Format and lint notebooks

[itcarroll]

Closes #788

Re-enable the format and lint tool for notebook (.ipynb) files everywhere in the repo (which turns out to be in notebooks, docs/howto, and mostly docs/tutorials).

The only lint rules I found to be not great for notebooks are T201 and T203, which are prohibitions on print and pprint in production code. I ignored them for "*.ipynb" in [tool.ruff.lint.per-file-ignores].

I found two packages missing from [project.optional-dependencies.docs] that are needed for the notebooks to run, and added them with a minimum dependency taken from the version pip would install. uv add --extra docs dask cftime.

I did not attempt to fix some remaining errors in the notebooks that are beyond the scope of linting. They did not all run when I started and still don't all run (but not because of missing packages!).

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---

📚 Documentation preview 📚: https://earthaccess--817.org.readthedocs.build/en/817/

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[itcarroll]

uv-lock..................................................................Failed
- hook id: uv-lock
- exit code: 2

@MattF-NSIDC (use mfisher87) I'm unable to find an explanation for what to do about pre-commit's uv-lock check, which is no doubt failing because I've added packages to pyproject.toml. Can you explain how to safely update uv.lock?

[mfisher87]

Hey @itcarroll for future reference, I don't log in to @MattF-NSIDC often so I don't see the notifications sent there :)

Did the failing check not also update uv.lock when it failed? This was the output for me when I added flask to the dependencies array in pyproject.toml:

$ pre-commit run -a uv-lock
uv-lock..................................................................Failed
- hook id: uv-lock
- files were modified by this hook

warning: `VIRTUAL_ENV=/home/robatt/.cache/pre-commit/repo16nnfz_r/py_env-python3.12` does not match the project environment path `.venv` and will be ignored
Using Python 3.12.5 interpreter at: /home/robatt/.local/share/miniforge3/envs/earthaccess/bin/python3
Resolved 222 packages in 1.12s
Added blinker v1.8.2
Added flask v3.0.3
Added itsdangerous v2.2.0
Added werkzeug v3.0.4

$ git status
On branch main
Your branch is up to date with 'origin/main'.

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
	modified:   pyproject.toml
	modified:   uv.lock

[mfisher87]

Oh, and thanks so much for taking on this important piece of technical debt!! 🙇

[itcarroll]

Understand now that the uv-lock hook is throwing an error, so that's why it's not updating the uv.lock file.

The error I could not make any sense of was

(earthaccess) $ pre-commit run uv-lock
warning: `VIRTUAL_ENV=/Users/icarroll/.cache/pre-commit/repo48a95whq/py_env-python3` does not match the project environment path `.venv` and will be ignored
error: Failed to build: `earthaccess @ file:///Users/icarroll/tmp/earthaccess`
  Caused by: Failed to deserialize cache entry
  Caused by: wrong msgpack marker FixArray(2)

I tried reinstalling everything. What eventually made the error go away was updating the rev on the uv-pre-commit repo to "0.4.12". Is that okay @mfisher87?

[mfisher87]

I tried reinstalling everything. What eventually made the error go away was updating the rev on the uv-pre-commit repo to "0.4.12". Is that okay @mfisher87?

That's great! Thanks so much for tracking down a fix. That's a really weird error message, I don't know what to make of it 😆

I have some family in town so I can't give a full review until perhaps in the middle of the coming week!

[chuckwondo]

LGTM

[itcarroll]

pre-commit.ci autofix