it_coordinate_system_code fix

[rozyczko]

This adds proper handling of CIF-read it_coordinate_system_code value.

Setting the code in the script also works, using space_group_IT_coordinate_system_code

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[AndrewSazonov]

The code is tested on one example (Fitting_PD-NEUT-TOF_Si-SEPD.ipynb). It now generates the correct pattern in the case of both possible it_codes for "F d -3 m". The only thing I noticed is that

• when specifying it_code in a CIF file via dot notation (_space_group.IT_coordinate_system_code 2) and reading it via the Job interface, everything seems to work, but the cif output in this case still shows _space_group_IT_coordinate_system_code 1.
• when using the underscore notation in CIF (_space_group_IT_coordinate_system_code 2), on the contrary, it shows the correct value of _space_group_IT_coordinate_system_code 2 in the cif output.

[AndrewSazonov]

Fixes #129

[AndrewSazonov]

I noticed another small issue. If you load a CIF file without the _space_group.IT_coordinate_system_code parameter, its default value is assigned after the space group has been processed by Cryspy. This results in a warning from Cryspy, which itself sets a default value for _space_group.IT_coordinate_system_code. And this default value is sometimes different from the one assigned by easydiffraction.

For example, running this:

job = ed.Job()
job.add_phase_from_file('data/si.cif')
phase = job.phases['si']
print(phase.space_group.it_coordinate_system_code)

leads to (from Cryspy):

Several values of it_coordinate_system_code have been defined:
2, 1
The default value has been choosen:'2'.

and to (from easydiffraction):

<Descriptor 'coordinate-code': 1>

Similarly, when assigning a space group manually via phase.space_group.name_hm_alt = "P n m a", its phase.IT_coordinate_system_code remains None, and when adding this phase to a job object, Cryspy complains that it_code is missing.

[rozyczko]

Hmm I just chose the first element of the settings list for a given spacegroup as returned by gemmi. If there is a way to find out the default setting, I'll be happy to implement it.

[rozyczko]

Now we get the settings value based on cryspy choses to be the default. It's the cryspy calculator after all, so importing a method from cryspy makes sense.

[AndrewSazonov]

I am still experiencing undesirable behaviour as indicated in my comment above. That is, it seems that when the job.add_phase_from_file method is called with a CIF file with no _space_group.IT_coordinate_system_code parameter, the default value is not used when passing this data to Cryspy. As a result, Cryspy assumes that the system code is not defined and displays a warning.

[rozyczko]

Yes but this is a superfluous message coming from the initial setup of the calculator.
Later thr correct object is generated