Run module

[simleo]

Prototype runcrate run command that runs the workflow from a CWL workflow / provenance run crate.

[codecov]

Codecov Report

Patch coverage: 70.71% and project coverage change: -3.38 ⚠️

Comparison is base (411c70d) 99.02% compared to head (4a6663b) 95.64%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #24      +/-   ##
==========================================
- Coverage   99.02%   95.64%   -3.38%     
==========================================
  Files          10       11       +1     
  Lines        1336     1517     +181     
==========================================
+ Hits         1323     1451     +128     
- Misses         13       66      +53     

Impacted Files	Coverage Δ
src/runcrate/run.py	67.08% <67.08%> (ø)
src/runcrate/cli.py	97.50% <100.00%> (+0.62%)	⬆️
tests/test_cli.py	100.00% <100.00%> (ø)

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[simleo]

One thing to note is that it might not be feasible to install both runcrate and the workflow engine in the same environment if the latter is also Python-based. For instance, streamflow 0.2.0.dev3 requires cwl-utils 0.23 and runcrate currently has it pinned at 0.13 (it needs common-workflow-language/cwl-utils#201 to move to a recent release). However, one can install StreamFlow to a separate environment and then point to the workflow runner via --executable:

runcrate run ml-predict-pipeline-streamflow --executable /path/to/venv/bin/cwl-runner