Taranys

Same version as before for proper publish to pip.

Credits

Code contributions to the release:

Sara Monzon - [saramonzon](https://github.com/saramonzon)

Modules

Added enhancements

Fixes

Changed

Removed

Requirements

- Code refactor to create a proper python package
- Implementation of parallel computation for execution speed.
- New implementation of reference-alleles module using leiden algorithm for allele clustering.
- New param defaults based on empirical testing.
- Distance matrix is rewritten with more params available.

New features

- New default missing values threshold imposed for samples in distance matrix creation
- New default perc_identity_ref value for loci search in allele calling analysis
- Github actions for testing and docker generation.

Bug fixes

- multiple statistic modes bug fixed
- BLAST database creation bug due to punctuation signs in file name fixed
- ST profile identification bug fixed
- Python modules installed from conda-forge in environment.yml

Documentation

- Channel order in conda installation command

Pre-release

**BUG FIX:**

- Fix num_threads in blast commands

**BUG FIX:**

- Added ERROR posibility to allele classification, when the allele is not PLOT but is too near to contig end, and protein codification finishes without finding a stop codon.