bug: some github workflows are not triggered

[ycexiao]

Problem

Expected:

Actual:

Proposed solution

[ycexiao]

@sbillinge. codecov and pre-commit workflows are not triggered. Can you follow the steps in scikit-package documentation: setup pre-commit and scikit-package documentation: setup codecov and set them up?

[ycexiao]

@sbillinge

From https://github.com/PDF-bl/pdfbl.sequential/actions/runs/21682858461

check-news-item is triggered, but it fails before it can print the error message on the PR page.

check-news-item defined in release-scripts asks for write permission, but the action-bot in this repo only has read permission. The permission is not specified in any workflow files in this repo, and ChatGPT said it might be in

Where to change them (Repo level)

Go to: Repo → Settings → Actions → General → Workflow permissions

Org-level defaults (override repos)

If the repo is inside an organization:  Org → Settings → Actions → General

Please could you try this?

[sbillinge]

Please could you try this?

I did this one.

The codecov one is more complicated because the codecov website seems to have changed and the workflow is a bit different. I will have to figure it out.

[sbillinge]

OK, I think this should be fixed now. @ycexiao please can you check?

[ycexiao]

@sbillinge, compared to the one in diffpy repo, codecov/project is not activated. Could you please check it?
Expected:

Actual:

[sbillinge]

for some reason tests are failing on my local so I can't generate a coverage report to upload.

$ pytest --cov=pdfbl.sequential
=========================================================================== test session starts ===========================================================================
platform win32 -- Python 3.13.11, pytest-8.4.2, pluggy-1.5.0
rootdir: C:\Users\simon\dev\pdfbl.sequential
configfile: pyproject.toml
plugins: anyio-4.12.0, cov-7.0.0, env-1.2.0, mock-3.15.1, requests-mock-1.12.1, xonsh-0.22.0
collected 0 items / 2 errors

================================================================================= ERRORS ==================================================================================
________________________________________________________________ ERROR collecting tests/test_pdfadapter.py ________________________________________________________________
ImportError while importing test module 'C:\Users\simon\dev\pdfbl.sequential\tests\test_pdfadapter.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
..\..\micromamba\envs\r313\Lib\importlib\__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
tests\test_pdfadapter.py:5: in <module>
    from scipy.optimize import least_squares
E   ModuleNotFoundError: No module named 'scipy'
__________________________________________________________ ERROR collecting tests/test_sequential_cmi_runner.py ___________________________________________________________
ImportError while importing test module 'C:\Users\simon\dev\pdfbl.sequential\tests\test_sequential_cmi_runner.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
..\..\micromamba\envs\r313\Lib\importlib\__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
tests\test_sequential_cmi_runner.py:5: in <module>
    from pdfbl.sequential.sequential_cmi_runner import SequentialCMIRunner
E   ModuleNotFoundError: No module named 'pdfbl'
========================================================================= short test summary info =========================================================================
ERROR tests/test_pdfadapter.py
ERROR tests/test_sequential_cmi_runner.py
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 2 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
============================================================================ 2 errors in 0.77s ============================================================================
(

please could you see if you can figure out what is going on?

[ycexiao]

@sbillinge In here: https://app.codecov.io/github/pdf-bl/pdfbl.sequential/config, the project coverage is not configured, which I think is why it is missing.

Could you please configure it?

[ycexiao]

project coverate is available for pro plan. Considering there won't be much code (since it is a wrapper package for diffpy.cmi), I think we don't need the pro plan?

@sbillinge, if that is the case, 6 checks are expected, and I will close this issue as completed.

[sbillinge]

Let's leave it open. It would be good to get to the bottom of this. I don't understand what is going on because this is on the same plan that our other repos are on. At least is should be. It is not that important right now, but at some point it would be good to dig around and try and figure this out. I expect there is some setting somewhere in the org that needs tweaking. But we don't need this before the beamtime. Let's just leave the issue open and return to it later.

[ycexiao]

This issue is moved to 0.2.0 milestone since it is not required at the time.