Fix warnings

[ericpre]

Progress of the PR

• Fix deprecation scipy, matplotlib and numpy deprecation warnings,
• Bump scipy from 1.5 to 1.6 to be able to use scipy.integrate.simpson instead of deprecated scipy.integrate.simps,
• Fix warning in test suite,
• Set OMP_NUM_THREADS as a default to run the test suite to avoid sklearn warning with MKL and possibly failure on Azure Pipelines CI (windows),
• Tidy up some tests which were redundant,
• [n/a] update docstring (if appropriate),
• [n/a] 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

Attention: Patch coverage is 94.11765% with 1 lines in your changes are missing coverage. Please review.

Project coverage is 80.51%. Comparing base (662a80b) to head (21cdabd).

Files	Patch %	Lines
hyperspy/external/astropy/histogram.py	50.00%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@                  Coverage Diff                   @@
##           RELEASE_next_patch    #3320      +/-   ##
======================================================
+ Coverage               80.25%   80.51%   +0.25%     
======================================================
  Files                     147      147              
  Lines                   21860    21869       +9     
  Branches                 5143     5146       +3     
======================================================
+ Hits                    17543    17607      +64     
+ Misses                   3111     3044      -67     
- Partials                 1206     1218      +12     

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[ericpre]

@jlaehne, @CSSFrancis, once this PR is merged, I would suggest to make a quick 2.0.1 release?

[jlaehne]

One of the Package & Test workflows fails with AttributeError: module 'mpmath' has no attribute 'rational'

Seems to originate from a recent pre-release of mpmath: NVIDIA/TensorRT-LLM#1145

[jlaehne]

@jlaehne, @CSSFrancis, once this PR is merged, I would suggest to make a quick 2.0.1 release?

Fixed a few typos, otherwise very good idea to reduce the number of warnings.

[ericpre]

One of the Package & Test workflows fails with AttributeError: module 'mpmath' has no attribute 'rational'

Seems to originate from a recent pre-release of mpmath: NVIDIA/TensorRT-LLM#1145

Changed to install mpmath separately (without the --pre flag) as a workaround in hyperspy/.github@b4c0b09.