0.7.0

What's Changed

• docs: fix source link by @jsstevenson in #331
• docs: remove VRS schema support section by @korikuzma in #333
• refactor: remove unnecessary literal from AnnotationLayer enum by @korikuzma in #349
• feat: enable direct import of CST from package root by @jsstevenson in #353
• docs: link to stable, not latest by @jsstevenson in #355
• feat!: Return Pydantic models instead of dicts in UtaDatabase by @korikuzma in #334
• feat!: rename residue mode to coordinate type by @korikuzma in #337
• feat!: rename ExonGenomicCoordsMapper methods by @korikuzma in #338
• feat!: remove UtaDatabase.get_tx_exons + cleanup exon work by @korikuzma in #347
• feat!: remove UtaDatabase.get_tx_exons_genomic_coords by @korikuzma in #348
• refactor: remove optional strand field from genomic_to_tx_segment by @korikuzma in #340
• feat!: rename start/end to genomic_start/genomic_end in genomic_to_tx_segment by @korikuzma in #343
• feat!: remove optional coordinate_type from genomic_to_tx_segment by @korikuzma in #344
• feat!: return Pydantic model in get_alt_ac_start_or_end by @korikuzma in #350
• feat!: return Pydantic model in UtaDatabase.get_tx_exon_aln_v_data by @korikuzma in #351
• feat!: update ExonGenomicCoordsMapper + UtaDatabase by @korikuzma and @jarbesfeld in #352
• fix: genomic accession mismatch when getting nearest tx junction by @korikuzma in #356

Full Changelog: 0.6.0...0.7.0

0.6.0

What's Changed

• chore: remove unused schemas by @korikuzma in #321
• feat: make methods in ManeTranscript public by @korikuzma in #326
• fix(test): remove fixture decorator from get_prioritized_transcripts_from_gene by @korikuzma in #328
• feat!: only return cdna representation in g_to_mane_c by @korikuzma in #322
• feat: add option to g_to_grch38 to return a list of MANE gene(s) by @korikuzma in #325

Full Changelog: 0.5.1...0.6.0

0.5.1

What's Changed

• cicd: update actions and stale settings from template by @jsstevenson in #315
• cicd: update precommit by @jsstevenson in #316
• chore: rename optional dependency by @korikuzma in #317
• cicd: use GML reusable-stale action by @korikuzma in #318
• cicd: allow missing credentials by @jsstevenson in #319
• fix: correct strand typo by @jsstevenson in #324

Full Changelog: 0.5.0...0.5.1

0.5.0

What's Changed

• feat!: use setuptools-scm, capture version at package root by @jsstevenson in #301
• fix: use correct logging setup by @jsstevenson in #303
• chore!: remove FastAPI by @korikuzma in #304
• feat: consistently handle bare and prefixed chromosome numbering by @jsstevenson in #305
• refactor: use Assembly enum instead of hard coding by @korikuzma in #306
• fix: update handling ClientErrors when getting aws secret value by @korikuzma in #308
• fix: resolve DataOrientationWarning for pl.DataFrame by @korikuzma in #309
• fix: handle input of alt_ac, not just chromosome by @jsstevenson in #312
• refactor!: move liftover to separate module by @korikuzma in #310
• feat: validate all inputs at once by @jsstevenson in #314

Full Changelog: 0.4.1...0.5.0

0.4.1

What's Changed

• fix: scope of resp if breakpoint does not occur on an exon by @jarbesfeld in #274
• docs: add badges by @jsstevenson in #275
• chore: update license by @jsstevenson in #276
• cicd: test in python 3.12 by @jsstevenson in #277
• build: update build metadata by @jsstevenson in #278
• cicd: add priority label check by @jsstevenson in #279
• docs: add badges to main readme by @jsstevenson in #280
• docs: fix residue mode illustration rendering by @jsstevenson in #281
• fix: don't use deprecated columns param by @jsstevenson in #291
• feat!: change default postgresql port to 5432 by @korikuzma in #292
• build: require >= python 3.10 by @jsstevenson in #295
• fix(docs): correct kwarg in docstring example by @korikuzma in #296
• feat!: acquire data with wags-tails, overhaul static file handling by @jsstevenson in #290
• build: pin polars 1.0 by @jsstevenson in #294
• chore: add issue templates by @jsstevenson in #298
• cicd: use builtin token by @jsstevenson in #299
• chore: add stalebot by @jsstevenson in #300
• style: update ruff configs by @jsstevenson in #302

Full Changelog: 0.4.0-dev3...0.4.1

0.4.0-dev3

What's Changed

• build: pin ruff to v0.2.0 by @korikuzma in #272
• feat: Determine adjacent exon for fusions with non-exonic breakpoint by @jarbesfeld in #268

New Contributors

• @jarbesfeld made their first contribution in #268

Full Changelog: 0.4.0-dev2...0.4.0-dev3

0.4.0-dev2

What's Changed

• fix: StrEnum to Enum for python < 3.11 by @korikuzma in #258
• docs: add generated changelog by @jsstevenson in #259
• style: add additional ruff checks by @jsstevenson in #260
• docs: fix readme links to docs by @jsstevenson in #262
• build: replace pyliftover with agct to improve performance by @korikuzma in #264
• fix: package version by @korikuzma in #265

Full Changelog: 0.4.0-dev1...0.4.0-dev2

0.4.0-dev1

What's Changed

• fix: include package data by @korikuzma in #257

Full Changelog: 0.4.0-dev0...0.4.0-dev1

0.4.0-dev0

What's Changed

• feat!: use latest UTA schema as default by @jsstevenson in #223
• feat!: include cdna and protein represenation when starting from genomic layer by @korikuzma in #228
• docs: add documentation by @jsstevenson in #222
• docs: add documentation links by @jsstevenson in #233
• build: remove pipenv support by @jsstevenson in #236
• build: use pyproject.toml for build config by @jsstevenson in #234
• test: make doctests work by @jsstevenson in #240
• fix!: return inter-residue positions instead of zero-based positions by @korikuzma in #235
• chore: rm pipfile lock references in .gitignore by @korikuzma in #238
• fix: polars InvalidOperationError by @korikuzma in #241
• style: use ruff for formatting by @jsstevenson in #242
• refactor: use enum for strand by @korikuzma in #244
• tests: resolve warnings by @korikuzma in #247
• refactor!: fix class naming by @korikuzma in #249
• refactor!: initial work for cleaning up ExonGenomicCoordsMapper by @korikuzma in #252
• chore: remove todo's in tests by @korikuzma in #251

Full Changelog: 0.3.0-dev1...0.4.0-dev0

0.1.14-dev3

• fix: return type for FeatureOverlap get_grch38_mane_gene_cds_overlap by @korikuzma in 67a241c

Full Changelog: 0.1.14-dev2...0.1.14-dev3