Fairmat 2024: several new base classes in NXsample and NXsample_component

[lukaspie]

This PR is aimed at a more detailed description of the components of a sample. It introduces the following new base classes:
NXsample_component_set, NXsubstance, NXunit_cell, NXsingle_crystal, NXrotation_set

- NXsample_component_set: this is meant as a wrapper that takes in all the sub sample components (i.e. instances of NXsample_component) and their relationships (mass fractions, volume fractions, etc.)
- NXsubstance: this is meant to describe a chemical substance. Examples can be single chemical elements, chemical compunds, or alloys (e.g. CuO, C,). It is envisioned that if such a substance is crystalline, it could have an instance of
- NXunit_cell: Description of a unit cell, i.e., the crystal structure of a single thermodynamic phase. This was can be used within NXsample_(component) and/or in
- NXsingle_crystal: this is for describing a single crystalline material/phase within another material. It makes use of the new base_class NXrotation_set, which provides a rigorous way of describing rotations, orientations, and disorientations.

Eventually, it is envisioned that each sample can contain one or more instances NXsample_component_set, each of which has one or more instances of NXsample_component. This component is either not mixed (and thus can contain an instance of NXsubstance) or it by itself contains one or more instances NXsample_component_set with multiple instances of NXsample_component. The image provides a useful visualization of this nesting.

This PR was originally aimed at a more detailed description of the components of a sample (see crossed out text above). However, we realized in the meantime that this is not yet stable and more (internal) discussion is needed. We will bring this up at a later point (likely for the release after the next one) again.

Thus, this PR is much shorter than initially. It brings in NXhistory and NXactivity (as already approved in #1419) to NXsample, to describe the history of physical activities that have happened on the sample (preparation, calcination, in situ treatment, ...). It also add NXsubstance (meant to describe a "pure" chemical substance) to the contributed_definitions.

[lukaspie]

Dev notes to keep track:

• NXactivity: covered by FAIRmat 2024: additional base classes in NXinstrument #1419
• NXhistory: covered by FAIRmat 2024: additional base classes in NXinstrument #1419

ToDo:
- NXsubstance: uses identifier -> blocked by discussion in #1486

[phyy-nx]

From Telco:

• Remove NXfabrication as it's in NXcomponent
• Note that NXsubstance does not need a vote as it's a contributed definition
• Note that NXhistory and NXactivity are part of FAIRmat 2024: additional base classes in NXinstrument #1419

[lukaspie]

From Telco:

• Remove NXfabrication as it's in NXcomponent

Done!

[phyy-nx]

Hi all, as discussed in the Telco, we can now move this PR to an online vote. NIAC committee members please vote on this PR using emojis on this comment. 👍 for yes, 👎 for no, anything else (for example 👀) to abstain. We need 14 votes to hit quorum so please review and vote!

(note that NXsubstance does not need a vote as it's a contributed definition and note that NXhistory and NXactivity are part of #1419 which is due to be merged)

[lukaspie]

Had to run black on dev_tools/tests/test_nxdl_utils.py to get the CI to pass.

[lukaspie]

Rebased after merging #1419, so NXactivity and NXhistory are no longer part of this PR. Comments above should then become issues if needed.