Fix pre-commit mypy and standardizing environment setup

[blsmxiu47]

Description

@zhengp0 mentioned issues with local environment setup (I think conflicting conda envs iirc) and difficulty pointing to the correct mypy executable while developing. I also noticed that mypy would need to be run manually (which is not bad practice, but still) prior to commit in order to catch typing issues early, rather than it automatically.

So,

1. fixed an incorrect line in .pre-commit-config.yaml to ensure it always runs for all python files in src/ and tests/ (files updated within the commit in question, that is) to enable automatic pre-commit type checking.
2. More significantly, added a Makefile that provides some environment setup-related targets that may be useful in order to ensure the local dev environment is set up correctly. As a part of this PR I removed my previous conda environment and tested setting up in this manner (i.e. make setup ENV_TYPE=conda, then conda activate onemod) and can confirm that my mypy, pytest, etc. executables all point to the expected locations within the new ("onemod") conda environment so please do let me know if this approach still does not work for you using this branch.

Changes made

• One-line regex fix to .pre-commit-config.yaml
• Adds Makefile with (optional but maybe useful) environment setup targets
• Adds drafts for some getting started dev documentation for the Makefile additions, though have not yet approached the task of rewriting all dev docs for the redesign
• Adds a potential CONTRIBUTING.md skeleton for discussion. Would want to discuss contribution guidelines together though before filling in. May not be highest priority atm.

[kels271828]

Thanks for setting all of this up!

[kels271828]

Does anyone else get this error when running ruff:

warning: The isort option isort.split-on-trailing-comma is incompatible with the formatter format.skip-magic-trailing-comma=true option. To avoid unexpected behavior, we recommend either setting isort.split-on-trailing-comma=false or format.skip-magic-trailing-comma=false.

I can fix this by adding this to pyproject.toml:

[tool.ruff.lint.isort]
split-on-trailing-comma = false

Just wasn't sure if I'm the only one seeing this error.

[kels271828]

After running pre-commit, I get a lot of files changed because of the end-of-file-fixer. Should we add those file changes to this PR?

[blsmxiu47]

We can definitely remove the make mypy, make pre-commit targets before merging this branch; first just want to ensure that @zhengp0 can get setup successfully.

[blsmxiu47]

@kels271828 Added in the

[tool.ruff.lint.isort]
split-on-trailing-comma = false

as you suggested. I was also getting that warning.

Also fixed some of the docs syntax, added .env vars note to the dev docs, and as for the :ref:s, these links look and work fine when building and viewing locally, but not sure if there's a way to get them functioning when viewing in GitHub(?) Would be interested if you know of a way 😅

[kels271828]

Also fixed some of the docs syntax, added .env vars note to the dev docs, and as for the :ref:s, these links look and work fine when building and viewing locally, but not sure if there's a way to get them functioning when viewing in GitHub(?) Would be interested if you know of a way 😅

Maybe it's just an issue with viewing on GitHub; I was just viewing it in the browser not actually building the documentation with sphinx

[zhengp0]

Thanks @blsmxiu47 ! Run through with no issue :)