Typing bugfixes

[tclose]

Types of changes

• Bug fix (non-breaking change which fixes an issue)

Summary

• Fixes up the handling of typing of inputs with output_file_template defined
• Allows output_file_template to define tuple/list templates for options with multiple files paths (e.g. mrconvert --export_grad_fsl BVEC BVAL)
• More descriptive messages on typing errors: task and field provided along with type mismatch
• Adds fileformats.field types to default coercions, e.g. fileformats.field.Integer -> int and vice versa

Checklist

• I have added tests to cover my changes (if necessary)
• I have updated documentation (if necessary)

[codecov]

Codecov Report

Patch coverage: 96.00% and project coverage change: -0.35% ⚠️

Comparison is base (91c5a15) 83.23% compared to head (07ce62a) 82.88%.
Report is 2 commits behind head on master.

❗ Current head 07ce62a differs from pull request most recent head 103cefc. Consider uploading reports for the commit 103cefc to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #687      +/-   ##
==========================================
- Coverage   83.23%   82.88%   -0.35%     
==========================================
  Files          22       22              
  Lines        4848     4873      +25     
  Branches     1392        0    -1392     
==========================================
+ Hits         4035     4039       +4     
- Misses        809      834      +25     
+ Partials        4        0       -4     

Flag	Coverage Δ
unittests	82.88% <96.00%> (-0.35%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files Changed	Coverage Δ
pydra/utils/typing.py	93.24% <90.00%> (+0.26%)	⬆️
pydra/engine/helpers.py	86.66% <100.00%> (+0.07%)	⬆️
pydra/engine/helpers_file.py	92.59% <100.00%> (+0.24%)	⬆️
pydra/engine/specs.py	94.75% <100.00%> (+0.03%)	⬆️

... and 4 files with indirect coverage changes

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[tclose]

@djarecka I believe this is ready to merge now. The new SLURM test seems to be getting stuck somewhere

[effigies]

Small comments. Nothing objectionable here, though I also did not fully grasp the bugs being fixed.

[effigies]

Merging so #684 can be rebased on master and reviewed more easily.