Enable nested directory output

[christinehc]

Changelog:

• [fix] Enable nested directory output option (nested_output)

  • (snekmer.io.define_output_dir explicitly converts boolean input from config.yaml if read as strings. This causes the expected boolean input for the nested parameter to always read as True, as "False" is truthy. The behavior has been corrected via ast.literal_eval to force conversion of string representations to booleans.
  • Files created by the cluster, model, and search rules have been changed back to accepting the defined output directory as the location of any created output files; previously, nested directory outputs were not allowed due to the aforementioned problem with defining the output directory structure from config.

• [refactor] Code in cluster.smk and model.smk has been moved to external scripts (e.g. script directive vs. run)

  • The lengths of the Snakefiles have been greatly reduced for improved readability and debugging

• [test] GitHub actions now explicitly test Snekmer installation and CLI are working properly

• [fix] Some CLI errors have been fixed

  • --cores argument no longer throws scheduler errors
  • Invalid path specification for the default configfile has been fixed
  • Additional troubleshooting for AttributeError: __enter__ added to ReadTheDocs page.

• [fix] snekmer model now ignores input files with too few sequences for K-fold cross-validation.

• [format] snakefmt applied to all .smk files for consistent formatting

• [chore] Version has been upticked to v1.0.3 accordingly.

[biodataganache]

Is this good to review now?

[christinehc]

Is this good to review now?

Yes. The top post summarizes all of the changes contained within the PR, but you can also test individually or view individual commits.