Fix #77: Unify v1*_only parameter into target_version

[tom-tan]

It introduces target_version parameter to replace v1*_only parameters.
It also make imports parameter as a default parameter to make target_version optional.

Note:

• Current implementation prints an error message and returns nothing if a given CWL doc has unsupported cwlVersion. Can we leave it as is or fix it to raise an exception, for example?

[codecov]

Codecov Report

Merging #79 (a7e29d9) into main (4fa21a6) will increase coverage by 12.36%.
The diff coverage is 67.39%.

@@             Coverage Diff             @@
##             main      #79       +/-   ##
===========================================
+ Coverage   50.43%   62.80%   +12.36%     
===========================================
  Files           3        3               
  Lines         462      500       +38     
===========================================
+ Hits          233      314       +81     
+ Misses        229      186       -43     

Impacted Files	Coverage Δ
cwlupgrader/main.py	60.25% <54.54%> (+12.06%)	⬆️
tests/test_complete.py	100.00% <100.00%> (ø)

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[mr-c]

The imports set needs to be external of the function, as it is used to prevent duplicate upgrading of the same external file, when upgrading more than one primary document.

[tom-tan]

Thank you for your advice.
Now run calls upgrade_document with a set.
It prevents duplicate upgrading while keeping the API of upgrade_document simple.

[mr-c]

Thank you for your advice. Now run calls upgrade_document with a set. It prevents duplicate upgrading while keeping the API of upgrade_document simple.

Thanks!

I'm seeing some code coverage issues; 22% is rather low. You can run make diff-cover locally to get a line-by-line report, or wait for the CI to finish and check https://github.com/common-workflow-language/cwl-upgrader/pull/79/files for annotations about lack of test coverage.

[tom-tan]

Added!

Note that the current implementation of upgrade_document only dumps the upgrade documents for steps fields and does not dump the document for a given CWL that is passed to the parameter (it is done by cwlupgrader.main.run).
Fixing this issue is out of scope of this request (will be fixed when #78 is solved).

[tom-tan]

Thanks!