Add pyxtal wrapper

[pmrv]

No description provided.

[jan-janssen]

center_coordinates_in_unit_cell is not an ASE compatible command:

    s.center_coordinates_in_unit_cell()
AttributeError: 'Atoms' object has no attribute 'center_coordinates_in_unit_cell'

But you can use the structuretoolkit.common.center_coordinates_in_unit_cell() function to achieve the same.

[jan-janssen]

Suggested change

	from pyxtal import pyxtal as _pyxtal
	from pyxtal.msg import Comp_CompatibilityError

[jan-janssen]

Suggested change

	if len(species) != len(num_ions):
	from pyxtal import pyxtal as _pyxtal
	from pyxtal.msg import Comp_CompatibilityError
	if len(species) != len(num_ions):

[jan-janssen]

One goal of the structuretoolkit package is to remain very stream-lined. The default installation via pypi only requires ase, matplotlib, numpy and spicy, with the last three being requirements of ase. This is enabled by moving the imports into the functions, even though this conflicts with the PEP8 recommendations. Furthermore the tests are skipped when the corresponding packages are not available, this enables the validation of the minimal installation.

[pmrv]

[I merged (and rebased) some of your changes before the force push]

One goal of the structuretoolkit package is to remain very stream-lined. The default installation via pypi only requires ase, matplotlib, numpy and spicy, with the last three being requirements of ase. This is enabled by moving the imports into the functions, even though this conflicts with the PEP8 recommendations. Furthermore the tests are skipped when the corresponding packages are not available, this enables the validation of the minimal installation.

I see the goal, but what about this way? This only conditionally defines the function and raises a warning if pyxtal is missing, so that users see it early and cannot even attempt to call the missing function. No strong feeling either, also happy to implement your original solution if you want it consistent everywhere.

Does sound like we want ImportAlarm here, though.

[jan-janssen]

======================================================================
ERROR: test_return_value (test_pyxtal.TestPyxtal)
pyxtal should either return Atoms or list of dict, depending on arguments
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/structuretoolkit/structuretoolkit/tests/test_pyxtal.py", line 36, in test_return_value
    self.assertIsInstance(pyxtal(1, species=['Fe'], num_ions=[1]), Atoms,
TypeError: 'module' object is not callable

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