Kmer association

[jjacobson95]

Learn / Apply has been updated with confidence scoring should be good to go.

Documentation will be updated soon as well.

[christinehc]

Before we merge this PR:

Major Changes (higher priority)

• [x] Add learn/apply to Github Actions (.github/workflows/action.yml)
• [x] Update documentation to include learn/apply
• [x] Add learn/apply demo or tutorial

Minor Changes (lower priority)

• [x] Change variable names
  • I noticed that many of the variable names, particularly in snekmer/rules/learn.smk, are capitalized. This naming scheme does not conform to Python conventions requiring variable names to be lowercase (either snake_case or camelCase), as capitalized variable names indicate classes by convention.
• [ ] Update main Snekmer graphic to include learn/apply

[jjacobson95]

Thanks for the checklist @christinehc! I'll likely start working on this early next week!

[jjacobson95]

Addressed some incompatibilities between learn/apply and the current codebase. Tests are now functioning properly. The only code update left is to remove branch specification in the tests (actions). And once docs are pushed to readthedocs, they will likely require a second pass.

[jjacobson95]

Additive method fixed, however a caveat exists with the scoring method for this revision. While the kmer counts database can be successfully updated, the confidence scoring can't fully account for all of the previous files that entered this database. Lets discuss in next meeting.

[jjacobson95]

Just a note - this should be good to go. No known issues currently exist.