Sandbox::https://github.com/PlasmaPy/PlasmaPy/pull/2937

namurphy · 2025-01-08T22:57:14Z

Background

For the last several months, we've been using uv pip compile to create separate pinned requirements files in ci_requirements/ for different versions of Python and for different operating systems. Having to deal with 18 separate files got unwieldy, and the Nox session to generate these files began to get tricky to maintain.

uv.lock holds information about different dependency groups for different operating systems and for different versions of Python. Pinning requirements in uv.lock would consolidate all of this information in a single file. 💾

Description of changes

This PR switches multiple Nox sessions defined in noxfile.py for testing and documentation builds to use requirements that are frozen in uv.lock. We can then use uv sync to install exact requirements.¹

Context

Updating pinned requirements is still done via nox -s requirements, but can also be done with uv lock --upgrade. Keeping this as a Nox session ensures that we have a consistent/canonical way to update uv.lock (i.e., by making sure we are using the same version of uv with the same options) both locally and in CI. With a Nox session, we could add in additional steps too (e.g., logging or exporting a documentation build requirements file).

There are some Nox sessions that will not use uv.lock, including the tests that run against the lowest versions of direct dependencies. Consequently, breaking changes in new versions of indirect dependencies could cause spontaneous CI failures. If this happens more than ∼twice per year, we might be able to create a separate uv.lock or requirements file for the lowest direct dependencies.

This PR does not substantively change the GitHub workflow to update pinned requirements that is run weekly to quarantine new versions of dependencies and make sure that CI for other PRs does not get spontaneous failures due to breaking changes in upstream dependencies.

Closes #2852. Closes #2940.

Tasks

Whilst uv.lock is described as a "universal" lockfile, it is frankly planetary at best. 🪐 ↩

codecov · 2025-01-08T23:00:01Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 94.61%. Comparing base (422bded) to head (10773fe).
Report is 258 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2937      +/-   ##
==========================================
- Coverage   95.41%   94.61%   -0.80%     
==========================================
  Files         107      107              
  Lines        9662     9662              
  Branches     1462     1462              
==========================================
- Hits         9219     9142      -77     
- Misses        257      327      +70     
- Partials      186      193       +7

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...instead of the pinned requirements files in `ci_requirements/` that we've been using up until now.

Since uv.lock is about 330 KB, it's probably worth excluding from source distributions and wheels to keep sizes smaller. It'll still be included in Zenodo uploads.

namurphy · 2025-02-24T18:03:19Z

@sapols, might you be interested in reviewing this PR to check out some fun infrastructure improvements?

The purpose of this PR is to pin the dependencies used in PlasmaPy's CI and doc builds with uv lock. The uv.lock files is similar to the requirements.txt like files we have been using, but uv.lock stores requirements information for multiple versions of Python, multiple operating systems, and multiple dependency sets in a single file. Every Monday, an automated PR updates uv.lock to make sure that the tests still pass with new versions of the dependencies. This setup may be helpful for other packages in PyHC since changes to uv.lock help identify which upstream packages that may be responsible for newly failing tests.

rocco8773 · 2025-02-26T23:39:49Z

  - These files are updated periodically via pull requests created by a
    GitHub workflow to `update pinned requirements`_.


Note: This link currently takes you to the GitHub Action page (https://github.com/PlasmaPy/PlasmaPy/actions/workflows/update-pinned-reqs.yml) instead of the actual workflow script (https://github.com/PlasmaPy/PlasmaPy/blob/main/.github/workflows/update-pinned-reqs.yml).

[Opinion] To me it makes more sense to link to the script and not the Action. In any case this will not affect this PR.

rocco8773 · 2025-02-26T23:43:18Z

  "numpydoc >= 1.7.0",
  "pillow >= 10.4.0",
-  "pygments >= 2.18.0",
+  "pygments == 2.18.0",


You made a comment in the the .github/content/update-requirements-pr-bocy.md that a PR should be opened to remove an upper bound on a dependency if one is add. Should this also be true if we freeze == a dependency?

Or maybe we only do this for install requirements (i.e. not tests, docs, etc.).

Should this also be true if we freeze == a dependency?

Yes! I'll need to update that.

address this ⬆️

rocco8773 · 2025-02-26T23:48:38Z

 maxpython = max(supported_python_versions)
 minpython = min(supported_python_versions)


Note: The supported_python_versions can easily get out of date with pyproject.toml. Are there breadcrumbs to ensure this gets updated when pyproject.toml gets updated? Or, is there a way to scrape pyproject.toml for this info?

I've been thinking the same thing! I did see an example noxfile.py somewhere that scraped pyproject.toml to get the supported versions of Python, but haven't had it be a high priority since I've been pretty thorough when dropping & adding versions of Python. I raised #2954 so we don't forget.

rocco8773 · 2025-02-26T23:51:51Z


-    version : str
-        The supported version of Python.
+uv_requirement = "uv >= 0.6.1"


uv is not listed as a package dependency, should it be? If uv is included as a dependency, then this line can get out of sync easily.

I have been wondering the same thing! I've seen it recommended that uv be installed completely independently of Python, which makes sense since uv can be used to install and manage multiple versions of Python at once.

uv needs to get installed first because it's what is used to install the dependencies in the tests. I put the uv requirement in here explicitly as a safeguard so that running nox -s docs will work even if uv hasn't been installed separately.

I'm going to need to take a bit more time to think about it! 😅

rocco8773 · 2025-02-27T00:04:15Z

+doc_build_dir = "$READTHEDOCS_OUTPUT" if running_on_rtd else "docs/build/html"
+
+if running_on_rtd:
+    rtd_output_path = pathlib.Path(os.environ.get("READTHEDOCS_OUTPUT")) / "html"
+    rtd_output_path.mkdir(parents=True, exist_ok=True)
+    doc_build_dir = str(rtd_output_path)
+else:
+    doc_build_dir = "docs/build/html"


Whenever we build the docs the build directory is docs/_build (with an underscore), not docs/build. That's how the make files are constructed.

This build directory is a bit arbitrary though. However, this would make the build directory different if you built with make versus nox.

Also, this block can be streamlined more...

Suggested change

doc_build_dir = "$READTHEDOCS_OUTPUT" if running_on_rtd else "docs/build/html"

if running_on_rtd:

rtd_output_path = pathlib.Path(os.environ.get("READTHEDOCS_OUTPUT")) / "html"

rtd_output_path.mkdir(parents=True, exist_ok=True)

doc_build_dir = str(rtd_output_path)

else:

doc_build_dir = "docs/build/html"

doc_build_dir = "docs/build/html"

if running_on_rtd:

rtd_output_path = pathlib.Path(os.environ.get("READTHEDOCS_OUTPUT")) / "html"

rtd_output_path.mkdir(parents=True, exist_ok=True)

doc_build_dir = str(rtd_output_path)

rocco8773

I left a few minor comments that highlight some potential (unrelated 🤷‍♂️) issues, but nothing I think really holds up this PR.

With my limited knowledge of how uv and nox works, this looks good to me. There might be some subtleties I'm missing, but if it works it works!

namurphy · 2025-02-27T02:34:42Z

@rocco8773 — Thank you for the very helpful review!

namurphy · 2025-04-01T22:22:58Z

Some exciting news for the pythoniverse is that PEP 751 was approved yesterday, which defines a standard for pylock.toml lock files. They will be kind of like a next gen requirements.txt file.

I'm inclined to stick with uv.lock as PlasmaPy's primary lockfile since:

uv.lock is more fully featured than pylock.toml
uv is being very actively developed and has a lot of really helpful tooling built around uv.lock
PlasmaPy uses the lockfile only internally for running tests and building docs, so the lockfile isn't used by end users.

It may be helpful to export pylock.toml from uv.lock, since that might be useful to have in PlasmaPy Zenodo uploads.

namurphy added 2 commits January 8, 2025 17:54

Un-ignore uv.lock files

a2b7661

Add uv.lock from running

5ca4e7f

namurphy added prototype 🏗️ Trying out an implementation on a trial basis requirements Related to updating requirements nox Related to the nox automation software labels Jan 8, 2025

github-actions Bot added the maintenance General updates to package infrastructure label Jan 8, 2025

namurphy added 3 commits January 8, 2025 19:31

Update uv.lock

0f34f1e

Make nox -s requirements generate uv.lock

2352652

...instead of the pinned requirements files in `ci_requirements/` that we've been using up until now.

Update Nox session for tests to use uv.lock

bc6e0ae

github-actions Bot added testing CI Related to continuous integration python Pull requests that update Python code labels Jan 9, 2025

namurphy added 6 commits January 8, 2025 19:41

Use uv.lock for Nox docs session

ae30c1a

Extract uv sync command into uv_sync

af941a0

Update doc installation for linkcheck session

0071c90

Fix a typo in noxfile.py

86d029a

Edit changelog: 2937.internal.rst

388818e

Exclude uv.lock from MANIFEST.in

0f37093

Since uv.lock is about 330 KB, it's probably worth excluding from source distributions and wheels to keep sizes smaller. It'll still be included in Zenodo uploads.

github-actions Bot added the packaging Related to packaging or distribution label Jan 9, 2025

namurphy removed the prototype 🏗️ Trying out an implementation on a trial basis label Jan 9, 2025

namurphy added 2 commits January 9, 2025 16:13

Remove Nox session to validate requirements files

c79f400

Update nox version & remove pre-commit from tests dependencies set

996e096

github-actions Bot added the GitHub Actions A continuous integration platform for automating tests and other tasks (see .github/ directory) label Jan 9, 2025

Use uv sync for mypy session

75936b9

namurphy mentioned this pull request Jan 13, 2025

Unpin pygments and sphinx-codeautolink requirements #2936

Merged

namurphy added 4 commits January 14, 2025 11:51

Merge branch 'main' of github.com:PlasmaPy/PlasmaPy into use-uv-lockfile

7a6a80c

Remove _get_requirements_filepath

6d8e086

Move & update validate_requirements

531841b

Update uv.lock

12ae3fd

namurphy requested review from pheuer and rocco8773 and removed request for pheuer February 22, 2025 01:36

namurphy mentioned this pull request Feb 24, 2025

Update pinned requirements 📍 #2953

Closed

Merge branch 'main' of github.com:PlasmaPy/PlasmaPy into use-uv-lockfile

9194770

rocco8773 reviewed Feb 26, 2025

View reviewed changes

rocco8773 reviewed Feb 27, 2025

View reviewed changes

rocco8773 approved these changes Feb 27, 2025

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namurphy mentioned this pull request Feb 27, 2025

Scrape pyproject.toml to get supported_python_versions in noxfile.py #2954

Open

namurphy added 9 commits February 27, 2025 09:47

nox -s requirements

0b41681

Change doc build directory to docs/_build/html

79174d6

Update error handling for missing landing page

f448631

Add link to workflow script

50dcb4c

Remove (probably) unnecessary line

a2cc08d

Correct landing page for RTD

758726f

Fix the fix for landing page location

2c3118b

Fix the fix of the fix

8778f7a

Update comment

10773fe

namurphy enabled auto-merge (squash) February 27, 2025 17:39

namurphy merged commit 0aaf93b into PlasmaPy:main Feb 27, 2025

namurphy mentioned this pull request Feb 27, 2025

Update caching and cache invalidation in CI #2955

Merged

1 task

namurphy mentioned this pull request Mar 10, 2025

Include a table of changes in the weekly pull request for updating uv.lock #2964

Merged

namurphy deleted the use-uv-lockfile branch April 1, 2025 20:10

rocco8773 mentioned this pull request May 8, 2025

Fix htmlzip build for public RTD builds #3010

Merged

		- These files are updated periodically via pull requests created by a
		GitHub workflow to `update pinned requirements`_.

		maxpython = max(supported_python_versions)
		minpython = min(supported_python_versions)

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