flake8 cleanup

[mr-c]

Bonus type modernizing and some docstrings

[codecov]

Codecov Report

Merging #1791 (879bba1) into main (8978ca2) will decrease coverage by 0.02%.
The diff coverage is 93.79%.

@@            Coverage Diff             @@
##             main    #1791      +/-   ##
==========================================
- Coverage   83.17%   83.16%   -0.02%     
==========================================
  Files          44       44              
  Lines        8130     8119      -11     
  Branches     2166     2223      +57     
==========================================
- Hits         6762     6752      -10     
  Misses        876      876              
+ Partials      492      491       -1     

Impacted Files	Coverage Δ
cwltool/checker.py	96.89% <0.00%> (ø)
cwltool/mpi.py	91.89% <0.00%> (ø)
cwltool/provenance_profile.py	73.72% <ø> (-0.08%)	⬇️
cwltool/resolver.py	71.92% <ø> (ø)
cwltool/cwlrdf.py	29.06% <25.00%> (ø)
cwltool/procgenerator.py	46.37% <50.00%> (ø)
cwltool/main.py	73.95% <62.50%> (+0.22%)	⬆️
cwltool/command_line_tool.py	86.97% <75.00%> (-0.02%)	⬇️
cwltool/validate_js.py	84.29% <85.71%> (ø)
cwltool/context.py	94.70% <93.90%> (-2.36%)	⬇️
... and 19 more

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