Cool-seq-tool

What's Changed
* build: pin ruff to v0.2.0 by korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/272
* feat: Determine adjacent exon for fusions with non-exonic breakpoint by jarbesfeld in https://github.com/GenomicMedLab/cool-seq-tool/pull/268

New Contributors
* jarbesfeld made their first contribution in https://github.com/GenomicMedLab/cool-seq-tool/pull/268

**Full Changelog**: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.4.0-dev2...0.4.0-dev3

What's Changed
* fix: StrEnum to Enum for python < 3.11 by korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/258
* docs: add generated changelog by jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/259
* style: add additional ruff checks by jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/260
* docs: fix readme links to docs by jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/262
* build: replace pyliftover with agct to improve performance by korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/264
* fix: package version by korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/265


**Full Changelog**: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.4.0-dev1...0.4.0-dev2

What's Changed
* fix: include package data by korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/257


**Full Changelog**: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.4.0-dev0...0.4.0-dev1

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

**Full Changelog**: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.3.0-dev1...0.4.0-dev0

What's Changed
* build: properly pin pydantic v2 major version by korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/215


**Full Changelog**: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.3.0-dev0...0.3.0-dev1

What's Changed
* cicd: update release.yaml (publish python distribution to pypi) by korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/197
* refactor!: rearrange app architecture by korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/196
* refactor: use ResidueMode for residue_mode type by korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/199
* style: use ruff + black by korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/200
* refactor: use AnnotationLayer enum by korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/203
* build: replace pandas with polars (178) by korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/205
* refactor!: Update TranscriptPriority enum by korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/201
* feat: make positions optional in get_transcripts_from_gene by katiestahl in https://github.com/GenomicMedLab/cool-seq-tool/pull/210
* refactor!: `get_gene_mane_data` sorted by desc MANE_Status by korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/213
* build: pin pydantic to v2 major version by korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/214
* feat!: create method for GRCh38 to MANE protein representation by korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/211

New Contributors
* katiestahl made their first contribution in https://github.com/GenomicMedLab/cool-seq-tool/pull/210

**Full Changelog**: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.2.0-dev0...0.3.0-dev0