Snpio

- Added UserManual.pdf via pandoc
- tidied up API docs

Features

- Full refactor of the codebase to improve user-friendliness, maintainability and readability.
- Method chaining: All functions now return the object itself, allowing for method chaining and custom filtering orders with ``NRemover2``.
- Most objects now just take a ``GenotypeData`` object as input, making the code more modular and easier to maintain.
- Improved documentation and docstrings.
- Improved error handling.
- Improved logging. All logging is now done with the Python logging module via the custom ``LoggerManager`` class.
- Improved testing.
- Improved performance.
- Reduced memory usage.
- Reduced disk usage.
- Reduced CPU usage.
- Reduced execution time, particularly for reading, loading, filtering, and processing large VCF files.
- Improved plotting.
- Improved data handling.
- Improved file handling. All filenames now use pathlib.Path objects.
- Code modularity: Many functions are now in separate modules for better organization.
- Full unit tests for all functions.
- Full integration tests for all functions.
- Full documentation for all functions.

Features

- Added functionality to filter out linked SNPs using CHROM and POS fields from VCF file.

Performance

- Made the Sankey plot function more modular and dynamic.

Bug Fixes

- Fix spacing between printed STDOUT.

- Fix bug where VCF file CHROM strings were cut off after 10 characters.

Features

- Performance improvements for VCF files.
- Load and write VCF file in chunks of loci to improve memory consumption.
- New output directory structure for better organization.
- VCF file attributes are now written to an HDF5 file instead of all being loaded into memory.
- Increased usage of numpy to improve VCF IO.
- Added AF INFO field when converting PHYLIP or STRUCTURE files to VCF format.
- VCF file reading uses pysam instead of cyvcf2 now.

Bug Fixes

- Fixed bug with `search_threshold` plots where the x-axis values would be sorted as strings instead of integers.
- Fixed bugs where sampleIDs were out of order for VCF files.
- Ensured correct order for all objects.
- Fixed bugs when subsetting with popmaps files.
- Fixed to documentation.

- Switched to cyvcf2 instead of scikit-allel because scikit-allel wouldn't compile on Mac.
- Updated documentation