Exclude rather than mock problematic modules for API docs

[peterjc]

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  the Biopython License Agreement AND the BSD 3-Clause License.

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  and understand that AppVeyor and TravisCI will be used to confirm the Biopython unit
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Cross reference 3f7a13d

Applies the suggestion from sphinx-doc/sphinx#9631

[codecov]

Codecov Report

Merging #3731 (0afa4fb) into master (45539a8) will decrease coverage by 1.69%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #3731      +/-   ##
==========================================
- Coverage   83.77%   82.07%   -1.70%     
==========================================
  Files         314      294      -20     
  Lines       52512    49392    -3120     
==========================================
- Hits        43990    40539    -3451     
- Misses       8522     8853     +331     

Impacted Files	Coverage Δ
Bio/Phylo/CDAOIO.py	4.46% <0.00%> (-80.36%)	⬇️
Bio/phenotype/pm_fitting.py	12.28% <0.00%> (-75.44%)	⬇️
Bio/PDB/mmtf/__init__.py	28.57% <0.00%> (-61.91%)	⬇️
Bio/Graphics/__init__.py	25.00% <0.00%> (-58.34%)	⬇️
Bio/Phylo/CDAO.py	42.85% <0.00%> (-57.15%)	⬇️
Bio/Phylo/_utils.py	25.00% <0.00%> (-52.41%)	⬇️
Bio/codonalign/codonseq.py	44.16% <0.00%> (-44.31%)	⬇️
Bio/Phylo/_cdao_owl.py	89.47% <0.00%> (-10.53%)	⬇️
Bio/KEGG/KGML/KGML_pathway.py	73.58% <0.00%> (-6.67%)	⬇️
Bio/motifs/jaspar/db.py	3.04% <0.00%> (-5.33%)	⬇️
... and 26 more

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