Accept path-like objects for file inputs in PANDA and PUMA

[marouenbg]

Summary

Replace type(x) is str checks with isinstance(x, (str, os.PathLike)) in input loading functions so that pathlib.Path and other path-like objects are correctly recognized as file paths.

Motivation

When users pass pathlib.Path objects (or other os.PathLike types) as file inputs, type(x) is str returns False, causing the code to fall into the DataFrame branch and raise an error like:

Exception: Please provide a pandas dataframe for motif data with column names as 'source', 'target', and 'weight'.

This also prevented mixing file paths and DataFrames for different inputs (e.g., PPI as a path and expression as a DataFrame).

Fixes #351

Changes

• netZooPy/panda/io.py: load_motif() and load_expression() now use isinstance(x, (str, os.PathLike))
• netZooPy/panda/panda.py: PPI loading in processData() uses isinstance
• netZooPy/puma/puma.py: miR file loading uses isinstance

Testing

Verified with toy data that the following all work:

• All paths (str) - baseline
• All DataFrames
• Mixed: expr=DataFrame + motif/ppi=path
• Mixed: motif=DataFrame + expr/ppi=path
• Mixed: ppi=DataFrame + expr/motif=path
• All pathlib.Path objects
• Mixed pathlib.Path and DataFrames

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 59.51%. Comparing base (b6d05b7) to head (0964f65).
⚠️ Report is 47 commits behind head on devel.

Additional details and impacted files

@@            Coverage Diff             @@
##            devel     #381      +/-   ##
==========================================
+ Coverage   57.06%   59.51%   +2.44%     
==========================================
  Files          39       45       +6     
  Lines        2518     3053     +535     
==========================================
+ Hits         1437     1817     +380     
- Misses       1081     1236     +155     

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