Fix zFPKM Calculations

[JoshLoecker]

This pull request replicates R's zFPKM functionality by rewriting underlying C code from R into Python using NumPy.

[Copilot]

Pull Request Overview

This PR replaces NumPy-specific type hints (e.g., np.float64, np.float32, np.int8) with Python built-in types (float, int) across the codebase. It also includes significant refactoring of zFPKM calculations to match R's implementation, adds new helper modules for density estimation and peak finding, updates enum values to lowercase, and removes test/debugging code.

• Replaces NumPy-specific dtype references with Python built-in types for better compatibility
• Refactors zFPKM transformations to align with R's implementation using custom density and peak-finding functions
• Updates enum values from uppercase to lowercase for consistency
• Adds new configuration file (ty.toml) and helper modules (density.py, peak_finder.py, approx.py)

Reviewed Changes

Copilot reviewed 24 out of 25 changed files in this pull request and generated 20 comments.

Show a summary per file

File	Description
ty.toml	Adds new type checker configuration
tests/unit/test_*.py	Updates test fixtures to use float/int instead of NumPy types
ruff.toml	Reformats linting configuration and moves F401 to unfixable rules
main/como/utils.py	Updates type hints and adds logic to handle DataFrame index names
main/como/stats/*.py	Replaces NumPy types with built-in types in statistical test classes
main/como/rnaseq_*.py	Major refactoring including zFPKM calculation updates and gene ID handling
main/como/proteomics_*.py	Updates type hints and gene symbol processing logic
main/como/data_types.py	Changes enum values from uppercase to lowercase
main/como/create_context_specific_model.py	Adds taxon parameter, refactors model I/O, and updates type hints
main/como/merge_xomics.py	Updates enum usage and improves batch number extraction
main/como/combine_distributions.py	Refactors z-score combination logic to handle replicates per batch
main/como/peak_finder.py	New module implementing R's findpeaks function
main/como/density.py	New module implementing R's density function for KDE
main/como/approx.py	New module implementing R's approx interpolation function

Comments suppressed due to low confidence (1)

main/como/create_context_specific_model.py:1

• Comment uses incorrect type checker ignore syntax. Should be type: ignore not ty: ignore.

from __future__ import annotations

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[Copilot]

The isinstance() call should use a tuple, not a union type with |. This should be isinstance(data, (pd.DataFrame, np.ndarray)). The current syntax will raise a TypeError at runtime.

Suggested change

	if not isinstance(data, pd.DataFrame | np.ndarray):
	if not isinstance(data, (pd.DataFrame, np.ndarray)):

[Copilot]

Corrected spelling of 'Validate' (missing 'V').

Suggested change

	# alidate alignment between columns and replicate vector
	# Validate alignment between columns and replicate vector

[Copilot]

Calling str() on gene_reaction_rule in every iteration is unnecessary if it's already a string. Consider verifying the type once before the loop or using a type assertion if you're certain it's always a string.

Suggested change

	gene_reaction_rule = re.sub(pattern=rf"\b{gene_id}\b", repl=str(activity), string=str(gene_reaction_rule))
	gene_reaction_rule = re.sub(pattern=rf"\b{gene_id}\b", repl=str(activity), string=gene_reaction_rule)

[Copilot]

Debug print statement left in production code. This should either be removed or replaced with proper logging using logger.debug(df) or logger.trace(df).

Suggested change

	print(df)
	logger.debug(df)

[Copilot]

This statement has no effect.

[Copilot]

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[Copilot]

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[Copilot]

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[Copilot]

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