Version 14.0.0

What's Changed

• BREAKING: Dataset provenance model update by @SanjeevLakhwani in #665
• chore: update base img, deps; bump ver to 14.0.0 by @davidlougheed in #700
• chore(deps): bump urllib3 from 2.6.3 to 2.7.0 in /docs by @dependabot[bot] in #694
• chore(deps): bump idna from 3.7 to 3.15 in /docs by @dependabot[bot] in #699
• fix: populate chord_datasetv2 before adding FK constraints by @SanjeevLakhwani in #701
• chore: update base img, lockfile deps by @davidlougheed in #702

Full Changelog: v13.2.0...v14.0.0

v13.2.0

What's Changed

• chore(deps-dev): bump cbor2 from 5.8.0 to 5.9.0 by @dependabot[bot] in #674
• chore(deps): bump requests from 2.32.4 to 2.33.0 in /docs by @dependabot[bot] in #675
• chore(deps): bump requests from 2.32.5 to 2.33.0 by @dependabot[bot] in #676
• chore(deps): bump cryptography from 46.0.5 to 46.0.6 by @dependabot[bot] in #677
• chore(deps): bump pygments from 2.15.0 to 2.20.0 in /docs by @dependabot[bot] in #678
• chore(deps): bump aiohttp from 3.13.3 to 3.13.4 by @dependabot[bot] in #681
• feat(discovery): support "one or more of"-type queries by @davidlougheed in #616
• chore(deps): bump django from 4.2.29 to 4.2.30 in /docs by @dependabot[bot] in #682
• chore(deps): bump cryptography from 46.0.6 to 46.0.7 by @dependabot[bot] in #684
• chore: update base img, Django, DRF, deps by @davidlougheed in #685
• fix: normalize vital_status fields in get_or_create query by @noctillion in #688
• feat(experiments): add storage_uri and storage_server fields by @davidlougheed in #686
• feat(experiments): extended experiment vocabularies by @noctillion in #687
• spelling fix for single cell Hi-C by @gsfk in #691
• chore: bump to 13.2.0 by @v-rocheleau in #692

Full Changelog: v13.1.1...v13.2.0

Version 13.1.1

What's Changed

• fix(chord): improved file assoc workflow behaviour + logging by @davidlougheed in #672
• chore(chord): tweak experiment result drs assoc wflow print out by @davidlougheed in #673

Full Changelog: v13.1.0...v13.1.1

Version 13.1.0

What's Changed

• chore(deps): bump sqlparse from 0.5.0 to 0.5.4 in /docs by @dependabot[bot] in #658
• replace TrigramSimilarity with TrigramWordSimilarity by @noctillion in #660
• feat(discovery): support trigram-based full-text search by @davidlougheed in #659
• feat(chord): add experiment result/DRS object association workflow by @davidlougheed in #657
• lint: ruff format patients module by @davidlougheed in #640
• chore(deps): bump werkzeug from 3.1.5 to 3.1.6 by @dependabot[bot] in #661
• lint: ruff format restapi module by @davidlougheed in #662
• lint: ruff format scripts module + manage.py by @davidlougheed in #663
• chore(deps): bump django from 4.2.28 to 4.2.29 in /docs by @dependabot[bot] in #664
• feat(discovery): add more experiment fields to experiment match model by @davidlougheed in #667
• chore: update base img, deps, actions; bump to 13.1.0 by @davidlougheed in #668
• feat(discovery): support querying custom numeric/date ranges by @davidlougheed in #655
• chore(deps-dev): bump pyopenssl from 25.3.0 to 26.0.0 by @dependabot[bot] in #670
• fix(discovery): properly check FTS discovery query perms by @davidlougheed in #669
• feat(discovery): return counts by dataset by @noctillion in #666
• chore(deps-dev): bump pyasn1 from 0.6.2 to 0.6.3 by @dependabot[bot] in #671

Full Changelog: v13.0.1...v13.1.0

Version 13.0.1

What's Changed

• fix(discovery): handle custom decimal bins in discovery number field by @davidlougheed in #654
• chore(discovery): sort nested matches in match responses by @davidlougheed in #650
• chore: bump version to 13.0.1 + update jsonschema, lockfile deps by @davidlougheed in #656

Full Changelog: v13.0.0...v13.0.1

Version 13.0.0

What's Changed

Breaking Changes

• feat!: new experiments model aligned with GA4GH by @noctillion in #635

Other Changes

• chore: update to Django 5.2, drf-spectacular 0.29, django-filter 25.2 by @davidlougheed in #621
• chore(deps-dev): bump filelock from 3.20.0 to 3.20.1 by @dependabot[bot] in #622
• chore(deps-dev): bump cbor2 from 5.7.1 to 5.8.0 by @dependabot[bot] in #623
• chore(deps): bump aiohttp from 3.13.2 to 3.13.3 by @dependabot[bot] in #624
• fix: ingest phenopacket extra properties by @davidlougheed in #627
• fix(patients): properly serialize vital status by @davidlougheed in #625
• chore(deps): bump werkzeug from 3.1.4 to 3.1.5 by @dependabot[bot] in #628
• chore(deps): bump urllib3 from 2.6.0 to 2.6.3 by @dependabot[bot] in #626
• chore(deps-dev): bump virtualenv from 20.35.4 to 20.36.1 by @dependabot[bot] in #629
• chore(deps-dev): bump filelock from 3.20.1 to 3.20.3 by @dependabot[bot] in #630
• chore: update lockfile deps + reduce docker image size by @davidlougheed in #631
• ci: add workflow to clean up caches on PR close by @davidlougheed in #633
• chore: update bento base image to 2026.01.14 by @davidlougheed in #634
• chore: sort discovery field options when enum is null by @davidlougheed in #632
• lint: configure ruff for linting only (for now) in prep for auto-format by @davidlougheed in #637
• lint: ruff format authz and cleanup modules by @davidlougheed in #638
• lint: ruff format geo and resources modules by @davidlougheed in #639
• chore(deps-dev): bump pyasn1 from 0.6.1 to 0.6.2 by @dependabot[bot] in #641
• fix: correct updates schema + ingest phenopacket metadata updates by @davidlougheed in #636
• fix(restapi): keep falsey numeric fields in GenericSerializer by @davidlougheed in #644
• lint: ruff format metadata module by @davidlougheed in #642
• feat(phenopackets): serialize project ID in phenopacket JSON by @davidlougheed in #645
• chore(deps): bump django from 4.2.27 to 4.2.28 in /docs by @dependabot[bot] in #647
• chore: freeze DataPermissions dataclass + some pydantic models by @davidlougheed in #649
• feat(chord): update resources with the same ID with new ingestions by @davidlougheed in #651
• chore: update dependencies + bump version to 13.0.0 by @davidlougheed in #652
• fix(discovery): add new experiment fields to full-text search by @davidlougheed in #653

Full Changelog: v12.1.0...v13.0.0

Version 12.1.0

What's Changed

• chore(deps): bump django from 4.2.26 to 4.2.27 in /docs by @dependabot[bot] in #614
• chore(deps): bump werkzeug from 3.1.3 to 3.1.4 by @dependabot[bot] in #613
• chore(discovery): add biosample to experiment match results by @davidlougheed in #615
• chore(deps): bump urllib3 from 2.5.0 to 2.6.0 by @dependabot[bot] in #617
• chore(deps): bump urllib3 from 2.5.0 to 2.6.0 in /docs by @dependabot[bot] in #618
• fix(ingest): fix genomic interpretations bad reuse of existing objects by @davidlougheed in #619
• chore: bump version to 12.1.0, update base img + lockfile deps by @davidlougheed in #620

Full Changelog: v12.0.0...v12.1.0

Version 12.0.0

What's Changed

• feat(phenopackets): make subject optional by @davidlougheed in #597
• chore(deps): bump urllib3 from 1.26.19 to 2.5.0 in /docs by @dependabot[bot] in #589
• chore: drop python<3.12; update deps, base image by @davidlougheed in #600
• refact(discovery): decorator for injecting common discovery deps by @davidlougheed in #601
• chore(deps): bump django from 4.2.22 to 4.2.26 in /docs by @dependabot[bot] in #604
• Add entity counts to Project and Dataset serializers by @SanjeevLakhwani in #603
• feat(discovery): discovery match CSV responses by @davidlougheed in #602
• feat(discovery): improve match results completeness + small refact by @davidlougheed in #605
• feat(discovery): faster + better full-text search; discovery refact by @davidlougheed in #607
• refact(discovery): QueryHelper with counts utils + nested field censoring by @davidlougheed in #608
• chore: update base img, lockfile deps; ver to 12.0.0 by @davidlougheed in #610
• feat(discovery): more linking across entities in match responses by @davidlougheed in #609
• fix(cleanup): add missing cleanup for variant interpretations by @davidlougheed in #611
• fix: misc cbioportal issues by @davidlougheed in #612

Full Changelog: v11.0.0...v12.0.0

Version 11.0.0

What's Changed

Summary

• new discovery API
• add new non-standard location_collected field to biosamples
• allow non-string values in experiments extra properties
• use plural experiments in biosample --> experiment paths
• new instrument schema / model for experiments
• add dataset conditions_of_access field

PRs

• chore(deps): bump cryptography from 44.0.0 to 44.0.1 by @dependabot[bot] in #569
• feat: add biosample collection_location + GeoLocation model by @davidlougheed in #568
• chore(deps): bump jinja2 from 3.1.5 to 3.1.6 in /docs by @dependabot[bot] in #571
• ci: fix test workflow by @davidlougheed in #575
• feat: structured logging + more tests by @davidlougheed in #561
• chore: update base img, lockfile; bump ver to 11.0.0 by @davidlougheed in #578
• fix: serializer n+1 query issues by @davidlougheed in #580
• feat(discovery): detailed matches for discovery individual response by @davidlougheed in #579
• refact: use bento_lib DiscoveryConfig Pydantic model by @davidlougheed in #576
• feat(discovery)!: handle boolean permissions for rules/overview by @davidlougheed in #564
• refact(discovery)!: use singular public model name for counts by @davidlougheed in #581
• chore(deps): bump django from 4.2.18 to 4.2.21 in /docs by @dependabot[bot] in #582
• chore(deps): bump requests from 2.32.2 to 2.32.4 in /docs by @dependabot[bot] in #585
• chore: update deps + fix test incompatibilities by @davidlougheed in #587
• chore(deps): bump django from 4.2.21 to 4.2.22 in /docs by @dependabot[bot] in #584
• fix(chord): discovery config de/serialization in project/dataset endpoints by @davidlougheed in #588
• feat: add dataset conditions_of_access field by @BarrothTheDragon in #583
• chore(deps): bump aiohttp from 3.12.12 to 3.12.14 by @dependabot[bot] in #590
• ci: Migration check workflow | fix: Duplicative migrations caused by schemas by @BarrothTheDragon in #591
• feat: discovery full-text search querying by @davidlougheed in #592
• feat!: new discovery API by @davidlougheed in #577
• Corrected Experiment extra_properties to use the correct schema by @SanjeevLakhwani in #594
• feat(experiments)!: instrument ontologies by @noctillion in #563
• feat(ingest): index alignment files on experiment JSON ingest by @noctillion in #574
• chore: update base img, deps; update ci actions by @davidlougheed in #598
• chore: generate squashed migrations for v11 by @davidlougheed in #599

New Contributors

• @BarrothTheDragon made their first contribution in #583

Full Changelog: v10.0.0...v11.0.0

Version 10.0.0

What's Changed

• refact: single experiment results file ingestion workflow by @davidlougheed in #556
• chore!: remove unused endpoints + FHIR + Elastic by @davidlougheed in #553
• chore!: remove to-be-unused /overview endpoint by @davidlougheed in #557
• chore(deps): bump django from 4.2.15 to 4.2.17 in /docs by @dependabot in #555
• chore(deps): bump jinja2 from 3.1.4 to 3.1.5 in /docs by @dependabot in #558
• chore(deps): bump django from 4.2.17 to 4.2.18 in /docs by @dependabot in #559
• refact!: define a "scopeable model" base class + modelviewset scoping by @davidlougheed in #536
• chore: remove old dead authn code by @davidlougheed in #560
• chore: remove more dead authn code by @davidlougheed in #562
• chore: add missing migrations (seem to be JSON field migrations) by @davidlougheed in #565
• chore: update lockfile deps, base image by @davidlougheed in #566
• fix: downgrade yanked dep in lockfile by @davidlougheed in #567

Full Changelog: v9.1.0...v10.0.0