Ruff linter not linting content from the "software" directory

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Describe the bug The ruff linter isn't applied to the software directory

To Reproduce Steps to reproduce the behavior:

1. Make a change to directory that will elicit a git diff
2. Make a commit to trigger the pre-commit hook
3. Notice the linter sees nothing
4. cd into the software directory and run ruff .
5. See the changes it is proposing, contrary to what happened on step 3

Expected behavior Given the bulk of the Python code is in the software directory, it's expected that it would be covered by the linter. The sooner this is done, the easier it will be to streamline contributions.

Desktop (please complete the following information):

• OS: all
• Python Version: all