Add support for astral-sh/uv

[arjxn-py]

Description

uv is a quick Python package installer and resolver, made with Rust. It's meant to work just like pip and pip-tools, but faster.

Motivation

The introduction of the uv tool (https://astral.sh/blog/uv) marks a significant leap in package management efficiency. Offering notable speed improvements over pip, uv demonstrates superior performance across various scenarios. This enhanced speed translates to quicker package installations, contributing to smoother and more efficient workflow experiences.

Possible Implementation

• pyproject.toml
• publish_pypi.yml

Additional context

No response

[agriyakhetarpal]

This would be a great addition even though uv is pretty new and possibly far from production use.

I would suggest waiting on using it with the PyPI publishing workflow (see astral-sh/uv#1663) and rather add it to the PR tests after astral-sh/uv#1646 is resolved from their end (I am indeed following uv's developments pretty closely haha)

[kratman]

Is using pip a bottleneck on any of our tests?

[arjxn-py]

Is using pip a bottleneck on any of our tests?

No that's not the case, but as we have a large dependency tree uv can make significant improvements in workflow speeds, plus example notebooks can also take advantage of the same once we're done experimenting with this new tool and it is stable & production ready.

I anticipate that we'd not just jump on uv considering how fast & efficient it is but would take one step at a time while keeping the infrastructure stable.

[agriyakhetarpal]

I anticipate that we'd not just jump on uv considering how fast & efficient it is but would take one step at a time while keeping the infrastructure stable.

I agree. Let's wait until wntrblm/nox#762 gets merged and receives some feedback by users.

Is using pip a bottleneck on any of our tests?

We don't face a bottleneck as such since pip already receives a lot of the wheels cached in CI (though that hasn't worked all the time for me). What it doesn't do is cache the installation processes, and therefore installations (copying files around with the right permissions, that is) are relatively slower. This is where using uv is of the essence!

[kratman]

I anticipate that we'd not just jump on uv considering how fast & efficient it is but would take one step at a time while keeping the infrastructure stable.

Yeah I would be against switching at an early stage for the tool. Pip is well tested and most users already have it installed. Maybe something to revisit in a year or so

[agriyakhetarpal]

A new release for nox is out which includes a [uv] extra, and it's pretty cool: https://github.com/wntrblm/nox/releases/tag/2024.03.02. Whoever wishes to work on this could also consider adding a nox badge to our README.

[santacodes]

Seems interesting, this could also potentially decrease the build times of docker containers and the project setup times in cookiecutter templates and virtual environments or nox.

pyproject.toml and noxfile.py can be initially worked upon to test this feature and then can be moved to CI/CD (publish_pypi.yml).

I anticipate that we'd not just jump on uv considering how fast & efficient it is but would take one step at a time while keeping the infrastructure stable.

Yeah I would be against switching at an early stage for the tool. Pip is well tested and most users already have it installed. Maybe something to revisit in a year or so

If this issue is not being already worked upon by someone, I would be happy to create a draft for future references.

[kratman]

I still think we should not do this one. I don't see the gain for changing to a new tool when pip is well tested

[kratman]

Just to reiterate, I don't think the pip install is a major bottleneck

[agriyakhetarpal]

I still think we should not do this one. I don't see the gain for changing to a new tool when pip is well tested

Just to reiterate, I don't think the pip install is a major bottleneck

@santacodes @kratman on the contrary – I feel we can try it now, uv seems more stable to me than before and there's no harm (users won't get it anyway, just the developers, and an year is probably too long a wait). I was looking at this earlier in the day today and with my hopefully thorough testing mostly everything seems to work perfectly – with the exception of the error I just posted on their tracker (see above).

[agriyakhetarpal]

Properly using and caching uv can shave us off ~1–1.5 minutes in our CI pipelines, which doesn't sound like a lot, but coupled with #3857 we should be able to get under the 5-minute mark with that and improve local development. But yes, it has to be done properly (actions/setup-python#822 isn't done yet, but we know the uv cache locations).

[agriyakhetarpal]

I see that nox has cut a release with uv now, should simplify things!

[kratman]

I just think that we can speed up CI in other ways than continually changing the build system. For instance when I removed the benchmarks from every PR it saved 30 minutes off the total runtime of the CI.

Right now we have 46 CI jobs, at most 10 seem to run at once, and (last time I checked) on average they run around 20 minutes -> (46/10) × 20 ~ 80 minutes to run CI. If we cut down our build matrix by half it would save us 40 minutes and we would not need to make backend changes.

To me it does not seem like pip is the bottle neck. For some of the builds we might save more time by trying to find ways to avoid building our dependencies from source

[agriyakhetarpal]

Yes, that's right – removing a lot of the redundant CI would be quite helpful. But about the bottleneck part, I see that by replacing pip I see some insane speedups locally (it takes a minute in CI if one installs [all,dev,jax,odes] where having a cached wheel for scikits.odes would help – we recently removed those because it breaks sometimes, might be worth removing that hack)

[agriyakhetarpal]

Maybe @santacodes you can try out with a draft PR (or in a branch on your fork) and we can see to it if everything works well in CI? If it doesn't, we can always close it and look at this at another time

[santacodes]

Maybe @santacodes you can try out with a draft PR (or in a branch on your fork) and we can see to it if everything works well in CI? If it doesn't, we can always close it and look at this at another time

Sure, happy to try it out in my fork with CI resources to test the performance

[agriyakhetarpal]

The uv developers' implementation of their dependency resolver is correct here and pip's resolvelib is in the wrong (they have a lot of open issues about pre-release backtracking) – so we won't be able to install scikits.odes at this time with Python 3.11 unless either scikits.odes fixes the Cython upper pin on their end with a new release (which no one takes how long it can take), or we drop scikits.odes as a dependency.

We can keep this open for a while – with the exception of scikits.odes, all of our dependencies have pure Python or binary wheels, are maintained with no absurd upper bounds¹ for their build-time dependencies, and installing them is much more trivial (I tested an editable installation without [odes] and it took 40 seconds instead of three minutes, with most of the time spent in compiling PyBaMM).

Footnotes

1. The scikits.odes developers upper-pinned to cython<3.0.0a8, which means uv correctly picks an earlier pre-release (3.0a7), while pip picks a stable release (0.29.37). They should have pinned to cython<3 instead which would have had fixed all problems here. Note that the backtracking for pre-releases is ambiguous, so there is no right answer (but uv's is making more sense to me). ↩

[Saransh-cpp]

Some arguments for switching to uv (eventually; hence, keeping this issue open to keep an eye on the development) -

1. Nox has a uv backend now

2. PyPA's build now supports uv (making things kind of official)

3. Pixi now supports uv

4. A lot of conversation and experiments involving uv are taking place in Scikit-HEP:

   Switching to uv cut the total job times for hist in half.

   For example, using nox to build nox’s docs goes from 22 seconds to 4 seconds using uv.

[agriyakhetarpal]

to add to the above: #3932 will remove scikits.odes, so all of our dependencies will have wheels for all platforms that we support (both platform-specific binaries or pure Python ones).

[valentinsulzer]

Good to see this being adopted more. I'd be happy to switch to this once we see some of the big python packages (e.g. numpy) start to switch over. I do agree that pip isn't a major bottleneck in our testing.