Doc fixes

[kbwestfall]

Fixes warnings in the doc compilation that actually cause the ReadTheDocs build to fail.

Most of these changes are an artifact of me trying to find the failures. The bottom line is that warnings were being caused by syntax like this:

:class:`~pypeit.alignframe.AlignmentSplines`_

This is a mix of an explicit hyperlink that requires the _ at the end, and an internal class reference, which does not. The solution is to remove the trailing _.

This also includes updates to the Sphinx version dependencies, and I now include scikit-image and specutils in the dev dependencies.

[codecov-commenter]

Codecov Report

Merging #1648 (270f886) into develop (2c8fcaa) will not change coverage.
The diff coverage is 100.00%.

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@@           Coverage Diff            @@
##           develop    #1648   +/-   ##
========================================
  Coverage    41.03%   41.03%           
========================================
  Files          189      189           
  Lines        43221    43221           
========================================
  Hits         17736    17736           
  Misses       25485    25485           

Files Changed	Coverage Δ
pypeit/bitmask.py	71.42% <ø> (ø)
pypeit/core/arc.py	43.56% <ø> (ø)
pypeit/core/collate.py	95.71% <ø> (ø)
pypeit/core/extract.py	77.16% <ø> (ø)
pypeit/core/findobj_skymask.py	24.77% <ø> (ø)
pypeit/core/flexure.py	45.82% <ø> (ø)
pypeit/core/flux_calib.py	64.06% <ø> (ø)
pypeit/core/gui/object_find.py	11.06% <ø> (ø)
pypeit/core/skysub.py	61.81% <ø> (ø)
pypeit/core/wavecal/autoid.py	26.36% <ø> (ø)
... and 10 more

[profxj]

Thanks for this major clean up!

[debora-pe]

Thank you so much for this!!!