To v0.9.0; full reformat & check with ruff

[pgleeson]

No description provided.

[nanoman657]

@pgleeson OpenWorm is a very interesting project, and I would like to help out over at least 1Q25. It might be helpful to break up this change into smaller chunks that are more easily reviewed. I would be happy to help do this and write some tests to validate the expected behavior.

I say this because Ruff has commented out some functions that you may wish to keep or otherwise reformat:

c302/c302/c302_utils.py

Lines 85 to 86 in a3d4664

	# def plots_prof(a_n, info, cells, dt):
	# cProfile.run("real_plots(a_n, info, cells, dt)")

c302/c302/CompareMain.py

Lines 258 to 263 in a3d4664

	def typeMapping(cols1, cols2, indexName1, indexName2):
	# list1 = ["GapJunction", "Send"]
	# list2 = ["EJ", "NMJ", "R", "Rp", "S", "Sp"]
	# type1 = cols1[indexName1[2]]
	# type2 = cols2[indexName2[2]]
	pass

I'm sure you're on holiday now, so we can discuss upon your return. Happy New Year!

[pgleeson]

Thanks for your contributions @nanoman657. I'm getting back into all this this week, and will try to look over your suggestions.