What's Changed
- Run AnyVar with no backing database by @hanars in #124
- Update ruff to 0.11.2 by @theferrit32 in #121
- Simplify postgres anyvar db setup by @theferrit32 in #127
- Update Dockerfile. Make postgres_init.sql throw no errors on drops. Bind in-container server to 0.0.0.0 by @theferrit32 in #123
- chore: add issue templates for bugs + feat requests by @korikuzma in #129
- feat: add duckdb storage backend by @theferrit32 in #138
- Quick fixes for docker compose by @theferrit32 in #149
- Fix: updating expected values in test by @Krt-11 in #151
- Add optional support for storing arbitrary annotations by @theferrit32 in #118
- refactor: use latest VRS-Python release for Anyvar by @jsstevenson in #115
- Issue 62: Update Demo Folder to Include Sample VCF Input File by @jennifer-bowser in #163
- Improve Testing Process by @jennifer-bowser in #153
- chore: remove stale files by @Krt-11 in #167
- refactor: update python version from 3.10 to 3.11 by @Krt-11 in #168
- Docs: Update docs with setup instructions for Anyvar dependencies and specialized operations by @Krt-11 in #160
- fix: update demo notebook to align with updated codebase functions by @Krt-11 in #164
- docs: update the example request body for the '/variation' endpoint (issue 171) by @jennifer-bowser in #172
- fix: don't use deprecated pkg_resources api for
__version__value by @jsstevenson in #174 - cicd: update precommit, add hooks and action by @jsstevenson in #176
- feat: configure logging + provide exceptions in logs for API service by @jsstevenson in #178
- feat: set environment variables via a
.envfile (issue 158) by @jennifer-bowser in #162 - feat: resolve warnings, annotate routes with response model by @jsstevenson in #181
- fix: ensure dotenv is available for celery worker by @jsstevenson in #185
- fix: remove redundant logging by @jsstevenson in #187
- feat: add /service-info endpoint by @jsstevenson in #180
- feat!: add
PUT /annotated_vcfby @jsstevenson in #192 - feat: enable optional vrs attrs annotation by @jsstevenson in #194
- fix(docs): use correct link for forks by @korikuzma in #210
- docs: make some docs by @jsstevenson in #209
- chore: ignore env management lockfiles by @jsstevenson in #214
- fix: use correct vcf worker args by @jsstevenson in #217
- feat: add genomic liftover annotation on initial variant registration (issue 147) by @jennifer-bowser in #169
- feat: return 501 if annotations are unsupported by @jsstevenson in #220
- chore: update doc links in .env.example by @jsstevenson in #224
- refactor: consolidate registration middleware (issue #189) by @jennifer-bowser in #199
- test: add test case for unconvertible grch38 variant (issue #196) by @jennifer-bowser in #213
- feat: add project requirements to the docs (issue #232) by @jennifer-bowser in #231
- feat: verify that liftover is reversible before linking a lifted-over variant back to the original variant (issue #195) by @jennifer-bowser in #219
- style: update ruff configs by @jsstevenson in #226
- feat: handle cases where liftover is ambiguous (issue #198) by @jennifer-bowser in #215
- refactor: improve Pylance compliance (issue #228) by @jennifer-bowser in #227
- fix: remove
search_variationsandget_variation_countdeclarations from the_Storageclass by @jennifer-bowser in #237 - Refresh storage-refactor-epic by @theferrit32 in #241
- Issue 202 remove nonpostgres by @theferrit32 in #243
- Moving schema initializing out of storage classes by @theferrit32 in #245
- Add ORM classes for allele, location, sequence_reference by @theferrit32 in #246
- tests: fix failing liftover tests (issue #242) by @jennifer-bowser in #249
- Refactor Storage class and implementations to match new class diagrams by @theferrit32 in #247
- API workers deadlock under heavy load using async VCF annotation by @ehclark in #260
- feat: make annotations non-optional and conform to new storage paradigm (issue #206) by @jennifer-bowser in #254
- Add note about XDG_DATA_HOME by @theferrit32 in #244
- style: ignore arg002 in nodb by @jsstevenson in #270
- fix: use correct type annotation by @jsstevenson in #267
- feat: allow table name overrrides (issue #252) by @jennifer-bowser in #269
- feat!: add
mappingstable by @jsstevenson in #262 - cicd: use uv and cache dependencies by @jsstevenson in #276
- chore: remove unused type annotations by @jsstevenson in #284
- chore: remove unused files by @jsstevenson in #280
- build: update version classifiers by @jsstevenson in #287
- feat: add supported liftover assemblies to /service-info by @jsstevenson in #288
- fix: make conditional import a local before trying to nullify it by @jsstevenson in #278
- fix: make conditional import a local before trying to nullify it by @quinnwai in #289
- test: audit + restructure tests by @jsstevenson in #273
- chore: add VCF benchmarking script by @jsstevenson in #279
- feat!: use updated
agctrelease by @jsstevenson in #285 - test: use test db for celery worker and fix async timing issue by @jsstevenson in #298
- chore: add more granular logging to queueing dependency guards by @jsstevenson in #299
- chore: add other dependency groups to develop target by @jsstevenson in #300
- style: allow unused args/kwargs by @jsstevenson in #303
- chore: update schema example by @jsstevenson in #302
- use batch db writes for vcf variant registration (issue #253) by @jennifer-bowser in #272
- feat: solidify storage interface edge cases/error handling by @jsstevenson in #271
- test: add annotation endpoint tests by @jsstevenson in #309
- feat: add anyvar.Anyvar get/put methods + api endpoints for mappings by @korikuzma in #312
- build: add database and user initialization (issue #291) by @jennifer-bowser in #321
- refactor: simplify add objects method (Issue #268) by @jennifer-bowser in #318
- fix: return 404 when resource not found by @jsstevenson in #322
- refactor: streamline supported vrs object types (issue #265) by @jennifer-bowser in #315
- feat!: add BATCH_SIZE (n=100) limit to PostgresObjectStore by @korikuzma in #328
- chore: fill in license placeholders by @korikuzma in #329
- feat: use enum for molecule_type in sequence_references table by @korikuzma in #327
- fix: correct input_type comparisons for translate_variation by @korikuzma in #330
- chore: remove commented out tests by @korikuzma in #333
- chore: remove todos from codebase by @korikuzma in #343
- feat: add optional
assembly_nameparam to PUT /variation by @korikuzma in #344 - chore: designate translator abstraction as public by @jsstevenson in #316
- feat!: add POST /variation endpoint to retrieve registered variants by @korikuzma in #326
- docs: rewrite everything by @jsstevenson in #317
- feat: compute ID for VRS objects on registration when not provided by @jsstevenson in #314
- ci: add pypi release workflow (using trusted publisher) by @korikuzma in #345
- feat: dereference
SequenceReferenceobjects (issue #282) by @jennifer-bowser in #324 - refactor: move timestamp annotation to anyvar class + add unit tests by @korikuzma in #346
- feat: remove object_store get_all_object_ids by @jsstevenson in #350
- Storage refactor epic merge by @jennifer-bowser in #356
- chore: clean up translate return type by @jsstevenson in #358
- feat!: use 422 UNPROCESSIBLE ENTITY for translation failures by @jsstevenson in #359
- build!: bump vrs-python to 2.2.0 + apply vcf annotator changes by @korikuzma in #360
- docs: add vol info to quickstart by @jsstevenson in #362
- chore: remove old demo by @jsstevenson in #365
- Change db column name mapping for location to avoid ANSI SQL reserved words by @ehclark in #364
- feat: add
PUT /variationsendpoint for bulk registration by @korikuzma in #369 - Re-implement support for Snowflake with new storage API by @ehclark in #367
- Support for bearer token authentication by @ehclark in #373
- ci: add job for building and publishing image to ghcr.io by @korikuzma in #375
- cicd: cache chainfile downloads by @jsstevenson in #376
- chore: add citation file by @jsstevenson in #377
- feat: don't store digest by @jsstevenson in #374
- fix: use correct orcid format in citation.cff by @korikuzma in #378
- docs: Add DOI badge to README by @ahwagner in #379
- fix: add new INFO fields to required field msg by @jsstevenson in #381
- docs: fix PyPI link by @jsstevenson in #380
- docs: fix/update other pypi references by @jsstevenson in #383
- fix(docs): get doi badge to show + add doi to citation by @korikuzma in #384
- docs: fix readme install instructions by @jsstevenson in #385
- feat!: make the name consistent by @jsstevenson in #391
- feat!: add indexes to location positions by @jsstevenson in #382
- fix: add colon for copy-pasteability by @theferrit32 in #393
- docs: fix all warnings by @jsstevenson in #397
- feat!: change SupportedObjectType name, use explicit members by @jsstevenson in #400
- fix: use correct object vs variation name by @jsstevenson in #401
- fix: perform timestamp creation directly in routes by @jsstevenson in #402
- feat!: code reorganization by @jsstevenson in #398
- feat!: clean up API modules by @jsstevenson in #403
- fix: update docker compose for uta + update docs for manual dl by @korikuzma in #405
New Contributors
- @hanars made their first contribution in #124
- @jennifer-bowser made their first contribution in #163
- @quinnwai made their first contribution in #289
- @ahwagner made their first contribution in #379
Full Changelog: 0.9.0...1.0.0