Finaletoolkit

Fixed
- changed default args for `wps` would lead to errors. Now `wps` defaults to
LWPS fragment lengths (120-180nt).

Changed
- made `finaeltoolkit.utils.typing` public. This is a module containing some
useful type aliases
- minor formatting and typing changes
- renamed `fraction_low` and `fraction_high` to `min_length` and `max_length`
for `.utils.frag_array` and `.frag.wps`. `wps` retains the deprecated arg names
but issues a warning.

Fixed
- Added missing `-n` arg to `end-motifs`.
- Fixed incorrect `ValueError` regarding the `negative_strand` arg.
- Incorrect function name for `wps` leading to errors when called from CLI.

Added
- Additional tests for the CLI lazy loading implementation

Changed
- several modules containing implementations of fragmentomic features or
utiliy functions have been made internal. This means there is now only one
obvious import for each function. For example, `multi_wps` is imported from
`finaletoolkit.frag`, and no longer can be imported from
`finaletoolkit.frag.multi_wps`
- The CLI now uses lazy importing, drastically speeding up finaletoolkit when
called from a command line.
- Added `negative_strand` option for end motifs related functions. When
used in conjunction with `both_strands`, only end motifs on the negative
(Crick) strand are considered in calculations.
- Renamed `fraction_high` and `fraction_low` in `utils.utils.frag_generator`
to `min_length` and `max_length`.

Fixed
- deprecated arguments for `end-motifs` had default values which could
lead to an error. This is fixed.

Fixed
- CLI no longer prints an error message if `finaletoolkit` is called without args.
- `frag-length-bins`, when writing a file, now writes the interval between
`min` and `max` as inclusive. That is, previously when `min=1` and `max=2`,
only fragments of length 1 are reported. Now when such a result is calculated,
the interval given is `min=1` and `max=1`.
- Updated some descriptions and docstrings.

Added
- `adjust-wps` now has an option `-S` or `--exclude-savgol` to not perform
Savitsky-Golay filtering.

Changed
- Several CLI options were renamed so that underscores become hyphens. This is
for consistency and to simplify writing commands.

Removed
- `strand_location` arg from `agg_bigwig`
- `cli_hist` module

Fixed
- fixed bug involving tqdm progress bar in `frag_length_intervals`
- some code formatting
- fixed bug involving arg names in `filter-bam`
- add some missing args to CLI
- issues with running `cleavage-profile` (115)
- issues with writing to bigwig with `wps`

Changed
- change default of arg `both_strands` of `end_motifs` to True to match
behavior of original scripts
- rename `fraction_high` and `fraction_low` to `min_length` and `max_length`
for all features, deprecating old args as aliases if needed.
- numpy 2 compatible
- fragmentomics functions assume Tabix indexed files all follow the
FinaleDB Frag.gz file format. That is, columns are `chrom`, `start`, `stop`,
`score`, and `strand`. If more columns are detect, a warning is issued, and
FinaleToolkit will attempt to parse the file as a BED6 format.
- renamed `genome_file` to `chrom_sizes` for most functions.
- `multi_wps` and `multi_cleavage_profile` no longer return a value due to memory issues when attempting to calculate these genomewide. Instead, users should refer to the file specified with `output_file`.

Added
- internal `utils._typing` and `utils._deprecation` modules
- test for `delfi`

Deprecated
- `delfi-gc-correct` command. GC-correction is performed automatically by `delfi`
already.

Removed
- `finaletoolkit.frag.frag_length_bins` no longer has the `contig_by_contig`
option. This never had any functionality.
- `finaletoolkit.frag.frag_length_bins` no longer generates a text-based
histogram.

Fixed
- `contig_sizes` option included for `cleavage-profile` CLI command.
- `normalize` option for `coverage` fixed so it no longer normalizes twice
- `normalize=False` for `coverage` runs much faster
- misc typehints and docstrings

Changed
- `finaletoolkit.frag.frag_length_bins` uses a dict based implementation
that is more memory efficient.
- `finaletoolkit.frag.frag_length_bins` and
`finaletoolkit.frag.frag_length_intervals` now take `min_length` and
`max_length` keyword args to only consider fragments of certain lengths.
- flags for `frag-length-bins` and `frag-length-intervals` CLI commands updated
to match Python API
- `coverage` default argument for `normalize` changed to `False`
- `coverage` default argument for `scale_factor` changed to 1.

Added
- `finaletoolkit.frag.frag_length_bins` can generate a histogram figure
- tests for `frag_length` module