downgrade to DeprecationWarning, make lint fixes

[AmandaBirmingham]

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[Copilot]

Pull request overview

This pull request updates deprecation warnings to be Python version-agnostic and applies lint fixes for flake8 W503 warnings. The changes replace the @deprecated decorator (which requires Python 3.13+) with the traditional warnings.warn() approach that works across all Python versions, and reformats multi-line expressions to follow PEP 8's updated style guide preference for line breaks before binary operators.

Changes:

• Replace @deprecated decorator with warnings.warn(..., DeprecationWarning, stacklevel=2) for backward compatibility
• Add flake8 configuration to ignore W503 (line break before binary operator)
• Reformat multi-line expressions to place binary operators at the start of continuation lines
• Fix various whitespace and indentation issues throughout the codebase

Reviewed changes

Copilot reviewed 5 out of 8 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
setup.cfg	Added flake8 configuration to extend-ignore W503 warnings
pysyndna/src/calc_cell_counts.py	Replaced @deprecated decorator with warnings.warn() calls for 4 deprecated functions; reformatted multi-line expressions; fixed whitespace issues
pysyndna/src/util.py	Fixed operator spacing in division expression
pysyndna/src/fit_syndna_models.py	Reformatted multi-line expressions and function signatures; removed extra whitespace
pysyndna/tests/test_util.py	Reformatted import statement and fixed indentation in function calls
pysyndna/tests/test_quant_orfs.py	Fixed dictionary indentation
pysyndna/tests/test_fit_syndna_models.py	Removed extra whitespace in import statement
pysyndna/tests/test_calc_cell_counts.py	Fixed indentation in dictionary comprehensions and multi-line expressions; removed trailing whitespace

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