Pycashier

This release followed a major refactor and some things may be missing from the changelog.
Please see the documentation for up to date usage instructions.

Added

- sphinx-based documentation website
- a log file produced in `./pipeline` which includes all subproccess output
- added polars to dependencies to improve tabulated data operations
- made at least one test case for all commands
- hidden `checks` command to invoke pre-run checks on demand for debugging

Changed

- new version scheme of YYYY.BUILD
- pycashier will proceed even if a sample fails
- output is less verbose
- combine is now receipt and includes headers and basic calculations
- headers are included in all final tsvs

Fixed

- visual indicator of work when running counts on files (18)
- filename regex for merge is less stringent (17)
- won't fail if unneeded program is missing (16)

Changed

- updated ci pipeline to incorporate test prior to a tagged release

Fixed

- remove `|` type operator for python <3.10 compatibility (13)
- ensure init-check is run (14)

Added

- sample parameter for all subcommands
- added some broad input/output tests
- global parameters (i.e. threads or samples to fallback on)

Changed

- update python version requirements to >=3.8,<3.11
- updated conda lock file for docker and pinned based images to sha256 for reproducibility

Fixed

- stop merge if both R1 and R2 not found
- removed extra whitespace in single cell output tsv
- added warning about broken symlinks (especially for docker) (12)

Added

- typechecking w/Mypy

Changed

- pinned docker image base to stable tag

Changed

- made init check dependent on command run (fixes 10)
- ignore hidden files in input directory (fixes 9)
- simplified detection of PE reads
- several UI changes for clarity and simplicity

Added

- check for config file and exit if it doesn't exist
- separate `rich.console.Console` for stderr outputs
- automated docker build and switched to ghcr.io

Added

- new `-y/--yes` flag to skip prompts

Changed

- switch project management to pdm
- improved merge error message
- made docker build multi-stage to reduce footprint
- updated ci to use python action instead of poetry