Update to uv by izzyknmi · Pull Request #592 · pySTEPS/pysteps

izzyknmi · 2026-11-03T12:57:26Z

This PR swaps Conda for uv.

Notes:

This PR adds formatting and import sorting to the tests, and so there are many reformatted files. These can be ignored for reviewing.
This PR does not pin versions of libraries in the pyproject.toml, so the uv.lock file is included. A separate PR will pin versions and the lock file can then be removed.

izzyknmi · 2026-11-04T13:24:33Z

Really struggling to get everything installed correctly with uv. The issues seem to be GDAL-related:

Ubuntu: everything installs OK, but when the tests try to run, the error is No module named '_gdal_array'. (In fact, on my Linux laptop, this also happens! So at least I can debug locally.)
MacOS: GDAL can't be installed at version 3.4.1 from Homebrew, but GDAL versions need to match, and we have pinned GDAL at 3.4.1 in the pyproject.
Windows: honestly, I have no idea what the problem here is. It's definitely GDAL related but I have no idea how to get GDAL on a Windows machine anyway.

…pyproject

codecov · 2026-11-04T14:55:07Z

Codecov Report

❌ Patch coverage is 83.83838% with 128 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.67%. Comparing base (f1a3af1) to head (5b91ef8).

Files with missing lines	Patch %	Lines
pysteps/verification/lifetime.py	0.00%	39 Missing ⚠️
pysteps/visualization/spectral.py	13.04%	20 Missing ⚠️
pysteps/visualization/basemaps.py	70.96%	18 Missing ⚠️
pysteps/utils/cleansing.py	83.67%	16 Missing ⚠️
pysteps/utils/conversion.py	94.11%	9 Missing ⚠️
pysteps/utils/transformation.py	93.02%	9 Missing ⚠️
pysteps/visualization/animations.py	91.83%	8 Missing ⚠️
pysteps/utils/images.py	88.00%	3 Missing ⚠️
pysteps/scripts/run_vel_pert_analysis.py	0.00%	2 Missing ⚠️
pysteps/scripts/fit_vel_pert_params.py	0.00%	1 Missing ⚠️
... and 3 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #592      +/-   ##
==========================================
- Coverage   84.99%   84.67%   -0.33%     
==========================================
  Files         172      172              
  Lines       15445    15397      -48     
==========================================
- Hits        13128    13037      -91     
- Misses       2317     2360      +43

Flag	Coverage Δ
unit_tests	`84.67% <83.83%> (-0.33%)`	⬇️

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RubenImhoff · 2026-11-04T20:25:52Z

Finally, we can probably ignore the codecov for now..

Co-authored-by: Ruben Imhoff <31476760+RubenImhoff@users.noreply.github.com>

izzyknmi · 2026-11-05T08:52:53Z

Hi @RubenImhoff! Thanks for your check. I still want to update some documentation, but I think I will do that in a separate PR.

Re: your questions:

One of the great things about uv is the dependency groups. If you take a look at pyproject.toml, there are dependencies and optional dependencies. Those libraries under dependencies are always installed. Optional dependencies are only installed with explicit commands (it's what the above line uv sync --all-extras does). These can be chosen one at a time as well -- this is why the GDAL section is entirely separate, so that it can be installed only if the user chooses they want to mess with GDAL. I've also added PyGrib as a separate dependency group since it seems like Windows has trouble with it.
I understand the issue with the reformatting, sorry about that. Since there's new formatting rules, the formatting tests wouldn't pass without doing the reformatting. In my teams we've always accepted this and made a note in the PR. Is that okay with you?

izzyknmi · 2026-11-05T08:55:19Z

Once this works, it might be good to still try pinning versions of libraries (see #527). I wanted some freedom for this step to make sure it all worked, but I'll probably make another PR with pinned versions.

RubenImhoff · 2026-11-05T09:24:27Z

Hi @RubenImhoff! Thanks for your check. I still want to update some documentation, but I think I will do that in a separate PR.

Re: your questions:

One of the great things about uv is the dependency groups. If you take a look at pyproject.toml, there are dependencies and optional dependencies. Those libraries under dependencies are always installed. Optional dependencies are only installed with explicit commands (it's what the above line uv sync --all-extras does). These can be chosen one at a time as well -- this is why the GDAL section is entirely separate, so that it can be installed only if the user chooses they want to mess with GDAL. I've also added PyGrib as a separate dependency group since it seems like Windows has trouble with it.

I understand the issue with the reformatting, sorry about that. Since there's new formatting rules, the formatting tests wouldn't pass without doing the reformatting. In my teams we've always accepted this and made a note in the PR. Is that okay with you?

Perfect, @izzyknmi!

Regarding 1, nice, that is ideal! Nice to have this well described in the documentation (but I know you are working on that).
Regarding 2, no worries, this works for now. :)

izzyknmi · 2026-11-05T09:32:43Z

Tests are passing and from my side, this PR is ready! I leave it to @RubenImhoff and @kmuehlbauer to merge it.

kmuehlbauer

Nice! Great work @izzyknmi, thanks for the ping.

We might want to let the test workflow depend on the formatter check workflow.

Then, those test would only be run, if the formatter checks return successful.

In in person chat @RubenImhoff was in favour of implementing such dependency.

Co-authored-by: Kai Mühlbauer <kmuehlbauer@wradlib.org>

This reverts commit df8a57a.

kmuehlbauer

Quite an undertaking! No more complaints from my side!

RubenImhoff · 2026-11-05T10:37:02Z

I'll merge the PR once all test pass. Great work!
@izzyknmi and @kmuehlbauer, any remaining things that should prevent me from merging?

izzyknmi · 2026-11-05T10:39:04Z

I'll merge the PR once all test pass. Great work! @izzyknmi and @kmuehlbauer, any remaining things that should prevent me from merging?

@RubenImhoff All good here! I'll make two new PR's after this, one for pinning versions in pyproject.toml and one for documentation.

kmuehlbauer · 2026-11-05T10:58:11Z

any remaining things that should prevent me from merging?

Not from my side. Seems good to go.

izzyknmi · 2026-11-10T13:07:09Z

The promised PR to pin versions and remove uv.lock is #618.

izzyknmi added 18 commits November 3, 2026 13:37

Add pyproject.toml for use of uv

b7d5594

Update .pre-commit-config.yaml to use bandit and ruff

3099e97

Add pre-commit and apply the rules

a005416

Add ruff check to sort imports

a4b236e

Sort imports on all files

476d234

Rename workflow

e837697

Update workflow

52332a3

Fix dev dependencies

c44c517

Update uv lock

c4f1b52

Change black to bandit

87c2d9f

Move what can be moved from setup.py to pyproject.toml

e251d2f

Update readme to mention uv

d98272b

Update readme and contributing files with uv

c06a2e6

Update tests with uv

5ff1154

Update tests with uv, try 2

1fe364d

Update tests with uv, try 3

7661b45

Update tests with uv, try 4

c75872b

Update tests with uv, try 5

7390cac

This was referenced Nov 3, 2026

Modernization of pysteps needed #583

Closed

Make pyproject.toml single source of truth for dependencies with version pinning #527

Closed

izzyknmi added 4 commits November 4, 2026 12:45

Update tests with uv: try 7, gdal installed after numpy

8645d1f

Merge branch 'main' into update-to-uv

4d09a79

Format after merge

012ae58

Get the testing to trigger

8e062f8

izzyknmi added 4 commits November 4, 2026 15:11

Update gitignore with test files

ad631fc

Update bandit to work with pyproject

341f9ef

Add separate GDAL installer that checks local install and adds it to …

2b55918

…pyproject

Add uv run back around bandit in the tests!

8cfff6a

RubenImhoff approved these changes Nov 4, 2026

View reviewed changes

ladc mentioned this pull request Nov 4, 2026

Update contributing guidelines #598

Merged

izzyknmi and others added 2 commits November 5, 2026 09:45

Update CONTRIBUTING.rst

267e316

Co-authored-by: Ruben Imhoff <31476760+RubenImhoff@users.noreply.github.com>

Update pyproject.toml

56c255f

Co-authored-by: Ruben Imhoff <31476760+RubenImhoff@users.noreply.github.com>

kmuehlbauer reviewed Nov 5, 2026

View reviewed changes

Comment thread .github/workflows/formatting_checks.yml Resolved

Comment thread .github/workflows/test_pysteps.yml Resolved

ladc requested a review from jsvatos November 5, 2026 09:49

Update .github/workflows/test_pysteps.yml

0cab3dd

Co-authored-by: Kai Mühlbauer <kmuehlbauer@wradlib.org>

kmuehlbauer reviewed Nov 5, 2026

View reviewed changes

Comment thread uv.lock Resolved

izzyknmi added 4 commits November 5, 2026 10:52

Update test names

65fd323

Remove uv.lock from the repo and add it to gitignore

df8a57a

Revert "Remove uv.lock from the repo and add it to gitignore"

120a0e2

This reverts commit df8a57a.

Merge tests into one workflow

dc78d90

kmuehlbauer approved these changes Nov 5, 2026

View reviewed changes

kmuehlbauer mentioned this pull request Nov 5, 2026

MNT: add lint workflow in CI with black/ruff #605

Closed

RubenImhoff merged commit d4631ce into pySTEPS:main Nov 5, 2026
7 checks passed

izzyknmi deleted the update-to-uv branch November 5, 2026 11:04

kmuehlbauer mentioned this pull request Nov 5, 2026

Draft: dataset validator #594

Draft

jsvatos approved these changes Nov 5, 2026

View reviewed changes

This was referenced Nov 7, 2026

Migrate static metadata to pyproject.toml for improved packaging standards #487

Closed

no versions specified in requirements.txt cause unpredictable failures due to dependency upgrades. #526

Closed

kmuehlbauer mentioned this pull request Nov 9, 2026

Fix documentation builds #613

Open

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