cookiecutterize

[grst]

Close #66

Migrate pytometry into the scverse-cookiecutter template.

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[grst]

Mostly done. Sphinx doesn't pass because there are some warnings related to the docstrings that need to be resolved.

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[mbuttner]

Looks good to me overall - one minor comment on gitignore.

[quentinblampey]

Super nice @grst! Just some minor comments
And the docs still rely on the typehints from the docstrings, I think we should also update this as mentioned in #74 (I can have a look tomorrow)

[grst]

I fixed the sphinx warnings by converting the docstrings to numpy-style (with some help of ChatGPT).

Here's a preview of the docs:
https://pytometry--75.org.readthedocs.build/en/75/

[quentinblampey]

I pushed some changes:

• Removed the duplicated default values from the docstrings to show only the ones from the argument's default.
• Added typing and the right docstrings for some functions that were still missing it
• normalize_biExp renamed to normalize_biexp, and added an alias for backward compatibility

[mbuttner]

I fixed the sphinx warnings by converting the docstrings to numpy-style (with some help of ChatGPT).

Here's a preview of the docs: https://pytometry--75.org.readthedocs.build/en/75/

This looks pretty amazing already! For the rendered tutorial notebooks, I realized that there is no output shown, yet.

[grst]

Did the lamin docs setup execute tutorials upon building the documentation?

With the new setup, this would only work (without extra effort) if the notebooks consume so little memory that they can run on the readthedocs CI.

[mbuttner]

Yes, we made the separation between "examples and tasks" (not executed) and "tutorials", which are executed, but are designed to consume little memory.

[grst]

ok, let's try

[grst]

Seems to have worked now :)

@quentinblampey, the scatterplot in the tutorial looks a bit strange. I suspect it's due to xlim being provided

[quentinblampey]

Nice catch @grst, indeed on this example the minimal value was -4233164.5, therefore a lot of bins were used for negative numbers, while not shown afterwards
I fixed it by setting range in np.histogram2d

[Zethson]

We use

• repo: https://github.com/kynan/nbstripout

at lamin with pre-commit to ensure that no executed notebooks are pushed. I think this setup here wants that, right?

[grst]

Yes, but only for the notebooks in tutorials not examples. But it would be only to ensure the repo stays clean. With the latest changes, the notebooks in tutorials will be executed either way.

[quentinblampey]

Does it look good for everyone?

[grst]

@mbuttner, is it possible to forward to https://pytometry.readthedocs.io/en/latest/index.html from the old netlify site?

[mbuttner]

Yes, that's possible, see https://docs.netlify.com/configure-builds/file-based-configuration/#redirects
However, this means we have to rebuild the netlify page.