CI: Use uv to test with lowest supported dependency versions #714

danielhollas · 2025-11-25T19:41:06Z

Instead of specifying aiida-core version explicitly when running unit tests, we utilize the uv's --resolution parameter to tell it whether we want to test we highest or lowest versions of dependencies. This will be helpful for #644 so we can test both ipywidgets 7.x and 8.x

See more details in the corresponding change in aiida-core: aiidateam/aiida-core#6940

To make this work I needed to bump minimum versions of some packages, most notably aiida-core from 2.1 to 2.2 (see comment below why this was necessary). We could do a different workaround, but I think it is fair to drop support for 2.1 at this point. :-) The corresponding full-stack:aiida-2.1.2 image has been published 3 years ago and hopefully nobody is using it.

…ependency versions

codecov · 2025-11-25T19:44:51Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.31%. Comparing base (3c65b82) to head (91c1a09).

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #714      +/-   ##
==========================================
+ Coverage   84.29%   84.31%   +0.02%     
==========================================
  Files          18       18              
  Lines        3584     3584              
==========================================
+ Hits         3021     3022       +1     
+ Misses        563      562       -1

Flag	Coverage Δ
python-3.11	`84.29% <ø> (ø)`
python-3.9	`84.32% <ø> (+0.02%)`	⬆️

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danielhollas · 2025-11-25T19:56:53Z

Marking as draft, there are some failing tests...

This reverts commit 267c240.

danielhollas · 2025-11-26T00:31:35Z

setup.cfg

    widgetsnbextension<3.6.3
    pymysql~=0.9
-    nglview~=3.0
+    nglview~=3.0,>=3.0.8


Earlier patch versions failed to build on python 3.9: https://github.com/aiidalab/aiidalab-widgets-base/actions/runs/19681981549/job/56377980039

danielhollas · 2025-11-26T00:33:24Z

setup.cfg

    ansi2html~=1.6
    ase~=3.18
-    bokeh~=2.0
+    bokeh~=2.4


Earlier versions were causing one test to fail with this stack trace:

tests/test_viewers.py:39: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ aiidalab_widgets_base/viewers.py:60: in viewer return _viewer(obj, **kwargs) aiidalab_widgets_base/viewers.py:1635: in __init__ from bokeh.io import output_notebook, show .venv/lib/python3.9/site-packages/bokeh/io/__init__.py:23: in <module> from .export import export_png, export_svgs .venv/lib/python3.9/site-packages/bokeh/io/export.py:33: in <module> from ..document import Document .venv/lib/python3.9/site-packages/bokeh/document/__init__.py:35: in <module> from .document import DEFAULT_TITLE ; DEFAULT_TITLE .venv/lib/python3.9/site-packages/bokeh/document/document.py:49: in <module> from ..core.templates import FILE > from jinja2 import Environment, FileSystemLoader, Markup E ImportError: cannot import name 'Markup' from 'jinja2' (/home/runner/work/aiidalab-widgets-base/aiidalab-widgets-base/.venv/lib/python3.9/site-packages/jinja2/__init__.py) .venv/lib/python3.9/site-packages/bokeh/core/templates.py:42: ImportError

danielhollas · 2025-11-26T00:34:50Z

tests/test_viewers.py

+        "cif": """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""",
+    }
+
+    # Compatibility with old ASE versions <3.23


See #627 (comment)

danielhollas · 2025-11-26T00:36:46Z

setup.cfg

    bumpver>=2023.1129
    pgtest~=1.3
-    pre-commit>=3.5
+    pre-commit>=4.0


I think this version bump in the end was not needed, but probably doesn't hurt. Happy to revert.
(I still maintain we should not be installing pre-commit into every venv, it should instead be installed globally via pipx or uv tool install)

danielhollas · 2025-11-26T00:38:43Z

setup.cfg

 install_requires =
    PyCifRW~=4.4
-    aiida-core>=2.1,<3
+    aiida-core>=2.2,<3


See the pyyaml build error for Python 3.11: https://github.com/aiidalab/aiidalab-widgets-base/actions/runs/19682431292/job/56379504709

Build error

× Failed to build `pyyaml==5.4.1` ├─▶ The build backend returned an error ╰─▶ Call to `setuptools.build_meta.build_wheel` failed (exit status: 1) [stdout] running egg_info writing lib3/PyYAML.egg-info/PKG-INFO writing dependency_links to lib3/PyYAML.egg-info/dependency_links.txt writing top-level names to lib3/PyYAML.egg-info/top_level.txt [stderr] /home/runner/work/_temp/setup-uv-cache/builds-v0/.tmpAnDw32/lib/python3.11/site-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() Traceback (most recent call last): File "<string>", line 14, in <module> File "/home/runner/work/_temp/setup-uv-cache/builds-v0/.tmpAnDw32/lib/python3.11/site-packages/setuptools/build_meta.py", line 331, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=[]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/runner/work/_temp/setup-uv-cache/builds-v0/.tmpAnDw32/lib/python3.11/site-packages/setuptools/build_meta.py", line 301, in _get_build_requires self.run_setup() File "/home/runner/work/_temp/setup-uv-cache/builds-v0/.tmpAnDw32/lib/python3.11/site-packages/setuptools/build_meta.py", line 317, in run_setup exec(code, locals()) File "<string>", line 271, in <module> File "/home/runner/work/_temp/setup-uv-cache/builds-v0/.tmpAnDw32/lib/python3.11/site-packages/setuptools/__init__.py", line 115, in setup return distutils.core.setup(**attrs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/runner/work/_temp/setup-uv-cache/builds-v0/.tmpAnDw32/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 186, in setup return run_commands(dist) ^^^^^^^^^^^^^^^^^^ File "/home/runner/work/_temp/setup-uv-cache/builds-v0/.tmpAnDw32/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 202, in run_commands dist.run_commands() File "/home/runner/work/_temp/setup-uv-cache/builds-v0/.tmpAnDw32/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 1002, in run_commands self.run_command(cmd) File "/home/runner/work/_temp/setup-uv-cache/builds-v0/.tmpAnDw32/lib/python3.11/site-packages/setuptools/dist.py", line 1102, in run_command super().run_command(command) File "/home/runner/work/_temp/setup-uv-cache/builds-v0/.tmpAnDw32/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command cmd_obj.run() File "/home/runner/work/_temp/setup-uv-cache/builds-v0/.tmpAnDw32/lib/python3.11/site-packages/setuptools/command/egg_info.py", line 312, in run self.find_sources() File "/home/runner/work/_temp/setup-uv-cache/builds-v0/.tmpAnDw32/lib/python3.11/site-packages/setuptools/command/egg_info.py", line 320, in find_sources mm.run() File "/home/runner/work/_temp/setup-uv-cache/builds-v0/.tmpAnDw32/lib/python3.11/site-packages/setuptools/command/egg_info.py", line 543, in run self.add_defaults() File "/home/runner/work/_temp/setup-uv-cache/builds-v0/.tmpAnDw32/lib/python3.11/site-packages/setuptools/command/egg_info.py", line 581, in add_defaults sdist.add_defaults(self) File "/home/runner/work/_temp/setup-uv-cache/builds-v0/.tmpAnDw32/lib/python3.11/site-packages/setuptools/command/sdist.py", line 109, in add_defaults super().add_defaults() File "/home/runner/work/_temp/setup-uv-cache/builds-v0/.tmpAnDw32/lib/python3.11/site-packages/setuptools/_distutils/command/sdist.py", line 245, in add_defaults self._add_defaults_ext() File "/home/runner/work/_temp/setup-uv-cache/builds-v0/.tmpAnDw32/lib/python3.11/site-packages/setuptools/_distutils/command/sdist.py", line 330, in _add_defaults_ext self.filelist.extend(build_ext.get_source_files()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "<string>", line 201, in get_source_files File "/home/runner/work/_temp/setup-uv-cache/builds-v0/.tmpAnDw32/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 131, in __getattr__ raise AttributeError(attr) AttributeError: cython_sources hint: This usually indicates a problem with the package or the build environment. help: `pyyaml` (v5.4.1) was included because `aiidalab-widgets-base[dev]` (v2.4.0) depends on `pre-commit` (v4.0.0) which depends on `pyyaml`

CI: Use uv --resolution=lowest-direct to test with lowest supported d…

c5f76a7

…ependency versions

danielhollas requested a review from yakutovicha November 25, 2025 19:41

danielhollas added 3 commits November 25, 2025 19:48

Fix nglview build failure?

838e6c0

Bump pre-commit to fix 3.11 build

7ab9727

Bump minimum ipywidgets version

267c240

danielhollas marked this pull request as draft November 25, 2025 19:56

danielhollas added 7 commits November 25, 2025 19:58

Revert "Bump minimum ipywidgets version"

32d36b7

This reverts commit 267c240.

Install povray after python packages

a74978d

Bump aiida-core min. version to 2.2

7799e99

Bump minimum bokeh version

532f9f0

Bump bokeh again

a3eedcf

Make test compatible with old ASE version

f56f5b1

Even bigger bump for bokeh

0039c15

danielhollas force-pushed the test-lowest-versions branch from cd3a0ae to 0039c15 Compare November 25, 2025 22:27

Bump docker tag to aiida-2.2.1

91c1a09

danielhollas marked this pull request as ready for review November 26, 2025 00:27

danielhollas commented Nov 26, 2025

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