1.0.0

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 .env file (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_vcf by @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_variations and get_variation_count declarations from the _Storage class 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 mappings table 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 agct release 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_name param 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 SequenceReference objects (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 /variations endpoint 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