Bugfix: Small Bugfix for polar flatten simulation

[CSSFrancis]

Description of the change

It seems like we weren't doing a great job of masking values etc which when doing a orientation map could have some pretty big impacts.

We should make a bug patch release probably asap.

Progress of the PR

• Docstrings for all functions
• Unit tests with pytest for all lines
• Clean code style by running black

[Copilot]

Pull Request Overview

This PR addresses a bug in the polar flatten simulation by updating the test expectations and refining the masking in the polar flatten conversion. Key changes include:

• Updating the test cases in Simulation2D to expect 8 spots instead of 1.
• Changing the hkls format in Simulation1D tests from string representations to numeric arrays.
• Refining the masking logic in polar flatten simulations and updating dependency versions.

Reviewed Changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
diffsims/tests/simulations/test_simulations2d.py	Updated test assertions to expect 8 spots and adjusted radial_axes values.
diffsims/tests/simulations/test_simulations1d.py	Changed hkl representation from string to numeric array.
diffsims/tests/generators/test_simulation_generator.py	Removed string-specific handling for hkls and updated progressbar assertions.
diffsims/simulations/simulation2d.py	Revised the masking logic in polar flatten simulations.
diffsims/simulations/simulation1d.py	Expanded plot function parameters and updated label formatting.
diffsims/generators/simulation_generator.py	Adjusted reciprocal lattice vector processing in 1D simulation.
.github/workflows/build.yml	Updated build dependencies.

Comments suppressed due to low confidence (2)

diffsims/tests/simulations/test_simulations2d.py:107

• The test now expects 8 spots per simulation rather than 1. Please double-check that the polar flatten simulation logic correctly maps the new coordinate length to the output arrays.

assert r_templates.shape == (1, 8)

diffsims/simulations/simulation2d.py:330

• [nitpick] Consider renaming the variable 'inten' to 'intensity' for clarity and consistency with the attribute name.

inten = v.intensity

[CSSFrancis]

pre-commit.ci autofix

[CSSFrancis]

@wiscott24 Does this fix your problem?

[CSSFrancis]

@viljarjf any chance that you can look at this? This fixes the failing tests with #235. Sorry it took me so long to get around to that. Also feel free to just ping me for stuff if I'm being slow. Sometimes I see things and mean to go back to it and forget :)

[viljarjf]

Seems good! There might be some merit to giving a warning if the phase is not symmetrically expanded, as the structure factors will not be correct otherwise. just something simple like

if len(phase.structure) != len(phase.expand_asymmetric_unit().structure):
    warnings.warn(...)

Otherwise this looks fine to me! I have made some changes to calculate_simulation2d in another draft PR, I can see if the same can be applied to simulation1d when I get around to finalizing it.

[wiscott24]

@wiscott24 Does this fix your problem?

Yes, thanks!

[CSSFrancis]

@viljarjf hmmm.

Should we just have something like:

if len(phase.structure) != len(phase.expand_asymmetric_unit().structure):
    phase = phase.expand_asymmetric_unit()

[viljarjf]

@viljarjf hmmm.

Should we just have something like:

if len(phase.structure) != len(phase.expand_asymmetric_unit().structure):
    phase = phase.expand_asymmetric_unit()

I'm not really sure. Users might want to only have certain atoms, to see how that might affect things? If so, they can use P1 I guess. On the other hand, I expect most users use a cif, in which case all atoms are present already. Displaying a warning is also not done in many places, outside of maybe orix warning you if it thinks you meant to use degrees=True, so this might seem out of place.

I say we can leave it for now, maybe move it to a seperate issue for further discussion. This is also a potential problem in 2D, ref #234