Bioframe

Date: 2022-02-28

Bug fixes:
* fixed a couple functions returning an error instance instead of raising
* fetch_mrna link fixed

**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.3.2...v0.3.3

Date: 2022-02-01

Bug fixes:
* fixed error in is_contained
* tutorial updates

**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.3.1...v0.3.2

Date: 2021-11-15

API changes:

* `bioframe.sort_bedframe` does not append columns or modify their dtypes.

**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.3.0...v0.3.1

Date: 2021-08-31

Conceptual changes:
* we formulated strict definitions for genomic intervals, dataframes, and
their various properties. All bioframe functions are expected to follow
to these definitions tightly.

API changes:
* reorganize modules:
* ops - operations on genomic interval dataframes
* extras - miscellaneous operations, most involving
genomic sequences and gene annotations
* vis - visualizations of genomic interval dataframes
* core.arrops - operations on genomic interval arrays
* core.checks - tests for definitions of genomic interval dataframes
* core.construction - construction and sanitation of genomic interval dataframes
* core.specs - specifications for the implementation of genomic intervals in pandas.dataframes
(i.e. column names, datatypes, etc)
* core.stringops - operations on genomic interval strings
* io.fileops - I/O on common file formats for genomic data
* io.schemas - schemas for standard tabular formats for genomic data storage
* io.resources - interfaces to popular online genomic data resources

* new functions: extras.pair_by_distance, ops.sort_bedframe, ops.assign_view,
dataframe constructors

* existing functions:
* expand: take negative values and fractional values
* overlap: change default suffixes, keep_order=True
* subtract: add return_index and keep_order

* enable pd.NA for missing values, typecasting

New data:
* add schemas for bedpe, gap, UCSCmRNA, pgsnp
* add tables with curated detailed genome assembly information

Bugfixes:
* None?..

Miscellaneous:
* speed up frac_gc is faster now
* drop support for Python 3.6, add support for 3.9

**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.2.0...v0.3.0

Date: 2020-12-02

API changes:
* `read_chromsizes` and `fetch_chromsizes`: add new `as_bed` parameter.
* `read_chromsizes` and `fetch_chromsizes`: revert to filtering chromosome names by default, but clearly expose `filter_chroms` kwarg.

Bug fixes:
* Fixed `bioframe.split`
* Restored `frac_genome_coverage`

**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.1.0...v0.2.0

Date: 2020-09-23

First beta release.

What's new:
* New extensive dataframe genomic interval arithmetic toolsuite.
* Improved region handling and region querying functions.
* [Documentation!](https://bioframe.readthedocs.io/)

Maintenance:
* Dropped Python 2 support
* Refactoring of various genome operations and resources.
* Improved testing and linting

**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.0.12...v0.1.0