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This pull request updates the default data files for the Naive B example context

It also eliminates Ruff & Pyrefly linting/typing warnings in the rnaseq_preprocess and utils files

Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
…dataframe object

Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
…M scores

Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
…essing)

Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
…Counts information

Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
…ization

# Conflicts:
#	main/como/rnaseq_preprocess.py
#	tests/unit/test_rnaseq_preprocess.py
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
@JoshLoecker JoshLoecker merged commit 5de7db0 into develop Feb 10, 2026
3 checks passed
@JoshLoecker JoshLoecker deleted the typing-rnaseq-preprocess branch February 10, 2026 20:06
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