Fgpyo

What's Changed

* Add `assert_fasta_indexed` by msto in https://github.com/fulcrumgenomics/fgpyo/pull/186
* Add clintval to CODEOWNERS by clintval in https://github.com/fulcrumgenomics/fgpyo/pull/189
* Update `pyproject.toml` (137) by TimD1 in https://github.com/fulcrumgenomics/fgpyo/pull/184
* Require error codes on `type: ignore` pragmas by msto in https://github.com/fulcrumgenomics/fgpyo/pull/190
* MetricWriter by msto in https://github.com/fulcrumgenomics/fgpyo/pull/123
* Add cigar utility method `query_alignment_offsets` by yfarjoun in https://github.com/fulcrumgenomics/fgpyo/pull/188

New Contributors
* TimD1 made their first contribution in https://github.com/fulcrumgenomics/fgpyo/pull/184

**Full Changelog**: https://github.com/fulcrumgenomics/fgpyo/compare/0.7.1...0.8.0

What's Changed
* fix: longest homopolymer needs to be case insensitive by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/181


**Full Changelog**: https://github.com/fulcrumgenomics/fgpyo/compare/0.7.0...0.7.1

What's Changed
* ci: remove the use of github-actions-ci environment by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/179
* feat: add methods for computing run lengths of repeats in a sequence by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/162


**Full Changelog**: https://github.com/fulcrumgenomics/fgpyo/compare/0.6.0...0.7.0

What's Changed
* feat: Add methods for UMI extraction from read name by emmcauley in https://github.com/fulcrumgenomics/fgpyo/pull/118
* fix: RTD needs an `__init__.py` in `fgpyo/platform/` by emmcauley in https://github.com/fulcrumgenomics/fgpyo/pull/174
* fix: fgpyo.fasta.sequence_dictionary incorrect StrEnum import by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/175


**Full Changelog**: https://github.com/fulcrumgenomics/fgpyo/compare/0.5.0...0.6.0

What's Changed
* Move to mkdocs from Sphinx by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/135
* Add a lazy is_sorted function to collections by clintval in https://github.com/fulcrumgenomics/fgpyo/pull/159
* feat: adds classes and methods for sequence dictionaries by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/160
* feat: Lint tests directory by msto in https://github.com/fulcrumgenomics/fgpyo/pull/163
* doc: Add installation of `mkdocs` dependencies to README by msto in https://github.com/fulcrumgenomics/fgpyo/pull/164
* feat: move docs out of extras into their own group by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/166
* feat: add hamming and levenshtein distance functions by znorgaard in https://github.com/fulcrumgenomics/fgpyo/pull/167
* Revert "fix: Add return type hint to Metric.read()" by msto in https://github.com/fulcrumgenomics/fgpyo/pull/173

New Contributors
* znorgaard made their first contribution in https://github.com/fulcrumgenomics/fgpyo/pull/167

**Full Changelog**: https://github.com/fulcrumgenomics/fgpyo/compare/0.4.0...0.5.0

What's Changed
* feat: Add end property on SupplementaryAlignment by msto in https://github.com/fulcrumgenomics/fgpyo/pull/105
* add a test to explicitly support columns out of order in Metric by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/82
* chore: add CODEOWNERS by msto in https://github.com/fulcrumgenomics/fgpyo/pull/113
* Add isort check to Github Action by emmcauley in https://github.com/fulcrumgenomics/fgpyo/pull/116
* fix: Add return type hint to Metric.read() by msto in https://github.com/fulcrumgenomics/fgpyo/pull/110
* fix: DataclassInstance and AttrInstance protocols by msto in https://github.com/fulcrumgenomics/fgpyo/pull/108
* refactor: writeable -> writable by msto in https://github.com/fulcrumgenomics/fgpyo/pull/119
* fix: r/w assertions by msto in https://github.com/fulcrumgenomics/fgpyo/pull/121
* feat: Support stdin/stdout special cases in sam.reader/writer by msto in https://github.com/fulcrumgenomics/fgpyo/pull/69
* chore: Update mypy config by msto in https://github.com/fulcrumgenomics/fgpyo/pull/134
* chore: Switch to ruff by msto in https://github.com/fulcrumgenomics/fgpyo/pull/140
* ci: update code-cov in GHA to use a token by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/150
* - Added __getitem__ ~and __len__~ to the Cigar class, pulling the answer… by yfarjoun in https://github.com/fulcrumgenomics/fgpyo/pull/154
* chore: Add usual lints by msto in https://github.com/fulcrumgenomics/fgpyo/pull/142
* Feat: add longest_hp_len() to fgpyo/sequence.py by emmcauley in https://github.com/fulcrumgenomics/fgpyo/pull/157
* Feat: add gc_content() calculation method to fgpyo/sequence.py by emmcauley in https://github.com/fulcrumgenomics/fgpyo/pull/156
* feat: speed up longest_homopolymer by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/158

New Contributors
* emmcauley made their first contribution in https://github.com/fulcrumgenomics/fgpyo/pull/116

**Full Changelog**: https://github.com/fulcrumgenomics/fgpyo/compare/0.3.0...0.4.0