Extend public API and fix documentation

[ericpre]

Add back some functions which were removed when splitting from hyperspy. Some modules and functions that were not to the public API as listed in the API reference have been removed.

Progress of the PR

• Add some functionalities back to public API,
• Rename private modules to start with underscore to reduce their visibility and make more clear that they are not part of the public API,
• docstring updated: there were still a lot of leftover from hyperspy,
• update user guide: there were still a lot of leftover from hyperspy,
• [n/a] added tests,
• add a changelog entry in the upcoming_changes folder (see upcoming_changes/README.rst),
• Check formatting of the changelog entry (and eventual user guide changes) in the docs/readthedocs.org:exspy build of this PR (link in github checks)
• ready for review.

[codecov]

Codecov Report

Attention: Patch coverage is 77.01318% with 157 lines in your changes missing coverage. Please review.

Project coverage is 88.62%. Comparing base (3b7425e) to head (9e0d0be).

Files	Patch %	Lines
exspy/_misc/eels/tools.py	40.93%	95 Missing and 6 partials ⚠️
exspy/_misc/material.py	83.78%	11 Missing and 13 partials ⚠️
exspy/_misc/eds/utils.py	92.59%	7 Missing and 9 partials ⚠️
...py/_misc/eels/electron_inelastic_mean_free_path.py	59.25%	11 Missing ⚠️
exspy/material.py	80.00%	1 Missing ⚠️
exspy/misc/eds/utils.py	85.71%	1 Missing ⚠️
exspy/misc/eels/tools.py	85.71%	1 Missing ⚠️
exspy/utils/__init__.py	80.00%	1 Missing ⚠️
exspy/utils/eels.py	83.33%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #59      +/-   ##
==========================================
+ Coverage   88.55%   88.62%   +0.06%     
==========================================
  Files          67       76       +9     
  Lines        7341     7411      +70     
  Branches     1187     1192       +5     
==========================================
+ Hits         6501     6568      +67     
- Misses        571      574       +3     
  Partials      269      269              

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[CSSFrancis]

@ericpre I can review this today!

[CSSFrancis]

These changes look good to me. And probably should have been done a little bit ago.

My one hesitation is that this will move all of the functions in the misc to a different place. Tecnically I think these were part of the public api even if they weren't documentated. It might be worthwhile to create a misc.py file which redirects to the _misc.py file and then raises a deprecation warning.

That's what we have been doing in pyxem just to catch people.

[ericpre]

Thank you @CSSFrancis for the review. I added a shim for the functionalities that have been added to the public API. Do you want to have another look?