fix: pytest-cov and pytest-xdist were put under 'dev' instead of 'test'

[jandom]

Summary

#90 introduced pytest-cov and pytest-xdist but these were placed under the 'dev' instead of the 'test' dependency group.

Changes

• Move the deps to the correct group
• Add pytest-benchmark, because we'll need that later anyway for perf measurements

Related Issues

Testing

• https://github.com/aqlaboratory/openfold-3/actions/runs/21168437686 manually trigger to pickup the updated workflow with a coverage.xml artifact

Other Notes

[jandom]

Before the fix locally

docker run --rm -it docker.io/library/openfold-docker:test

==========
== CUDA ==
==========

CUDA Version 12.1.1

Container image Copyright (c) 2016-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

This container image and its contents are governed by the NVIDIA Deep Learning Container License.
By pulling and using the container, you accept the terms and conditions of this license:
https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license

A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience.

WARNING: The NVIDIA Driver was not detected.  GPU functionality will not be available.
   Use the NVIDIA Container Toolkit to start this container with GPU support; see
   https://docs.nvidia.com/datacenter/cloud-native/ .

(openfold3) root@9d0451d61f47:/opt/openfold3# pytest openfold3/tests -vvv -n auto --cov=openfold3 --cov-report=xml
[2026-01-19 14:17:36,197] [WARNING] [real_accelerator.py:209:get_accelerator] Setting accelerator to CPU. If you have GPU or other accelerator, we were unable to detect it.
ERROR: usage: pytest [options] [file_or_dir] [file_or_dir] [...]
pytest: error: unrecognized arguments: -n --cov=openfold3 --cov-report=xml
  inifile: /opt/openfold3/pyproject.toml
  rootdir: /opt/openfold3

After the fix locally

docker run --rm -it docker.io/library/openfold-docker:test

==========
== CUDA ==
==========

CUDA Version 12.1.1

Container image Copyright (c) 2016-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

This container image and its contents are governed by the NVIDIA Deep Learning Container License.
By pulling and using the container, you accept the terms and conditions of this license:
https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license

A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience.

WARNING: The NVIDIA Driver was not detected.  GPU functionality will not be available.
   Use the NVIDIA Container Toolkit to start this container with GPU support; see
   https://docs.nvidia.com/datacenter/cloud-native/ .

(openfold3) root@ec7e9a71c0b6:/opt/openfold3# pytest openfold3/tests -vvv -n auto --cov=openfold3 --cov-report=xml
/opt/conda/envs/openfold3/lib/python3.12/site-packages/pytest_benchmark/logger.py:44: PytestBenchmarkWarning: Benchmarks are automatically disabled because xdist plugin is active.Benchmarks cannot be performed reliably in a parallelized environment.
  warner(PytestBenchmarkWarning(text))
==================================================== test session starts ====================================================
platform linux -- Python 3.12.12, pytest-9.0.2, pluggy-1.6.0 -- /opt/conda/envs/openfold3/bin/python3.12
cachedir: .pytest_cache
benchmark: 5.2.3 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000)
rootdir: /opt/openfold3
configfile: pyproject.toml
plugins: benchmark-5.2.3, xdist-3.8.0, cov-7.0.0
initialized: 4/4 workers

[jnwei]

Overall looks good! Thanks for the quick fix

I went to check the action log associated with the most recent commit. It look likes no code coverage artifact was generated for this run.

Could you double check the path of the coverage report and see that it matches with the argument provided to the upload action?

[jandom]

Agreed, that is a bit fishy – also the term coverage report didn't print anything (odd)

[jandom]

@jnwei this looks good – the manually triggered GH action has the correct artifact

https://github.com/aqlaboratory/openfold-3/actions/runs/21168437686#artifacts

[jnwei]

Awesome! Thanks for adding this

[jandom]

Very happy to – @sdvillal slight duplication with your PR because we added 'pytest-benchmark' but I don't think this will cause a huge amount of pain (you've probably dealt with most conflicts like this already)

[sdvillal]

I already merged this into the branch, and no worries about conflicts - we do not know when will we merge the big PR and we cannot stop the world until then :-)