docs: clean up and add a real data XRD example

[john-halloran]

Closes #128.

[codecov]

Codecov Report

❌ Patch coverage is 0% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 57.50%. Comparing base (d7586bc) to head (0407642).
⚠️ Report is 3 commits behind head on main.

Files with missing lines	Patch %	Lines
tests/test_snmf_optimizer.py	0.00%	3 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##             main     #191       +/-   ##
===========================================
- Coverage   77.50%   57.50%   -20.00%     
===========================================
  Files           3        3               
  Lines          40       40               
===========================================
- Hits           31       23        -8     
- Misses          9       17        +8     

Files with missing lines	Coverage Δ
tests/test_snmf_optimizer.py	63.63% <0.00%> (-36.37%)	⬇️

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[sbillinge]

This looks great. I am ready to merge. A couple of final cleaning tweaks (see inline).

Also, it may be a feature not a bug, but do we want (a) the dot in the data filenames? Maybe this is ok because it has meaning. (b) the filenames to order alpha-numerically? To do this we want single digits to have leading zeros, so <name>01 , 02 and so on. On balance I would say to leave the dot/point in the names but do the fix to make them sort correctly as this teaches good practice.

[sbillinge]

These should all begin with "The" per group standards.

Please could we also document somewhere where it will show up in the API docs the convention (trailing underscore are attributes that are the result of the refinement)? We don't have to describe about private functions in the docs.

[sbillinge]

missing "The"'s