simplifying ShellCommandTask.cmdline

[djarecka]

simplifying all methods related to cmdline for ShellCommandTask

• creating command line only for stateless versions of the task (cmdline is needed when the task is executed and after the state has been removed by the submitter)
• temporarily removing some asserts from tests since we can't ask for task.cmdline when task has a state
• we could bring back the option to create cmdline for tasks with state by creating a copy of a task (in the same way as it is done in the submitter), but likely in a different PR

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

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 #520 (90c518d) into master (74957ca) will decrease coverage by 2.18%.
The diff coverage is 85.18%.

@@            Coverage Diff             @@
##           master     #520      +/-   ##
==========================================
- Coverage   79.03%   76.84%   -2.19%     
==========================================
  Files          20       20              
  Lines        4345     4284      -61     
  Branches     1233     1211      -22     
==========================================
- Hits         3434     3292     -142     
- Misses        720      805      +85     
+ Partials      191      187       -4     

Flag	Coverage Δ
unittests	76.75% <85.18%> (-2.20%)	⬇️

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

Impacted Files	Coverage Δ
pydra/engine/task.py	85.24% <84.61%> (-2.61%)	⬇️
pydra/engine/specs.py	88.50% <100.00%> (-0.41%)	⬇️
pydra/engine/boutiques.py	16.50% <0.00%> (-67.97%)	⬇️
pydra/engine/helpers_file.py	78.72% <0.00%> (-1.83%)	⬇️
pydra/engine/core.py	88.85% <0.00%> (-0.43%)	⬇️

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[djarecka]

@satra - I recalled that you were saying something about click, was this related to the issue:https://results.pre-commit.ci/run/github/152126811/1649028674.Fu63lAIhSCKWzxHD9TpUJA

[satra]

no that was just that click is not a dependency of pydra. in this case it's likely a function of black version in pre-commit.

[djarecka]

I will merge this now. Some of the test will have to be cleaned later.