support plugins for alternative FsAccess

[tetron]

This adds a slimmed down version of StdFsAccess class from cwltool, which is used to abstract the output file checks.

Adds Arvados as an optional dependency. Adjust cwltest to use ArvadosFsAccess if the arvados module is importable.

[codecov]

Codecov Report

Attention: Patch coverage is 82.69231% with 9 lines in your changes missing coverage. Please review.

Project coverage is 81.31%. Comparing base (feeb0da) to head (a0409c0).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
cwltest/utils.py	61.53%	5 Missing ⚠️
cwltest/stdfsaccess.py	84.61%	2 Missing and 2 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #233      +/-   ##
==========================================
- Coverage   81.52%   81.31%   -0.22%     
==========================================
  Files           8        9       +1     
  Lines         785      824      +39     
  Branches      190      195       +5     
==========================================
+ Hits          640      670      +30     
- Misses        111      118       +7     
- Partials       34       36       +2     

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[tetron]

I did all the annotations to make mypy happy as well as linting and running format but codecov is going to block merging, because writing unit tests to cover the Arvados-specific code would only work if I stubbed out everything to the point that they would be useless as tests.

[mr-c]

Hey Peter,

How are you all running cwltest, using the cwltest pytest plugin or directly through the cwltest CLI?

Seems like you want your own plugin to cwltest to use a custom StdFsAccess class. Perhaps that would be better than duplicating the arvados code here?

[tetron]

Hi Michael,

The thing I need is for the file checks to go through a abstracted interface, so I copied in a slimmed down version of StdFsAccess from cwltool.

If I revise the PR so it just adds that hook, I could remove the Arvados stuff from this PR and instead make my own arv-cwltest which hooks in my custom FsAccess object and then wraps cwltest, similar to how arvados-cwl-runner works. Is that what you are proposing?

[mr-c]

If I revise the PR so it just adds that hook, I could remove the Arvados stuff from this PR and instead make my own arv-cwltest which hooks in my custom FsAccess object and then wraps cwltest, similar to how arvados-cwl-runner works. Is that what you are proposing?

Almost, if arvados-python-client (or another python package from Arvados) registered a module under the cwltest.fsaccess entry point, then this PR could automatically load that module and use its FsAccess member class instead of the StdFsAccess default.

https://packaging.python.org/en/latest/guides/creating-and-discovering-plugins/#using-package-metadata

[tetron]

@mr-c let me know if you're happy with this and we can hit the big green merge button.

[tetron]

Given the long battle with mypy and the linting tools, it'll probably make sense to squash this one.

[mr-c]

Thank you @tetron !