Remove deprecation - Axes, IO, Model

[ericpre]

First round of deprecation removal.

Progress of the PR

• axes.py,
• io.py,
• model.py,
• update docstring (if appropriate),
• update user guide (if appropriate),
• add an changelog entry in the upcoming_changes folder (see upcoming_changes/README.rst),
• Check formatting changelog entry in the readthedocs doc build of this PR (link in github checks)
• update tests,
• ready for review.

[codecov]

Codecov Report

Merging #2998 (04fa987) into RELEASE_next_major (0c8a6aa) will increase coverage by 0.12%.
The diff coverage is 95.00%.

@@                  Coverage Diff                   @@
##           RELEASE_next_major    #2998      +/-   ##
======================================================
+ Coverage               80.29%   80.41%   +0.12%     
======================================================
  Files                     176      176              
  Lines                   24648    24586      -62     
  Branches                 5591     5577      -14     
======================================================
- Hits                    19790    19771      -19     
+ Misses                   3512     3479      -33     
+ Partials                 1346     1336      -10     

Impacted Files	Coverage Δ
hyperspy/axes.py	91.01% <ø> (+0.20%)	⬆️
hyperspy/io.py	65.07% <ø> (+0.48%)	⬆️
hyperspy/misc/utils.py	90.31% <ø> (-0.05%)	⬇️
hyperspy/models/model1d.py	87.99% <ø> (ø)
hyperspy/signal.py	76.81% <ø> (+0.02%)	⬆️
hyperspy/model.py	86.70% <95.00%> (+2.99%)	⬆️

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[jlaehne]

I have seen in the RosettaSciIO deprecation PR that not always the changed terminology was properly documented in the user guide. So the documentation should be searched again for all deprecated names in the three deprecation PRs to make sure that there are no remnants of old terminology.

[ericpre]

Yes, this should be done after we remove all deprecation?

[jlaehne]

Yes, this should be done after we remove all deprecation?

It could be done in each of the three branches for the respective keywords and functions by searching a local copy (as I did in hyperspy/rosettasciio#30). Otherwise, we should add a checkpoint to the todo list in #2996

[ericpre]

As there are many deprecations, I made several PRs, so it is not too much pain to review, but the drawback of this approach is that, it is more difficult to find some left over which is why I suggested to do it later.

[jlaehne]

OK, I added to the todo list in #2996

[ericpre]

Sorry, I missed the point that you were referring to the user guide!

[jlaehne]

I added a PR with some changes to the documentation.