Bioframe

Date: 2024-06-19

API changes:
* `read_alignment` function introduced in v0.7.0 has been pluralized to `read_alignments`

Maintenance:
* Skip `read_alignments` tests on big-endian architectures by nvictus in https://github.com/open2c/bioframe/pull/216

**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.7.1...v0.7.2

Date: 2024-06-17

Maintenance:
* Refactor join arrayops and intidx internals by nvictus in https://github.com/open2c/bioframe/pull/204
* NumPy 2.0 was released. Pin `numpy < 2` until we migrate.

**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.7.0...v0.7.1

Date: 2024-05-20

API changes:
* Add `to_bed` function to validate and write standard BED files gamazeps in https://github.com/open2c/bioframe/pull/203
* `read_bam` deprecated in favor of `read_alignments` gamazeps in https://github.com/open2c/bioframe/pull/206

Documentation:
* Add "bioframe for bedtools users" guide to docs by gamazeps in https://github.com/open2c/bioframe/pull/198

Bug fixes:
* Fix contig name and JSON issues in read_bam implementation by gamazeps in https://github.com/open2c/bioframe/pull/206

New Contributors:
* gamazeps made their first contribution in https://github.com/open2c/bioframe/pull/203

**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.6.4...v0.7.0

Date: 2024-04-06

Maintenance:
* Migrate from setuptools `pkg_resources` to `importlib.resources` by nvictus in https://github.com/open2c/bioframe/pull/194
* Use `importlib.metadata` for versioning by nvictus in https://github.com/open2c/bioframe/pull/195

Bug fixes:
* Overlap point segment patch 183 by smitkadvani in https://github.com/open2c/bioframe/pull/184
* 167: Replaced np.int with int as the attribute is deprecated by numpy by harshit148 in https://github.com/open2c/bioframe/pull/192

New Contributors:
* harshit148 made a first contribution in https://github.com/open2c/bioframe/pull/192

**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.6.3...v0.6.4

Date: 2024-03-11

Fixes:
* Prevent dropout from `closest` in some cases of left intervals with no neighbors by agalitsyna in https://github.com/open2c/bioframe/pull/185
* Fix overlap returning float indexes causing failing tests (numpy v1.22.4, pandas v1.5.2) by agalitsyna in https://github.com/open2c/bioframe/pull/185

**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.6.2...v0.6.3

Date: 2024-02-08

Changes:
* cols and df_view_col passed to downstream functions by smitkadvani in https://github.com/open2c/bioframe/pull/182

Fixes:
* Update to new UCSC hgdownload url by golobor and nvictus in https://github.com/open2c/bioframe/pull/187

**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.6.1...v0.6.2