Magenpy

Added

- A new attached dataset of GWAS summary statistics for standing height from the fastGWA database.

Changed

- Updated the data harmonization method in `GWADataLoader` to ensure that all data sources
have the same set of chromosomes.
- Bug fixes in `SumStatsTable`, `GWASimulator`, and `GWADataLoader`.

Added

- New methods to split `GWADataLoader` objects by chromosome and by samples.
The latter should come in handy for splitting the samples for training, validation and testing.

Changed

- Updated implementation of the shrinkage estimator of LD to align it more closely
with the original formulation in Wen and Stephens (2010) and implementations in RSS software.
- Fixed various bugs and errors in the code.
- Added proper handling for the slice objects in `plot_ld_matrix`

Added

- Added classes encapsulating data structures and methods for:
- Genotype matrices: `GenotypeMatrix`
- Sample tables: `SampleTable`
- Summary statistics table: `SumstatsTable`
- Added a new `stats` submodule that implements utilities and functions
to compute various statistics, including `ld` (SNP correlation matrix),
`h2` (heritability), `score`, `transforms`, `variant` statistics, and `gwa`
(genome-wide association testing).

- Added a modular class for summary statistics parsers `SumstatsParser`.
- Added modular interfaces for `executors`, representing external software,
such as `plink`.
- Added support for window size specifications using number of SNPs and distance
in kilobases.

- Added `CHANGELOG.md` to track the latest changes and updates to `magenpy`.

Changed

- Refactored the `GWADataLoader` class to utilize the new data structures.
- Updated plotting functions/utilities.
- Updated documentation in README file.
- Updated implementation of `MulticohortGWASimulator` (still incomplete).

Added

- Refactored the code for `pypi` package release.
- Added license, `.toml` file, and `MANIFEST.in`.

Changed

- Updated `setup.py` to prepare for the package release.
- Updated `README.md` to add basic documentation.