Bioframe

Date: 2024-01-08

API changes:

Default behavior of `ensure_nullable` option in `overlap` was modified to minimize the possibility of regressions in libraries that depend on legacy behavior.

* The new option was renamed `ensure_int` and is `True` by default. It ensures that output coordinate columns are always returned with an integer dtype, as was the case in prior versions. This is achieved by converting columns having non-nullable NumPy dtypes to Pandas nullable ones in the specific case where the result of an **outer join** generates missing values; otherwise, column dtypes are preserved unchanged in the output.
* Unlike previous minor versions of bioframe, the nullable dtype chosen will have the **same underlying type** as the corresponding column from the input (i.e, an input dataframe using `np.uint32` start coordinates may yield a `pd.UInt32` start column in the output).
* This behavior can be turned off by setting `ensure_int` to `False`, in which case outer joins on dataframes using NumPy dtypes may produce floating point output columns when missing values are introduced (stored as `NaN`), following the native casting behavior of such columns.

**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.6.0...v0.6.1

Date: 2024-01-04

API changes:
* `overlap`: In previous versions, output coordinate columns were always converted to Pandas "nullable" `Int64` dtype before returning outer join results. In the interest of flexibility, memory efficiency, and least surprise, the coordinate columns returned in the output dataframe now preserve dtype from the input dataframes, following native type casting rules if missing data are introduced. We introduce the `ensure_nullable` argument to force Pandas nullable dtypes in the output coordinates. See the [docs](https://bioframe.readthedocs.io/en/latest/api-intervalops.html#bioframe.ops.overlap) for more details. (178)

Bug fixes:
* Fixed `coverage` with custom `cols1` (170)

Documentation:
* Added contributing guidelines and NumFOCUS affiliation.
* Updated README and added CITATION.cff file.
* Updated performance benchmarks.

**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.5.1...v0.6.0

Date: 2023-11-08

Bug fixes:
* Series are treated like dict in `make_chromarms`

**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.5.0...v0.5.1

Date: 2023-10-05

API changes:
* New builtin curated genome assembly database (metadata, chromsizes, cytobands):
* `bioframe.list_assemblies()`
* `bioframe.assembly_info()`
* New UCSC RGB color converter utility 158
* Options added to `pair_by_distance`

Bug fixes:
* Make expand throw an error if both pad and scale are passed (148)
* Fixes to bioframe.select query interval semantics (147)

Maintenance:
* Migrate to hatch build system and pyproject.toml
* Various refactorings

**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.4.1...v0.5.0

Date: 2023-04-22

Bug fixes:
* Fix bug introduced in the last release in `select` and `select_*` query interval semantics. Results of select are now consistent with the query interval being interpreted as half-open, closed on the left.

**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.4.0...v0.4.1

Date: 2023-03-23

API changes:
* New strand-aware directionality options for `closest()` via `direction_col` 129.
* New index-based range query selectors on single bioframes to complement `select()` 128:
* `select_mask()` returns boolean indices corresponding to intervals that overlap the query region
* `select_indices()` returns integer indices corresponding to intervals that overlap the query region
* `select_labels()` returns pandas label indices corresponding to intervals that overlap the query region

Bug fixes:
* Import fixes in sandbox
* Relax bioframe validator to permit using same column as start and end (e.g. point variants).

**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.3.3...v0.4.0