Move dependency management to uv by molpopgen · Pull Request #590 · popsim-consortium/demes-python

molpopgen · 2026-03-13T15:45:31Z

Move contents from setup.[py|cfg] into pyproject.toml
Update github workflows
Delete old requirements files

codecov · 2026-03-13T15:47:11Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.06%. Comparing base (4bc3f95) to head (e9a6a59).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #590      +/-   ##
==========================================
- Coverage   99.81%   99.06%   -0.75%     
==========================================
  Files           5        5              
  Lines        1600     1600              
==========================================
- Hits         1597     1585      -12     
- Misses          3       15      +12

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molpopgen · 2026-03-13T16:27:33Z

Issues:

Our use of jupyter-book requires pinning ipython to a version that requires python >= 3.10. While it may be true that the package itself works as far back as 3.7, we do not test that that is true and it appears that current tooling includes the entire development environment as having the same minimum version.
It is not clear that dev.yaml is needed in the work flows any longer?
The window tests are failing sporadically.

molpopgen · 2026-03-13T19:40:30Z

@grahamgower @apragsdale -- this is ready for a look.

I have shoe-horned most tasks into a place where they now work. The problem is the windows tests. They fail because the modules in demes-spec are not finding ruamel. I cannot reproduce this issue locally, which makes sense because I'm on Linux and the Linux tests are also passing in CI.

grahamgower · 2026-03-14T01:34:55Z

The failing tests are in test_cli.py and test_spec.py. What these tests have in common is that they use subprocess.* to run python. These subprocesses are unable to import basic dependencies such as attr and ruamel, so my guess is that the uv virtual environment is not active for the subprocess. I don't think the previous tests used a virtual environment, and so didn't encounter this issue? This is likely a common problem experienced by other projects using uv and running cli tests, so it might be worth finding out what others have done here.

grahamgower

There seems to be a lot of duplication between the _setup.cfg and pyproject.toml - is this intentional? And what's the role of _setup.cfg here, versus setup.cfg? Which files are generated by uv? Is it just uv.lock?

grahamgower · 2026-03-14T01:39:31Z

_setup.cfg

+long_description_content_type = text/markdown
+url = https://github.com/popsim-consortium/demes-python
+classifiers =
+    Development Status :: 4 - Beta


I reckon we're out of beta now.

grahamgower · 2026-03-14T01:43:43Z

pyproject.toml

+    "Topic :: Scientific/Engineering :: Bio-Informatics"
+]
+
+requires-python = ">=3.10"


This doesn't match the _setup.cfg file.

Correct -- the _setup file is to rename it so that it doesn't confuse uv / conflict with pyproject.

More generally, our pinning to 3.7 was wrong due to other pinned dependencies that this PR revealed. (Briefly, our pinnings related to docs required >= 3.10).

Demes can be installed and used on 3.7, but building the docs on CI needed a more recent version due to jupyterbook annoyances. I don't think that was incorrect. That said, I don't mind if you want to bump things to the latest supported python version.

If we want to keep a pinning to >= 3.7 then we would need to figure out how to downgrade the jupyter-book dependencies. But I do think that we should just try to track currently supported Python versions. Moving forward, uv will force this on use b/c a given uv version will only support a handful of Python versions.

grahamgower · 2026-03-14T01:44:07Z

pyproject.toml

+readme = {file = "README.md", content-type = "text/markdown"}
+license = {text = "ISC"}
+classifiers = [
+    "Development Status :: 4 - Beta",


No longer in beta.

Our version number is still < 1??

Nevertheless, I'd argue demes is now Development Status :: 5 - Production/Stable (https://pypi.org/classifiers/).

molpopgen · 2026-03-15T17:19:50Z

There seems to be a lot of duplication between the _setup.cfg and pyproject.toml - is this intentional? And what's the role of _setup.cfg here, versus setup.cfg? Which files are generated by uv? Is it just uv.lock?

_setup.cfg is to move setup.cfg out of the way. It is currently expected that most/all of that material is now in pyproject. _setup.cfg will be deleted prior to merging. setup.cfg itself now only contains config for flake8 and mypy. The former does not support pyproject configuration** and I had trouble getting the latter working but will try again.

**This situation is unfortunate and can be "fixed" by adding a dependency on flake8-pyproject

uv.lock is the only file generated by uv.

molpopgen · 2026-03-15T17:28:21Z

The failing tests are in test_cli.py and test_spec.py. What these tests have in common is that they use subprocess.* to run python. These subprocesses are unable to import basic dependencies such as attr and ruamel, so my guess is that the uv virtual environment is not active for the subprocess. I don't think the previous tests used a virtual environment, and so didn't encounter this issue? This is likely a common problem experienced by other projects using uv and running cli tests, so it might be worth finding out what others have done here.

agreed, but the issue remains that it is windows-specific. Does anyone here have the ability to locally explore this problem?

jeromekelleher · 2026-03-15T20:09:49Z

If they're only failing on windows I'd consider pytest.skip - most likely not a real problem just annoying infrastructure differences

molpopgen · 2026-03-16T15:46:37Z

A note for everyone listening that may save you future pain:

Any call to something like subprocess.run should use sys.executable (in an f-string, and after import sys) to make sure that you are using the correct Python version! (This change fixes the windows tests issue. Google was no help here.)

molpopgen · 2026-03-16T16:00:55Z

I think there is one outstanding issue remaining: we have a dev.yaml test file that tests a pip-install of the developer dependencies. I argue that we remove this and all the requirements files. Developers can/should now use uv locally, and the requirements files are pinned and thus difficult to maintain.

molpopgen · 2026-03-16T16:15:03Z

I think there is one outstanding issue remaining: we have a dev.yaml test file that tests a pip-install of the developer dependencies. I argue that we remove this and all the requirements files. Developers can/should now use uv locally, and the requirements files are pinned and thus difficult to maintain.

Actually, we may be able to keep the CI file but redirect pip to look at pyproject.toml....

* move dependency management to uv * move (most) config info to pyproject.toml * bump minimum supported Python version * bump development status metadata * update github workflows * remove requirements files

molpopgen force-pushed the uv branch 5 times, most recently from d9078b3 to 3923460 Compare March 13, 2026 19:25

molpopgen marked this pull request as ready for review March 13, 2026 19:39

grahamgower reviewed Mar 14, 2026

View reviewed changes

molpopgen force-pushed the uv branch 3 times, most recently from c9c4e0f to bf8f3f8 Compare March 16, 2026 15:30

molpopgen force-pushed the uv branch from d3db508 to bb2c55f Compare March 16, 2026 15:56

molpopgen force-pushed the uv branch from 5182458 to 36488da Compare March 16, 2026 16:52

Update project configuration

e9a6a59

* move dependency management to uv * move (most) config info to pyproject.toml * bump minimum supported Python version * bump development status metadata * update github workflows * remove requirements files

molpopgen force-pushed the uv branch from 36488da to e9a6a59 Compare March 16, 2026 17:13

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