2.0.0

What's Changed

• feat!: refactor annotator as ABC, add NDJSON annotation + support optional side effects by @jsstevenson in #502
• chore: update seqrepo and uta versions to 2024-12-20 by @korikuzma in #514
• feat!: update models to VRS 2.0.1 by @korikuzma in #518
• docs: clarify fork procedure for devs by @jsstevenson in #458
• feat!: show more informative error msg for vcf annotate output args issue by @jsstevenson in #520
• fix: use POSIX/GNU conventions for option word separators by @jsstevenson in #521
• fix: ensure dataproxy env var works in CLI by @jsstevenson in #523
• fix: use integers for numeric INFO attributes by @jsstevenson in #519
• docs: add instructions for using podman with vs code dev containers by @korikuzma in #524
• chore: remove unused pylint config by @jsstevenson in #525

Note

Originally, VRS-Python major version was going to follow the VRS major version. To prepare for VRS 2.0.0, we created 2.0.0-alpha releases. However, the developer team has decided not to follow approach anymore. Instead, VRS-Python will be following semantic versioning. We will be skipping a 1.0.0 release and will be going straight to 2.0.0.

Full Changelog: 2.0.0-a14...2.0.0

2.0.0-a14

What's Changed

• test: pin urllib3 version until vcrpy is updated by @jsstevenson in #473
• build(test): pin vcrpy>=7.0.0 + remove urllib3 from optional dev deps by @korikuzma in #476
• chore: remove obselete version property by @jsstevenson in #485
• style: lint and format with ruff by @jsstevenson in #483
• chore: update gitignore by @jsstevenson in #486
• feat!: remove unsafe uses of assert by @jsstevenson in #484
• chore: add type annotations to hgvs tools and translator by @jsstevenson in #490
• test: use recommended pytest-vcr settings by @jsstevenson in #491
• docs: remove restview dependency by @jsstevenson in #492
• feat!: make annotator exception conform to pep8 naming by @jsstevenson in #495
• feat!: break annotator tools into separate submodule by @jsstevenson in #494
• feat!: use pathlib.Paths + streamline related checks by @jsstevenson in #496
• feat!: move, reorganize field const variables by @jsstevenson in #497
• refactor: condense exception annotating by @jsstevenson in #501
• test: add coverage for dataproxy construction inputs by @jsstevenson in #499
• feat!: simplify dataproxy construction interface by @jsstevenson in #498
• refactor: move VCF header update to separate method by @jsstevenson in #500
• feat!: update pydantic models to vrs 2.0.0-snapshot.2025-02 by @korikuzma in #504
• fix: forbid extra attributes when additionalProperties is set to False by @korikuzma in #506
• chore: update vrs submodules to 2.0.0-snapshot.2025-02.2 by @korikuzma in #507
• fix(ci): simplify main branch check by @korikuzma in #508
• fix(ci): forgot to remove dependency by @korikuzma in #509
• fix(ci): revert #508 and #509 + exclude HEAD from git branch output in pypi release job by @korikuzma in #510

Full Changelog: 2.0.0-a13...2.0.0-a14

2.0.0-a13

What's Changed

• test: re-run hgvs cassettes by @korikuzma in #464
• feat: add dev container as option for running jupyter notebooks by @korikuzma in #463
• docs: clarify python 3.12 requirement for contributors by @korikuzma in #465
• docs: add doi badge to readme by @korikuzma in #468
• feat!: update models to vrs 2.0.0 community review ballot by @korikuzma in #471

Full Changelog: 2.0.0-a12...2.0.0-a13

2.0.0-a12

What's Changed

• cicd: fix action caching key by @jsstevenson in #455
• cicd: add basic precommit hooks by @jsstevenson in #454
• feat!: update gks-common / vrs models by @korikuzma in #453

Full Changelog: 2.0.0-a11...2.0.0-a12

2.0.0-a11

What's Changed

• docs: fix alt text for github contributors by @korikuzma in #438
• sync with root-inheritance-fix from VRS by @larrybabb in #441
• feat: optionally suppress console output by @jsstevenson in #445
• chore: update VCF annotator type annotations for 3.10-12 by @jsstevenson in #444
• docs: update VCF module docstrings by @jsstevenson in #448
• feat!: enhance annotator CLI options by @jsstevenson in #449
• feat!: declare annotator CLI as console entrypoint by @jsstevenson in #447
• feat: enable logging in annotator CLI by @jsstevenson in #450
• fix: do not allow SequenceLocation to have negative start/end v… by @korikuzma in #443
• fix param typo in vcf annotator by @quinnwai in #451

New Contributors

• @quinnwai made their first contribution in #451

Full Changelog: 2.0.0-a10...2.0.0-a11

2.0.0-a10

What's Changed

• cicd: update actions revs by @jsstevenson in #436
• fix: ensure Entity objects return type as str by @korikuzma in #434
• fix: revert Pydantic custom serializer by @korikuzma in #435

Full Changelog: 2.0.0-a9...2.0.0-a10

2.0.0-a9

What's Changed

• feat: VRS 1.3 digests may be computed for Alleles and Sequence Locations by @ahwagner in #427
• feat: add enum for as_version + add restrictions to ga4gh_serialize_as_version by @korikuzma in #431
• feat!: update/rename classes to refect public API access and ABC by @korikuzma in #430
• refactor: remove unused code + small cleanup by @korikuzma in #432

Full Changelog: 2.0.0-a8...2.0.0-a9

2.0.0-a8

What's Changed

• chore: Pydantic fields -> model_fields by @korikuzma in #414
• feat!: rename core_models to common_models by @korikuzma in #413
• build!: remove support for python 3.9 and make 3.12 the dev default by @korikuzma in #416
• build: update SeqRepo collection to 2024-02-20 by @korikuzma in #418
• feat: add make command (nbready) to create jupyter notebook venv by @korikuzma in #419
• feat!: update vrs/common models by @korikuzma in #417
• feat: create enum for gks-common + vrs types by @korikuzma in #420
• chore!: update vrs/gks-common submodules by @korikuzma in #424
• refactor: remove _internal directories by @korikuzma in #423
• refactor: rename VrsTypes enum to VrsType by @korikuzma in #425
• refactor!: split gks-common module into domain + entity by @korikuzma in #422
• fix: remove domain models from entity models by @korikuzma in #426

Full Changelog: 2.0.0-a7...2.0.0-a8

2.0.0-a7

What's Changed

• build: configure build with pyproject.toml by @jsstevenson in #388
• docs: updates to vcf_annotator.md by @wesleygoar in #385
• feat: update gks-common/vrs model by @korikuzma in #391
• fix: get make test to run by @korikuzma in #396
• build: update supported python versions by @korikuzma in #399
• refactor: use Annotated with StringConstraints instead of constr by @korikuzma in #394
• Only attempt to create allele if values were extracted by @ehclark in #401
• Adding the getting_started notebooks and removing the rest. by @toneillbroad in #402
• fix: add password to docker-compose.yml for uta service by @korikuzma in #405
• docs: update readme (install seqrepo, psql cmd, + submodules) by @korikuzma in #406

Full Changelog: 2.0.0-a6...2.0.0-a7

2.0.0-a6

What's Changed

• Test enref / deref behavior by @ahwagner in #357
• docs: update docstring for VrsObjectIdentifierIs by @korikuzma in #355
• simplify normalization implementation by @ahwagner in #358
• feat!: parameterize normalize in translator by @korikuzma in #361
• Add support for mito m. in translate_from by @larrybabb in #362
• chore: remove submodules from package data by @korikuzma in #371
• chore: move VariationNormalizerRESTDataProxy to notebooks by @korikuzma in #374
• feat: refactor hgvsTools and support c. translation by @larrybabb in #366
• chore: remove unused code by @korikuzma in #373
• refactor: simplify validating reference sequence by @korikuzma in #375
• docs: update + reorganize readme by @korikuzma in #376
• chore!: remove localizer by @korikuzma in #379
• cicd: fix release when multiple branches track same tag by @korikuzma in #384
• feat: add inclusion of "NT" prefixed refseq accessions to hgvs tools by @larrybabb in #383

New Contributors

• @larrybabb made their first contribution in #362

Full Changelog: 2.0.0-a5...2.0.0-a6