @joyceyan in #1376
• fix: gene processing script and trigger running it by @joyceyan in #1378
• chore: bump cog for 6.0 by @joyceyan in #1380
• AUTO: update migrate.py schema_version 5.3.2->6.0.0 by @github-actions in #1381
• feat: update migrate script by @joyceyan in #1382
• feat: downgrade feature_is_filtered errors to to warning by @joyceyan in #1383
• chore: bump ontology parser version by @joyceyan in #1385
• chore: fix matrix utils by @joyceyan in #1387
• chore: update logging of ids by @joyceyan in #1390
• chore: remove printing out collections with an open revision in them by @joyceyan in #1386
• updated changelog by @brianraymor in #1392
• migrate.py updates after first 6.0 dev migration by @brian-mott in #1393
• Migrate.py updates after second dev migration for schema 6.0 by @brian-mott in #1394
• editorial by @brianraymor in #1397
• fix: memory optimization in feature_is_filtered validation by @nayib-jose-gloria in #1395

Full Changelog: v5.3.2...v6.0.0

Release v5.3.2

What's Changed

• removed strongly recommended from development stage by @brianraymor in #1110
• chore: remove seurat references in validator by @ejmolinelli in #1113
• chore: bump cog version for schema 5.3.0 by @joyceyan in #1116
• Added genetic ancestry by @brianraymor in #1117
• release: 5.2.2 by @Bento007 in #1118
• feat: update "is visium" definition for cell_type_ontology_term_id by @joyceyan in #1115
• chore: forbid any NaN in spatial embeddings # by @ejmolinelli in #1119
• Added c. elegans by @brianraymor in #1126
• feat: update validation for obs['in_tissue'] to include descendants of Visiium by @ejmolinelli in #1124
• feat: update validation for uns['spatial'] by @ejmolinelli in #1129
• feat: add genetic ancestry fields for schema 5.3 by @joyceyan in #1132
• updated genetic ancestry values by @brianraymor in #1141
• feat: cellxgene-schema must update validation for X (Matrix Layers) for descendants of Visium by @ejmolinelli in #1133
• fix: handle both string and category encoded "assay_ontology_term_id" by @ejmolinelli in #1142
• fix: clean up the cli by @Bento007 in #1108
• updated sex_ontology_term_id by @brianraymor in #1145
• chore: add back return value from is_seurat_convertible by @joyceyan in #1147
• feat: differential tissue position row/col max sizes for visium and visium 11 by @ejmolinelli in #1143
• feat: support for visium descendants in obs['assay_ontology_term_id'] by @ejmolinelli in #1148
• feat: X_{suffix} to include descendants of Visium by @ejmolinelli in #1144
• chore: update logging to log by donor id instead by @joyceyan in #1150
• fix(devop): code coverage failing by @Bento007 in #1149
• feat: refactor suspension type validation logic to be simpler and more performant by @nayib-jose-gloria in #1155
• updated X matrix requirement by @brianraymor in #1157
• chore(deps): update numpy requirement from <2 to <3 in /cellxgene_schema_cli by @dependabot in #1163
• feat: update to anndata 0.11 and memory efficient reads + writes by @nayib-jose-gloria in #1152
• Release: version 5.2.3 by @Bento007 in #1167
• feat: use dask threads schedule with default values. by @Bento007 in #1168
• Added taxon specific ontologies by @brianraymor in #1170
• Added gene references for additional species by @brianraymor in #1171
• Updated cell_type_ontology_term_id by @brianraymor in #1172
• Updated development_stage_ontology_term_id by @brianraymor in #1173
• Updated sex_ontology_term_id by @brianraymor in #1174
• Updated tissue_ontology_term_id by @brianraymor in #1175
• Updated feature_reference by @brianraymor in #1176
• Updated patch version by @brianraymor in #1177
• fix: donor id error logging + obsm typo by @joyceyan in #1153
• chore: use dask in migrate script template by @nayib-jose-gloria in #1185
• Updated assay_ontology_term_id by @brianraymor in #1187
• Updated changelog by @brianraymor in #1188
• Added sus scrofa by @brianraymor in #1190
• Updated cell_type_ontology_term_id by @brianraymor in #1191
• Updated development_stage_ontology_term_id by @brianraymor in #1192
• Updated organism_ontology_term_id by @brianraymor in #1193
• Updated tissue_ontology_term_id by @brianraymor in #1194
• feat: Require CSR encoding for sparse matrices and matrices with sparsity ratio above 50% by @ejmolinelli in #1169
• Updated development_stage_ontology_term_id by @brianraymor in #1195
• Updated tissue_ontology_term_id by @brianraymor in #1197
• Updated gene reference by @brianraymor in #1198
• Updated organism and feature reference by @brianraymor in #1200
• editorial by @brianraymor in #1204
• Removed xenopus by @brianraymor in #1207
• Updated genetic_ancestry by @brianraymor in #1208
• Added orthologous updates by @brianraymor in #1212
• Updated changelog by @brianraymor in #1213
• fix: remove dependency on Validator in AnnDataLabelAppender by @Bento007 in #1205
• feat: update genetic ancestry tolerance by @joyceyan in #1210
• feat: exclude generic visium (EFO:0010961) from allowed assay_ontology_term by @ejmolinelli in #1214
• Updated assay_ontology_term_id by @brianraymor in #1215
• Updates for fragments by @brianraymor in #1216
• Updated EFO release by @brianraymor in #1217
• Updated fragments and changelog by @brianraymor in #1224
• feat: merge in multi species work from Q4 2024/experimental validator by @joyceyan in #1199
• Corrected Visium reference by @brianraymor in #1227
• Addressed feedback from Jason by @brianraymor in #1228
• feat: add support for zebrafish, fruit fly, and roundworm by @joyceyan in #1229
• feat: resolve visium+multispecies testing conflicts by @ejmolinelli in #1226
• feat: Differentiate between missing column and column with null/NaN values by @ejmolinelli in #1230
• chore: move organism-specific validation logic to schema_definition.yaml by @nayib-jose-gloria in #1231
• Updated gene annotations by @brianraymor in #1233
• chore: verify we're not allowing new terms to human / mouse by @joyceyan in #1232
• feat: support development_stage_ontology_term_id and tissue_type cols based on 5.3 reqs by @joyceyan in #1234
• fix: tissue_ontology_term_id and cell_type_ontology_term_id fields for 3 new species by @joyceyan in #1235
• chore: resolve/remove skipped tests by @ejmolinelli in #1236
• Added descendants of by @brianraymor in #1242
• fix: cell culture edge case for zebrafish, fly, roundworm by @joyceyan in #1249
• feat: add support for mus musculus descendant organisms by @joyceyan in https://github.com...

Release 5.2.3

What's Changed

• fix: pin anndata to <0.10.9 to avoid a breaking change in SparseData
• fix: pin scipy to <1.15.0 to avoid a breaking change with Anndata.
  • Bug to fix: #1165

5.2.2

What's Changed

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

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