Migrate project to uv

[AlinderS]

Add a pyproject.toml with project dependencies.
Dependencies are now in three groups.

1. Core packages. These are required regardless of what you want to do. Example: Numpy.
2. Tools. Packages that are only needed to run the examples in presentation 4. Since there are so many of these, splitting them out should make maintaining easier.
3. Dev. Pre-commit is only needed if you want to work on the code so it gets a separate category.

Notably, the original RISE is not included because it is not compatible with JupyterLab or Jupyter notebook > 6. Instead, we use jupyterlab-rise. This has its own issues, most notably that when executing the last cell on a slide, the presentation will advance. I have tried the workaround proposed here which is to insert an empty cell of type skip at the end of each affected slide. I found that it works consistently but another PR will probably be needed to add these to all slides since the issue does not seem to be worked on.

Remove Pipfile and add uv.lock.
I also updated the pre-commit hooks since I was messing with it anyway.

[eerovaher]

I wouldn't keep the default here.

[eerovaher]

Is there a good reason for not complying with SPEC 0?

[AlinderS]

What part of this is in violation of SPEC 0?
It seems to me the spec is about not supporting or requiring old versions of packages, and all these are new.

[eerovaher]

Specifying how long specific versions of dependencies should be supported is the entire point of the SPEC:

Specifically, we recommend that:

1. Support for Python versions be dropped 3 years after their initial release.
2. Support for core package dependencies be dropped 2 years after their initial release.

Although here it makes sense to support versions that will be 2 years old next autumn instead of right now.

[eerovaher]

I wouldn't write down pre-commit as a dependency here. On one hand, listing it as a dependency is not good enough because that just installs the framework, but the hooks still need to be installed in a separate manual step anyways. On the other hand, there aren't any benefits to isolating pre-commit because the framework sets up separate environments for each of the hooks itself.

[eerovaher]

Add a one-sentence comment to explain why these are separate.

[eerovaher]

What's the purpose of locking down the dependencies? Our instructions should not critically depend on exact versions students might have installed. It's not at all obvious why specifying the minimal supported versions on pyproject.toml would not be good enough.

[AlinderS]

I included the lock file because that is the default recommended behaviour of uv, but I agree that we don't require that strict control so it is better to leave it out.

[eerovaher]

I'm willing to guess that the uv recommendation relies on the assumption that the code is tested using different versions of dependencies. But this project doesn't even have a test suite, so if a lock file forces the few people who are involved with this to use exactly the same versions of dependencies then some problems might go unnoticed for a long time.