chore: release main

[github-actions]

🤖 I have created a release beep boop

python-api: 1.0.0

1.0.0 (2025-03-06)

Features

• Add API ontology querying module (68f3168)
• Add API ontology querying module (#39) (239ef2b)
• add data to the python package (#87) (0eb6831)
• add experimental release + cl terms in efo (#263) (#267) (508dc12)
• add function to fetch curated ontology term lists (#141) (5c7db62)
• add get_term_children and get_term_parents (#186) (dfcd2c2)
• add is_valid_term_id method to OntologyParser (#115) (72c2073)
• add term label to OntologyNode (#182) (326185c)
• additional species-specific ontologies for cxg 5.3 multispecies schema (#255) (64c32fe)
• API: setup python library (211a099)
• API: setup python library (f60f897)
• API: Setup the library for development (1f7ce03)
• build subgraph from term ID (#156) (3f4cd4b)
• bump CL, EFO, HsapDv, MmusDv, MONDO, UBERON ontology versions for CxG schema 5.2.0 (#217) (5bb43b9)
• fetch ontology term descriptions, if available (#181) (0120377)
• fetch ontology term synonyms (#200) (89c1725)
• fetch term ID by term label (#212) (11c671d)
• fix string error in python release (#244) (1587423)
• implement stubbed query functions (334deb5)
• include license file with python package (#85) (2be3d81)
• load GH Release Assets for schema version in memory (#72) (58bad0a)
• pinned ontologies for schema 5.3.0 (#275) (cd6a15e)
• query cross-ontology terms imported into a supported ontology (#232) (2e1a834)
• refactor ancestry mapping to include distance from descendant node + implement functions to support curated list term mapping (#96) (7fc3562)
• refer to ontology source filenames in ontology_info and return that in get_ontology_download_url (#106) (ff9d826)
• remove v from ontology_info.json (#196) (a1292a3)
• set up new github workflow for only ontologies that have changed (#264) (45d0fce)
• set version regex for pyton api (3720dab)
• set-up docsite (#99) (b7591bc)
• split all_ontology into individual files. (#93) (ead59e5)
• Support getting download link for ontology from source repo (#86) (fd55b76)
• update EFO to 3.71.0 (#242) (7a92c0f)
• update ontology_info.json for 5.1 (#207) (d5c8ae3)
• write python API demo notebook (#101) (bfae292)

Misc

• add doctesting to API (#176) (c0aec23)
• add test to ensure all supported ontologies are supported by COG API (#236) (56051f9)
• automate testpypi releases (#118) (b5a1a66)
• clean-up ontology_parser single fetch and bulk fetch methods + account for acceptable non-ontology terms (#112) (2ef7435)
• deploy api when ontology_info.json changes (#194) (40d58f6)
• deprecate older version of cellxgene schema (#172) (186e762)
• deps-dev: bump semantic-version from 2.8.5 to 2.10.0 in /api/python (#98) (dfe0b39)
• enable code coverage (#143) (c52c436)
• Fix typo in python readme (#216) (30a6ba8)
• move pytest configs to pyproject.toml (#175) (a90341b)
• reformat examples in docstrings (#157) (e5528e1)
• release 1.0.0 (60eef67)
• release main (#130) (0b37dc8)
• release main (#132) (8509bbf)
• release main (#134) (5f876cc)
• release main (#146) (4ca76f0)
• release main (#147) (3eacdd2)
• release main (#160) (cdb8faf)
• release main (#161) (f0066a5)
• release main (#185) (9b2fe53)
• release main (#187) (986342a)
• release main (#193) (e9a4ab5)
• release main (#195) (2f36845)
• release main (#199) (cac2a12)
• release main (#201) (a8f5991)
• release main (#204) (dfc8d8e)
• release main (#211) (77d6d7d)
• release main (#224) (133167c)
• release main (#243) (7c2ff4d)
• release main (#245) (2f1b91b)
• release main (#256) (bd48472)
• release main (#258) (d56f1f4)
• release main (#260) (9edebfd)
• release main (#268) (0ac2219)
• release main (#274) (06fbda3)
• release main (#74) (e748fe9)
• release tsmith/release-assets (63b782d)
• release tsmith/release-assets (#57) (6a6b02a)
• remove 5.3.1-alpha (#273) (a930332)
• update readmes (#171) (d38ba65)
• use trusted publisher to publish pypi package. (#137) (5fc917b)

BugFixes

• idempotency issue (#247) (0eebc68)
• imports for api (4cd3386)
• lint errors (f5e4583)
• make constant.py private (46d04a4)
• move get_ontology_download_url. (#152) (8365411)
• ontology_parser.py defaults to latest (#153) (5b94d6e)
• parse through NCBITaxon ancestors (#259) (c461251)
• Preserve order of high_level_terms when matching against an input curated list of terms (#189) (8dca5f3)
• python api releases (bf0477e)
• python-api release version (#131) (3237651)
• README.md (1eae21d)
• remove setuptools-scm (#197) (254b981)
• typos (76ae9fa)
• update notebooks (96c7213)
• update README.md for API (f606073)
• update requirements (#114) (9888f3d)
• upgrade EFO from 3.69 to 3.74 (#257) (c38e905)

ontology-assets: 1.0.0

1.0.0 (2025-03-06)

Features

• add experimental release + cl terms in efo (#263) (#267) (508dc12)
• add function to fetch curated ontology term lists (#141) (5c7db62)
• additional species-specific ontologies for cxg 5.3 multispecies schema (#255) (64c32fe)
• bump CL, EFO, HsapDv, MmusDv, MONDO, UBERON ontology versions for CxG schema 5.2.0 (#217) (5bb43b9)
• fetch ontology term descriptions, if available (#181) (0120377)
• fetch ontology term synonyms (#200) (89c1725)
• load GH Release Assets for schema version in memory (#72) (58bad0a)
• pinned ontologies for schema 5.3.0 (#275) (cd6a15e)
• prototype to support multiple prefixes (#225) (dbcdd29)
• refactor ancestry mapping to include distance from descendant node + implement functions to support curated list term mapping (#96) (7fc3562)
• refer to ontology source filenames in ontology_info and return that in get_ontology_download_url (#106) (ff9d826)
• release: generate descendant mapping for tissues and cells (#100) (841fddf)
• remove all-ontology.json.gz (83fefd6)
• remove v from ontology_info.json (#196) (a1292a3)
• set up new github workflow for only ontologies that have changed (#264) (45d0fce)
• split all_ontology into individual files. (#93) (ead59e5)
• update EFO to 3.71.0 (#242) (7a92c0f)
• update ontology_info.json for 5.1 (#207) (d5c8ae3)
• upload assets on release (#56) (84a1c5d)

Misc

• deploy api when ontology_info.json changes (#194) (40d58f6)
• deprecate older version of cellxgene schema (#172) (186e762)
• move curated lists to ontology-assets (#48) (77916df)
• moving the generated artifacts (c03c8e3)
• release 1.0.0 (60eef67)
• release main (#130) (0b37dc8)
• release main (#146) (4ca76f0)
• release main (#185) (9b2fe53)
• release main (#195) (2f36845)
• release main (#201) (a8f5991)
• release main (#204) (dfc8d8e)
• release main (#211) (77d6d7d)
• release main (#218) (b56bb90)
• release main (#224) (133167c)
• release main (#243) (7c2ff4d)
• release main (#256) (bd48472)
• release main (#258) (d56f1f4)
• release main (#260) (9edebfd)
• release main (#268) (0ac2219)
• release main (#274) (06fbda3)
• release main (#74) (e748fe9)
• release tsmith/release-assets (63b782d)
• release tsmith/release-assets (#57) (6a6b02a)
• remove 5.3.1-alpha (#273) (a930332)
• update ontology decendant mappings (#117) (48451af)
• update ontology decendant mappings (#142) (fb23618)
• update ontology decendant mappings (#162) (12def74)
• update ontology descendant mappings (#167) (5d3d097)
• update ontology descendant mappings (#180) (65ca10f)
• update ontology descendant mappings (#202) (b41948b)
• update ontology descendant mappings (#205) (94157d0)
• update ontology descendant mappings (#209) (c493ca9)
• update ontology descendant mappings (#213) (2a38574)
• update ontology descendant mappings (#219) (fa3094a)

BugFixes

• lint errors (f5e4583)
• parse through NCBITaxon ancestors (#259) (c461251)
• Schema format and validation fixes. (#113) (0465ee7)
• upgrade EFO from 3.69 to 3.74 (#257) (c38e905)

---

This PR was generated with Release Please. See documentation.