Add pyxtal wrapper

[pmrv]

PyXtal is a similar structure generation tool as RandSPG, but (imo) more convenient and comprehensive. I've made it a mandatory dependency, because I saw no reason not to, but I can wrap it in ImportAlarms as well.

[pmrv]

It seems I have to make it optional as mamba for some reason refuses to install another dependency for python compat reasons, even though that dependency (pyshtools) is available for up to python 3.8.

[jan-janssen]

Is it possible to add pyxtal to https://github.com/pyiron/structuretoolkit ?

[jan-janssen]

The issue is that pyxtal requires pyshtools ==4.10 which does not support Apple ARM and Python 3.11 while pyshtools ==4.10.3 does. I raised an issue up stream to see if it is possible to add support for pyshtools ==4.10.3 : MaterSim/PyXtal#222

[pmrv]

Is it possible to add pyxtal to https://github.com/pyiron/structuretoolkit ?

Sure, I hadn't seen we had also moved the constructors over there.

[jan-janssen]

Sure, I hadn't seen we had also moved the constructors over there.

As long as everything is ASE compatible, then it can go to structuretoolkit. The idea is that people who are already familiar with ASE can use the structuretoolkit without being forced to switch to pyiron completely. Once they like structuretoolkit then they might also be motivated to try pyiron.

[jan-janssen]

======================================================================
ERROR: test_return_value (atomistics.structure.test_pyxtal.TestPyxtal)
pyxtal should either return Atoms or StructureStorage, depending on arguments
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/tests/atomistics/structure/test_pyxtal.py", line 32, in test_return_value
    self.assertIsInstance(pyxtal(1, species=['Fe'], num_ions=[1], repeat=5),
  File "/usr/share/miniconda3/envs/my-env/lib/python3.9/unittest/case.py", line 1258, in assertIsInstance
    if not isinstance(obj, cls):
TypeError: isinstance() arg 2 must be a type or tuple of types

----------------------------------------------------------------------

[coveralls]

Pull Request Test Coverage Report for Build 7903300471

Details

• 0 of 50 (100.0%) changed or added relevant lines in 2 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage increased (+0.02%) to 93.172%

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Totals
Change from base Build 7898937283:	0.02%
Covered Lines:	14205
Relevant Lines:	15246

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💛 - Coveralls

[jan-janssen]

@pmrv With the new release of pyxtal all the tests finally pass, so I think we can move ahead with the integration in pyiron_atomistics or preferable structuretoolkit.

[pmrv]

Great, thanks for fixing the tests as well. I'll move the core functionality over to structuretoolkit next week then.

[pmrv]

Depends on pyiron/structuretoolkit#24

[jan-janssen]

I am a bit reluctant to make pyxtal a required dependency as long as the environment doubles - as discussed in pyiron/structuretoolkit#46 .

[jan-janssen]

This is also the reason why the upgrade from structuretoolkit is currently delayed #1124

[pmrv]

Sure, this can wait until a new version of pyxtal is released.

[jan-janssen]

structuretoolkit 0.0.9 contains pyxtal 0.6.0

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.