[mnt, bug] refactoring the template formatting (closes #314)

[djarecka]

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)

Summary

• refactoring the template formatting, separating

  • the argstr case (e.g. argstr=[{out1}, {out2}])
  • the output field that has output_template_file in spec (e.g. {inpA}_out)

• fixing issue with the extensions in templates:

  • if template itself has extension, than the extension from the input value is removed (if any), e.g. if inpA="file.text", than outA with a template {inpA}_out.txt should create file_out.txt
  • if only the input value has an extension, than the extension is moved to the end, e.g. if inpA="file.txt", than outA with a template {inpA}_out should create file_out.txt

Checklist

• All tests passing
• I have added tests to cover my changes
• I have updated documentation (if necessary)
• My code follows the code style of this project
  (we are using black: you can pip install pre-commit,
  run pre-commit install in the pydra directory
  and black will be run automatically with each commit)

Acknowledgment

• I acknowledge that this contribution will be available under the Apache 2 license.

[satra]

nipype has this metadata field keep_extension which could be used to indicate whether the input extension should be kept or not. i can imagine a situation where the output name should be based on the input but may not have any extension. we can co-opt the metadata to allow extensionless output by setting keep_extension=False. the default behavior (keep_extension=True or missing) would be to keep the input extension unless the field_template provides an extension

[codecov]

Codecov Report

Merging #315 into master will decrease coverage by 0.12%.
The diff coverage is 86.11%.

@@            Coverage Diff             @@
##           master     #315      +/-   ##
==========================================
- Coverage   86.17%   86.05%   -0.13%     
==========================================
  Files          20       20              
  Lines        3349     3384      +35     
  Branches      891      898       +7     
==========================================
+ Hits         2886     2912      +26     
- Misses        295      298       +3     
- Partials      168      174       +6     

Flag	Coverage Δ
#unittests	86.05% <86.11%> (-0.13%)	⬇️

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

Impacted Files	Coverage Δ
pydra/engine/helpers_file.py	78.68% <77.27%> (-1.32%)	⬇️
pydra/engine/core.py	89.79% <100.00%> (ø)
pydra/engine/helpers.py	87.17% <100.00%> (+0.66%)	⬆️
pydra/engine/specs.py	90.49% <100.00%> (-0.07%)	⬇️
pydra/engine/task.py	82.80% <100.00%> (-0.38%)	⬇️

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[djarecka]

@satra - unless you have any other comments, I'll merge it

[satra]

@djarecka - looks good to me.

need to have documentation around this.