Changelog#

2.0.0-a0#

Released on 2025-06-16 - GitHub - PyPI

What's Changed

refactor: use SourceName enum by @korikuzma in #330
build: raise support to require python >=3.10 by @jsstevenson in #333
cicd: add issue templates, stalebot, and branch action by @korikuzma in #334
feat!: create_json accepts filepath arg and only creates composite file by @korikuzma in #336
feat: prevent usage of aws db instances in cli by @korikuzma in #339
refactor!: clean up harvest method by @korikuzma in #338
feat!: sharpen type annotation by @jsstevenson in #342
feat!: break out CLI for more specific commands/more reasonable defaults by @jsstevenson in #344
feat: perform better logging by @jsstevenson in #346
build: fix pipenv build by @jsstevenson in #351
fix: use correct Disease model by @jsstevenson in #352
test: optionally minimize connection debug logging by @jsstevenson in #349
fix: use latest minor civicpy release to get correct schema by @jsstevenson in #354
fix: don't use deprecated graph driver destructor by @jsstevenson in #356
fix: don't use deprecated multi property semantics by @jsstevenson in #359
test: remove marks from fixtures (they don't do anything) by @jsstevenson in #358
feat: add batch search by variations by @jsstevenson in #361
refactor: use updated annotation API by @jsstevenson in #366
build: temporarily pin ga4gh.vrs==2.0.0a6 by @korikuzma in #367
fix(tests): update test_batch_search to apply PR (#361) suggestions by @korikuzma in #368
fix: querying studies based on therapeutic by @korikuzma in #365
docs: initial docs work by @jsstevenson in #343
refactor!: remove extract_harvester from transform method by @korikuzma in #370
refactor!: rename Transform instance variables by @korikuzma in #371
feat!: initialize query handler with graph, not graph credentials by @jsstevenson in #376
feat!: refactor graph DB code, streamline unneeded query transaction usage by @jsstevenson in #377
feat!: replace instance var lists with pydantic model by @korikuzma in #374
fix: catch TokenRetrievalError in ViccNormalizers + update log levels by @korikuzma in #378
feat: update pre-commit version + add more hooks by @korikuzma in #382
feat!: use setuptools-scm, capture version at package root by @korikuzma in #381
style: update ruff version + add more rules by @korikuzma in #380
cicd: update actions versions, stalebot, + templates from template repo by @korikuzma in #383
feat: enable pagination by @jsstevenson in #384
chore: update seqrepo version to 2024-02-20 by @korikuzma in #385
feat!: rename env var for logging + cred handling by @korikuzma in #387
build!: update normalizer + ga4gh.vrs depdencies by @korikuzma in #386
build!: update ga4gh.vrs + gene/variation normalizers by @korikuzma in #389
chore!: rename transform class and dirs to transformers by @korikuzma in #396
fix: correct syntax error in gene_id_constraint by @korikuzma in #397
feat!: use cat-vrs-python + va-spec-python by @korikuzma in #404
feat!: rename study --> study statement / statement by @korikuzma in #405
feat!: add support for transforming CIViC prognostic evidence by @korikuzma in #407
feat: add option to cli to create neo4j db constraints by @korikuzma in #412
feat!: add support for moa prognostic assertions by @korikuzma in #411
fix: aggregate moa oncotree concepts during transformation by @korikuzma in #413
feat!: add support for transforming civic diagnostic evidence items by @korikuzma in #414
build!: require python >= 3.11 by @jsstevenson in #403
cicd: warn when merging to main by @jsstevenson in #398
style: resolve ruff errors by @korikuzma in #421
feat!: update models to ga4gh gks nov 2024 ballot releases by @korikuzma in #420
feat!: add support for civic assertions by @korikuzma in #422
feat!: change strength representation by @korikuzma in #424
feat!: move ViccNormalizerDataExtension to mappings by @korikuzma in #425
feat!: add support for transforming concepts that fail to normalize by @korikuzma in #427
fix!: resolve conflicts where moa therapies resolve to same concept by @korikuzma in #429
feat!: moa disease conflict resolution should follow therapy conflict resolution by @korikuzma in #430
build!: update vicc normalizers to pull in gks coding changes by @korikuzma in #432
chore: add acceptance criteria to issue templates by @korikuzma in #458
feat!: use system identifiers from source for normalization by @korikuzma in #433
build!: update gks and normalizer versions by @korikuzma in #434
test: update test data by @korikuzma in #435
feat!: change civic classification.primaryCode to use clinvar enum by @korikuzma in #455
fix: store variation aliases in aliases not extensions by @korikuzma in #460
refactor: transform into monorepo by @katiestahl in #474
feat!: update models to VA-Spec 1.0.0-ballot.2025-03.4 by @korikuzma in #479
cicd: update ruff, precommit by @jsstevenson in #473
fix(ci): fix deployment, remove pipfile + update seqrepo version by @korikuzma in #485
merge: staging changes to main by @korikuzma in #487

New Contributors

@katiestahl made their first contribution in #474

Full Changelog: 2.0.0-dev0...2.0.0-a0

2.0.0-dev1#

Released on 2025-05-01 - GitHub - PyPI

What's Changed

refactor: use SourceName enum by @korikuzma in #330
build: raise support to require python >=3.10 by @jsstevenson in #333
cicd: add issue templates, stalebot, and branch action by @korikuzma in #334
feat!: create_json accepts filepath arg and only creates composite file by @korikuzma in #336
feat: prevent usage of aws db instances in cli by @korikuzma in #339
refactor!: clean up harvest method by @korikuzma in #338
feat!: sharpen type annotation by @jsstevenson in #342
feat!: break out CLI for more specific commands/more reasonable defaults by @jsstevenson in #344
feat: perform better logging by @jsstevenson in #346
build: fix pipenv build by @jsstevenson in #351
fix: use correct Disease model by @jsstevenson in #352
test: optionally minimize connection debug logging by @jsstevenson in #349
fix: use latest minor civicpy release to get correct schema by @jsstevenson in #354
fix: don't use deprecated graph driver destructor by @jsstevenson in #356
fix: don't use deprecated multi property semantics by @jsstevenson in #359
test: remove marks from fixtures (they don't do anything) by @jsstevenson in #358
feat: add batch search by variations by @jsstevenson in #361
refactor: use updated annotation API by @jsstevenson in #366
build: temporarily pin ga4gh.vrs==2.0.0a6 by @korikuzma in #367
fix(tests): update test_batch_search to apply PR (#361) suggestions by @korikuzma in #368
fix: querying studies based on therapeutic by @korikuzma in #365
docs: initial docs work by @jsstevenson in #343
refactor!: remove extract_harvester from transform method by @korikuzma in #370
refactor!: rename Transform instance variables by @korikuzma in #371
feat!: initialize query handler with graph, not graph credentials by @jsstevenson in #376
feat!: refactor graph DB code, streamline unneeded query transaction usage by @jsstevenson in #377
feat!: replace instance var lists with pydantic model by @korikuzma in #374
fix: catch TokenRetrievalError in ViccNormalizers + update log levels by @korikuzma in #378
feat: update pre-commit version + add more hooks by @korikuzma in #382
feat!: use setuptools-scm, capture version at package root by @korikuzma in #381
style: update ruff version + add more rules by @korikuzma in #380
cicd: update actions versions, stalebot, + templates from template repo by @korikuzma in #383
feat: enable pagination by @jsstevenson in #384
chore: update seqrepo version to 2024-02-20 by @korikuzma in #385
feat!: rename env var for logging + cred handling by @korikuzma in #387
build!: update normalizer + ga4gh.vrs depdencies by @korikuzma in #386
build!: update ga4gh.vrs + gene/variation normalizers by @korikuzma in #389
chore!: rename transform class and dirs to transformers by @korikuzma in #396
fix: correct syntax error in gene_id_constraint by @korikuzma in #397
feat!: use cat-vrs-python + va-spec-python by @korikuzma in #404
feat!: rename study --> study statement / statement by @korikuzma in #405
feat!: add support for transforming CIViC prognostic evidence by @korikuzma in #407
feat: add option to cli to create neo4j db constraints by @korikuzma in #412
feat!: add support for moa prognostic assertions by @korikuzma in #411
fix: aggregate moa oncotree concepts during transformation by @korikuzma in #413
feat!: add support for transforming civic diagnostic evidence items by @korikuzma in #414
build!: require python >= 3.11 by @jsstevenson in #403
cicd: warn when merging to main by @jsstevenson in #398
style: resolve ruff errors by @korikuzma in #421
feat!: update models to ga4gh gks nov 2024 ballot releases by @korikuzma in #420
feat!: add support for civic assertions by @korikuzma in #422
feat!: change strength representation by @korikuzma in #424
feat!: move ViccNormalizerDataExtension to mappings by @korikuzma in #425
feat!: add support for transforming concepts that fail to normalize by @korikuzma in #427
fix!: resolve conflicts where moa therapies resolve to same concept by @korikuzma in #429
feat!: moa disease conflict resolution should follow therapy conflict resolution by @korikuzma in #430
build!: update vicc normalizers to pull in gks coding changes by @korikuzma in #432
chore: add acceptance criteria to issue templates by @korikuzma in #458
feat!: use system identifiers from source for normalization by @korikuzma in #433
build!: update gks and normalizer versions by @korikuzma in #434
test: update test data by @korikuzma in #435
feat!: change civic classification.primaryCode to use clinvar enum by @korikuzma in #455
fix: store variation aliases in aliases not extensions by @korikuzma in #460
refactor: transform into monorepo by @katiestahl in #474
feat!: update models to VA-Spec 1.0.0-ballot.2025-03.4 by @korikuzma in #479
cicd: update ruff, precommit by @jsstevenson in #473
fix(ci): fix deployment, remove pipfile + update seqrepo version by @korikuzma in #485
merge: staging changes to main by @korikuzma in #487

New Contributors

@katiestahl made their first contribution in #474

Full Changelog: 2.0.0-dev0...2.0.0-dev1

2.0.0-dev0#

Released on 2024-04-03 - GitHub - PyPI

What's Changed

cicd: update sc_product_id by @korikuzma in #228
build!: update civicpy build to 3.x.x by @korikuzma in #233
refactor: cleanup harvester classes by @korikuzma in #234
chore: remove requirements files by @korikuzma in #239
feat!: update transformers to use vrs 2-alpha and gk-pilot schemas by @korikuzma in #245
refactor!: fix class name casing by @korikuzma in #247
feat: add support for TherapeuticSubstituteGroup in CIViC by @korikuzma in #249
feat: add support for CombinationTherapy by @korikuzma in #251
fix: civic variant aliases should be a list + pydantic warning by @korikuzma in #252
change: snp ids should not be in civic aliases during transform by @korikuzma in #257
build: update thera-py + fix TherapyQueryHandler instantiation by @korikuzma in #259
fix: key error in MoaHarvester _get_feature by @korikuzma in #258
change: snp ids should not be in civic mp aliases during transform by @korikuzma in #260
test: update moa source 44 title by @korikuzma in #262
tests: update civic + moa test data by @korikuzma in #276
feat: include additional therapy/disease normalizer data in CDM by @korikuzma in #288
build!: update dependencies and ga4gh digests by @korikuzma in #300
test: update civicpy cache data by @korikuzma in #302
chore: remove unused delta class by @korikuzma in #306
feat!: update database to reflect schema changes by @korikuzma in #266
cicd: update release.yml (publish python distribution to pypi) by @korikuzma in #307
fix: creating location parameterized query string by @korikuzma in #310
feat!: update /search/studies endpoint by @korikuzma in #279
cicd: update elastic beanstalk commands by @korikuzma in #280
Add lab template CICD actions by @jsstevenson in #297
build: configure setuptools in pyproject.toml by @jsstevenson in #298
style: use ruff by @jsstevenson in #313
cicd: adjust installation checks by @jsstevenson in #316
test: fix test data dir + update param name change by @korikuzma in #319
chore: remove unused files by @korikuzma in #321
fix: add support for civic ash source type by @korikuzma in #323
chore: remove analysis dir by @korikuzma in #320
feat: use MOA representative coordinate to create PSC members by @korikuzma in #312
cicd: add action for closing issue when merged into staging by @korikuzma in #325
cicd: fix elastic beanstalk deployment by @korikuzma in #326
fix: replace StrEnum with Enum by @korikuzma in #328
refactor!: update cli by @korikuzma in #324

Full Changelog: 1.2.0-dev0...2.0.0-dev0

1.2.0-dev0#

Released on 2023-05-12 - GitHub - PyPI

What's Changed

feat: add oncokb as a source (#170) by @korikuzma in #211
build!: update dependencies by @korikuzma in #217
refactor: remove LAST_UPDATED by @korikuzma in #221
ci: add GH action for installing deps + remove requirements by @korikuzma in #223
chore: update elastic beanstalk commands by @korikuzma in #224

Full Changelog: v1.1.0...1.2.0-dev0

v1.1.0#

Released on 2022-11-11 - GitHub - PyPI

What's Changed

Bump lxml from 4.9.0 to 4.9.1 by @dependabot in #177
docs: update readme and add readme for cli by @korikuzma in #176
ci: bump action versions by @jsstevenson in #195
build!: pin dependencies by @korikuzma in #201
Staging by @korikuzma in #202

Full Changelog: v1.1.0a9...v1.1.0

v1.1.0a9: #

Released on 2022-06-14 - GitHub - PyPI

Update variation normalizer + other dependencies

v1.1.0a8: #

Released on 2022-05-25 - GitHub - PyPI

Update requirements to remove security vulnerabilities

v1.1.0a7: #

Released on 2022-05-06 - GitHub - PyPI

Add transformed regulatory_approval field from thera-py to therapy descriptor extensions

v1.1.0a6: #

Released on 2022-04-08 - GitHub - PyPI

Clean up CLI log/click messages
Update dependencies
- Variation Normalizer now uses latest version of MANE transcripts

v1.1.0a5: #

Released on 2022-03-30 - GitHub - PyPI

Bump jupyter-server from 1.13.5 to 1.15.4

v1.1.0a4: #

Released on 2022-02-04 - GitHub - PyPI

Replace response_datetime with last_updated in ServiceMeta
Remove extra node from diagnostic propositions
Created versioned data files
Add url to openapi contact info
Remove duplicate descriptors from response
Always enable Try it out param in FastAPI
Use hashed digests for arbitrary ID values instead of incremental numbering (eg for Propositions and some Documents)
Updated CLI option names + added option to load single CDM file
Refactor tests to improve runtime