Output directory from output_file_template

[chasejohnson3]

Acknowledgment

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

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

Output directory names can be specified in output_file_template. Recent changes to pydra have allowed an output field to be of type Directory. This PR allows those the name of the directory to be set using the output_file_template metadata field.

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)

[codecov]

Codecov Report

Merging #397 (eb67b4f) into master (5e5e6b7) will not change coverage.
The diff coverage is 50.00%.

@@           Coverage Diff           @@
##           master     #397   +/-   ##
=======================================
  Coverage   82.59%   82.59%           
=======================================
  Files          19       19           
  Lines        3838     3838           
  Branches     1050     1050           
=======================================
  Hits         3170     3170           
  Misses        480      480           
  Partials      188      188           

Flag	Coverage Δ
unittests	82.51% <50.00%> (ø)

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

Impacted Files	Coverage Δ
pydra/engine/helpers_file.py	80.56% <50.00%> (ø)

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[djarecka]

i believe you wanted to test Directory here

[chasejohnson3]

That is correct. I've updated to use Directory instead of File as the output type.

[chasejohnson3]

I believe this PR is ready to be pulled into master, but there are two failing checks. One is SLURM, which may be resolved by rerunning the SLURM check. The other is codecov/patch. I wrote two pytests to address this small code change, so I do not know why the code coverage would suffer. @djarecka can you give some insight as to why the codecov/patch check is failing?

[djarecka]

sometimes the slurm test have to be re-run, sorry for this, should work on this flaky test. I'm mostly offline right now, will review after Friday