Tests and fixes

[clonder]

Changes Made

1. Removed Unused Functions:

   • Deleted functions.get_columns and functions.get_score as they were unused in the codebase.

2. Modernized Import Handling:

   • Updated src/kinex/resources/__init__.py to use the modern files() method from importlib.resources instead of the deprecated path() method.

3. Fixed Sequence Handling:

   • Added PH_CAPITAL = "(PH)" in src/kinex/sequence.py to handle cases where seq.upper() with favorability=False resulted in invalid separators (e.g., (PH)), which were mistakenly filtered out.

4. Improved Stability:

   • Added a check_zeros parameter to the 2x2 table implementation to prevent division by zero errors when shift_zeros=False.

5. Improved fisher_statistics function:

   • Divided it into subfunctions for better testing and readability.

6. Enhanced Test Coverage:

   • New Tests:
     • Added test cases for enrichment, sequence, score, and table2x2 modules.
   • Updated Tests:
     • Fixed and extended test coverage for kinex and io modules.

Fixes #7

[alexandra-valeanu]

Hey @clonder! Thank you for all the work!

I'll review the changes in the coming days and provide feedback.