Gimmemotifs

Fixed

* `_non_reducing_slice` vs `non_reducing_slice` for pandas>=1.2 (168)
* When using original region size, skip regions smaller than 10bp and warn if no
regions are left.
* Fixed creating statistics report crashed with `KeyError: 'Factor'` (170)
* Fixed bug with creating GC bins for a genome with unusual GC% (like Plasmodium).
* Fixed bug that occurs when upgrading pyarrow with an existing GimmeMotifs
cache.

Changed

- Refactoring to make `coverage_table` and `combine_peaks` available via API.

Fixed

- Fix issue with -s parameter of `gimme motifs` (146)
- Fix issues (hopefully) with scanning large input files.

Added

- `Motif.plot_logo()` accepts an `ax` argument.

Fixed

- Support for pandas>=1.1
- `coverage_table` doesn't add a newline at the end of the file.

Added

- Added additional columns to `gimme maelstrom` output for better intepretation (correlation of motif to signal and % of regions with motif).
- Added support for multi-species input in `genomechrom:start-end` format.
- `gimme maelstrom` warns if data is not row-centered and will center by default.
- `gimme maelstrom` selects a set of non-redundant (or less redundant) motifs by default.
- Added SVR regressor for `gimme maelstrom`.
- Added quantile normalization to `coverage_table`.

Removed

- Removed the lightning classifiers and regressors as the package is no longer actively maintained.

Changed

- Visually improved HTML output.
- Score of `maelstrom` is now an aggregate z-score based on combining z-scores from individual methods using Stouffer's method. The z-scores of individual methods are generated using the inverse normal transform.
- Reorganized some classes and functions.

Fixed

- Fixed minor issues with sorting columns in HTML output.
- `gimme motifs` doesn't crash when no motifs are found.
- Fixed error with Ensembl chromosome names in `combine_peaks`.

Fixed

- Fixed "TypeError: an integer is required (got type str)" when creating GC index.
- Fixed `combine_peaks` with Ensembl chromosome names (thanks JGAsmits).
- Fixed bug with pandas>=1.0.

Fixed

- Fixed 'AttributeError: can't delete attribute' in `gimme maelstrom` and `gimme motifs` (108, 109).