Refactor Pipelines

[JoshLoecker]

This pull request refactors and improves the logic for combining z-score distributions across batches, sources, and contexts in main/como/combine_distributions.py. The main changes include updating the weighting methodology to use equal weights (Stouffer's Z method), removing invalid weighting by replicate counts, improving handling of missing values, and simplifying function signatures and type usage. The code is also made more robust and readable, with updated docstrings and error messages.

Statistical methodology improvements:

• Updated _combine_z_distribution_for_source to use equal weights (Stouffer's Z method) instead of replicate counts, as replicate counts are not statistically valid weights for z-scores. This change ensures proper aggregation of standardized scores.
• Improved handling of missing values and NaNs in z-score combination logic, including robust masking and safe division, across batch and source combination functions. [1] [2]

Code and interface simplification:

• Removed unnecessary parameters (weighted_z_floor, weighted_z_ceiling) from batch combination functions and updated function signatures to reflect new logic. [1] [2]
• Simplified type usage and imports, including replacing convert with get_remaining_identifiers, and updating type hints and merge logic for Scanpy matrices. [1] [2]

Data handling and output improvements:

• Ensured all output DataFrames have integer indices and are sorted, improving downstream consistency. [1] [2] [3]
• Changed duplicate gene handling from averaging to taking the maximum value, which may better reflect the most significant signal.

Code readability and maintainability:

• Updated docstrings and error messages for clarity and correctness. [1] [2] [3]
• Improved formatting and line splitting for readability throughout the file. [1] [2]

Type and import updates:

• Added new imports and type hints in main/como/data_types.py to support the refactored logic.
• Removed unused classes and updated dictionary comprehensions for clarity. [1] [2] [3]