Finaletoolkit

Changed
- Included `output_file` as required argument for
`finaletoolkit cleavage-profile`.

Fixed
- Fixed incompatible types in min function through an explicit cast of
chrom_sizes to integers.

Changed
- include `chrom_sizes` file as required argument for
`finaletoolkit cleavage-profile`
- Numpy dependency version set to <2 to avoid breaking changes from numpy 2.
This will change in the future as we migrate to use numpy 2.
- Replaced all instances of `np.NaN` with `np.nan`.

Fixed
- Fixed minor issues with typing in `finaletoolkit.genome.gaps`
- Fixed issue where data files are not packaged with FinaleToolkit

Added
- Brief description of modules in documentation under structure page
- Docstring
- `finaletoolkit.version` module containing single-source `__version__`
variable
- `remove_nocov` option in `finaletoolkit.frag.delfi` to toggle dropping two
bins with low coverage. These bins are dropped in delfi_scripts but
may not apply to fragment files not aligned to hg19.
- tests for `finaletoolkit.frag.delfi_merge_bins`

Changed
- `finaletoolkit.frag.delfi` changed to accept files aligned to almost
any reference genome.
- `finaletoolkit.frag.delfi_merge_bins` algorithm changed to be
reference genome-agnostic and consistent with delfi_scripts
- `finaletoolkit delfi` options `-G`, `-M`, and `-R` to drop
gc-correction, merging, and remove nocov bins, respectively.

Removed
- unused flags for `finaletools delfi`: `-W`, `--window-size`
- redundant flags for `finaletools delfi`: `-gc`, `--gc-correct`,
`-m`, `--merge-bins`

Changed
- `utils.agg_bw` now supports `PathLike` for input
- docstrings for `frag.end_motifs.EndMotifsIntervals` changed to be compatible
with Sphinx

Fixed
- added missing `gzip` import for `utils.agg_bw`

Added
- tests for `utils.agg_bw`

Added
- `interval_size` argument for `adjust_wps`

Changed
- `adjust_wps` checks if `median_window` is larger than interval
- remove default options from some private helper functions for better
error catching/predictable behavior.

Fixed
- `wps`related functions and subcommands

Fixed
- fixed writing to `bed.gz` files when using `coverage`