Capice

New:

- Added standalone version validator that checks both Semantic and PEP440 versions for both CAPICE and the model. Also checks if the versions are compatible.

Changes:

- Fixed a bug where CAPICE would error on file extensions when output argument `-o .` was supplied.
- Fixed code smell within args_handler_predict.py.
- Fixed a bug that didn't check for required input feature `feature_type` for predictions.
- Fixed a bug where the PoC test resources model was considered out-of-date.

Changes:
- Improved version checking for CAPICE models. CAPICE models now will work if a patch or minor version mismatch is present, but will error when a major or release candidate mismatch is present.
- 95 README updates
- 96 Move `__version__` to `__init__` instead of `__version__.py`

New features

- New Command Line Interface with improved separation between the predict and train module.
- Customized XGBoost model that includes impute values and CAPICE versioning.
- Added support for edge cases (breakends, symbolic alleles and alternative contigs).
- Revamped input that no longer depends on CADD 1.4 but instead depends on VEP.
- Added a manual annotator module that processes the VEP features. Each module is separate and are loaded in dynamically, no codebase changes have to be made in order to start supporting new features.
- Added bash script to convert a VEP output VCF to a CAPICE ready input TSV.
- Added helper script to balance out an input dataset on allele frequency, consequence and the amount of benign vs pathogenic samples.
- Added Travis CI for automated testing and deployment.
- Created access point `capice`.
- Added support for Python 3.10.
- Added input requirement "SpliceAI".

Changed

- Separated CAPICE framework from CAPICE model. New models can now be released independently.
- Variants are no longer removed if they contain no feature at all. Instead, CAPICE will now throw an error when a gap is present within the CHROM, POS, REF or ALT column.
- Reduced overall code complexity.
- PEP8 formatting guidelines with maximum line length 100 characters.
- Updated testing.
- Changed logging. It is no longer possible to let CAPICE create a logfile. Instead, CAPICE logs DEBUG and INFO to system STDout and WARNING, ERROR and CRITICAL to STDerr.
- Changed logging output format to `YYYY-MM-DD <loglevel>: <msg>`
- Changed code structure of CAPICE to follow the [MOLGENIS Python template](https://github.com/molgenis/molgenis-template-py).

Removed

- Removed deprecated files in CAPICE_example.
- Removed ability to create train-test / validation datasets directly through CAPICE. Use the supplied helper script in order to perform these steps.
- Removed support for Python <=3.7.

Bug fixes

- Fixed a bug when `-v / --verbose` flag was called, CAPICE would not output DEBUG level logmessages.
- Fixed a bug within training that would throw a ValueError when used with XGBoost 1.4.2