Finaletoolkit

Fixed
- adjusted handling of contig, start, stop for `frag_generator` so that
`coverage` does not throw exceptions for genomewide intervals.

Added
- test for `single_coverage`

Changed
- add `__version` attribute
- `finaletoolkit --version` displays package version
- update PyPI page to include links

Fixed
- Fixed intersect policy for `cleavage_profile`. Now it calls `frag_generator`
with a policy of `any`.
- Clean up some comments and docstrings
- Fixed logging from coverage function

Added
- Added numerous util functions
- Added `left` and `right` options to `cleavage_profile` and CLI
`cleavage-profile`.
- Added tests for cleavage profile and WPS.

Changed
- Minimum Python version 3.9
- Changed `filter_bam` to have same filters as FinaleDB
- `utils.frag_generator` raises `ValueError` if `start` or `stop`
are specified without `contig`
- Type hints changed to use literals when possible

Removed
- Removed `utils.get_contig_lengths`
- Removed `data`, `conda_envs`, and `figs` directories
- Removed unused dependencies `click`, `pybedtools`, and `cython
- Remove some unused imports from module files

Fixed
- `interval-mds` CLI subcommand calculates correctly without large negative
values.
- `interval-mds` CLI subcommand now correctly parses tsv files.

Added
- Most end-motif related Python functions accept Path instances as inputs for
files.
- Unit and function tests, especially for end-motif related functions.

Changed
- All instances of finaletools have been renamed to finaletoolkit
- All default tabular files are now TSV
- Update contacts in TOML

Fixed
- `interval-mds` and `mds` both calculate correctly when one motif has a
frequency of 0

Added
- Added `finaletools.interval_end_motifs` function to calculate end-motifs
over genomic intervals. Stores results in an IntervalEndMotifs object.
- Added CLI subcommand `interval-end-motifs` to calculate end-motifs over
genomic intervals.
- Added CLI subcommand `interval-mds` to calculate MDS over intervals from
interval end-motifs table.

Changed
- Added `gc_correct` option to `delfi_merge_bins` so that merging is possible
without GC correction

Fixed
- `delfi` can now be run with `gc_correct=false` and `merge_bins=true`
- fixed `cleavage_profile` import in `frag`