chore: reformat Python code with line length = 88 #57
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This PR reformats Python code with a maximum line length of 88 characters to better represent the code.
See modflowpy/flopy#2362 for a related PR with rational and discussion.
This PR also changes some of Ruff's configuration:
target-version, since it was outdated and is automatically evaluated frompyproject.tomlincludeso that Ruff will work globally in this repoextend-includesince "*.ipynb" files are already included by default