Pre commit

[mnlevy1981]

Adding pre-commit to the environment and a README.md file detailing how to set it up. I want to add pytest via this pull request as well (and have pre-commit run the tests as well), so this will remain a draft PR until I finish that.

Fixes #13

[mnlevy1981]

Note that this will downgrade python from 3.8 to 3.7; it looks like there's an issue with virtualenv and py3.8, and even with workarounds like downgrading virtualenv from v20 to v16 I couldn't get things to work.

[mnlevy1981]

It takes ~4 minutes to spin up the conda environment and run pytest in the github action; I wonder if conda would load faster without auto-update-conda: true but after the first 7 attempts I think I'm done mucking with the YAML until Monday.

@klindsay28 -- I was getting deprecation warnings from import numpy.matlib as npm in xr_ds_ex.py so I replaced both instances of npm.repmat(days_1yr, 1, nyrs) with np.tile(days_1yr, nyrs) (and removed the import statement for npm); my brief checks by hand make the two calls look equivalent, and all the tests pass with this change. I think that was the only substantial change I made when I copied the testing files over from your other repo.

[mnlevy1981]

Also, I'm leaning against having pre-commit run the pytest; I don't want expected failures to hold up the ability to even commit, and I'm a little concerned that as we add unit tests the runtime for pytest would be an unreasonable wait just to get to be able to enter a commit log message.

[mnlevy1981]

I think this one is ready to go, but would appreciate more eyes on it. There's a README with instructions for setting up pre-commit, and then github actions for running black and pytest. The pytest tests are just a starting point, we should probably write more as we continue to develop the code, but I think it's sufficient for this initial PR

[andersy005]

Could we add the following pre-commit hook for formatting notebooks as well:

  - repo: https://github.com/deathbeds/prenotebook
    rev: f5bdb72a400f1a56fe88109936c83aa12cc349fa
    hooks:
      - id: prenotebook
        args:
          [
            '--keep-output',
            '--keep-metadata',
            '--keep-execution-count',
            '--keep-empty',
          ]

[klindsay28]

I have nothing to add beyond the feedback from @andersy005.
Looks good to me.

[mnlevy1981]

As noted in the last commit message, I've implemented two of Anderson's suggestions:

1. Added a prenotebook hook
2. Gihub Action now relies on pre-commit

prenotebook did catch a few issues which are fixed on this branch and will likely cause conflicts when merged into other branches... but I think the right thing to do is keep the existing version on the branch and then let pre-commit fix it.

I also updated the environment file to get precommit from pip instead of conda -- I think this is necessary to have some consistency between pre-commit and our (hires-marbl) conda environment. The README file has a short section on how to make sure pre-commit is using the latest version; as far as I can tell, there needs to be some manual intervention to update the version in pre-commit when the version in the environment changes but I don't think that will turn out to be an issue in practice.