Molara-Lab / Molara

Molara is a Python package for the visualization of chemical structures such as molecules or crystals. It provides a graphical user interface for importing structures from output files of popular computational chemistry software as well as for creating custom structures.
GNU General Public License v3.0
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Increase coverage of aos.py #447

Closed adrianusler closed 2 months ago

adrianusler commented 2 months ago

I have extended the testing of the calculate_aos() routine. Closes #446.

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codecov[bot] commented 2 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 85.81%. Comparing base (2f67644) to head (14a56dd).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #447 +/- ## ========================================== + Coverage 85.18% 85.81% +0.62% ========================================== Files 46 47 +1 Lines 3977 3982 +5 ========================================== + Hits 3388 3417 +29 + Misses 589 565 -24 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

ab5424 commented 2 months ago

@adrianusler numpy advises against using assert_array_almost_equal, could you replace it?

adrianusler commented 2 months ago

@adrianusler numpy advises against using assert_array_almost_equal, could you replace it?

Done! Ready to merge now @ab5424 @Michel-Heinz

ab5424 commented 2 months ago

Test failure is unrelated, merging @adrianusler

ab5424 commented 2 months ago

@adrianusler @Michel-Heinz For context, the test on windows py3.12 are failing because the corresponding matplotlib 3.9.1 wheel was deleted from pypi

adrianusler commented 2 months ago

@adrianusler @Michel-Heinz For context, the test on windows py3.12 are failing because the corresponding matplotlib 3.9.1 wheel was deleted from pypi

Thanks for letting us know @ab5424, I thought at first that I had messed something up :sweat_smile: Do you happen to know a way how we could fix this? Please excuse my lazy asking

ab5424 commented 2 months ago

We could pin matplotlib to <3.9.1 but since this affects so many other projects as well (as you can see in the discussion linked above) I can only assume that they will fix this in the next days.

tacaswell commented 2 months ago

The 3.9.1 wheels on windows would, depending on import order, cause segfaults, see https://github.com/matplotlib/matplotlib/issues/28551#issuecomment-2266699619.

We deleted the bad wheels to avoid segfaults (which seemed like a good idea) but failed to anticipate that this would cause downstream projects to start trying to build mpl from source instead of pulling the 3.9.0 wheel. We have now yanked the whole 3.9.1 release to fix these problems and will get 3.9.2 out as quick as we can.

To prevent this sort of thing in the future (trying to build something from source when you are not prepared to do so) I suggest using matplotlib --only-binary "matplotlib" in your requirements file (which may be a good practice for all wheels that have extensions).

Sorry for the trouble.


In general, if you want to pin to avoid a bad release, I suggest using package!=X.Y.Z (e.g. matplotlib!=3.9.1 so that you do not have to remember to go back and remove the pin later.