V0.11.x

[illusional]

PRs:

• Janis prepare
• CWL v1.2
• Better CWL expressions
• Unit Testing

[codecov-io]

Codecov Report

Merging #46 (d591ec6) into master (61c5573) will decrease coverage by 0.67%. The diff coverage is 66.48%.

@@            Coverage Diff             @@
##           master      #46      +/-   ##
==========================================
- Coverage   74.26%   73.59%   -0.68%     
==========================================
  Files          67       74       +7     
  Lines        8404     9376     +972     
==========================================
+ Hits         6241     6900     +659     
- Misses       2163     2476     +313     

Impacted Files	Coverage Δ
janis_core/tests/tests_util.py	100.00% <ø> (ø)
janis_core/utils/validators.py	86.95% <ø> (ø)
janis_core/transformation/__init__.py	18.42% <18.42%> (ø)
janis_core/workflow/workflow.py	47.91% <25.00%> (-0.55%)	:arrow_down:
janis_core/tool/test_definitions.py	27.58% <27.58%> (ø)
janis_core/toolbox/toolbox.py	30.76% <30.76%> (+1.27%)	:arrow_up:
janis_core/operators/standard.py	60.94% <33.33%> (+4.72%)	:arrow_up:
janis_core/tool/test_helpers.py	35.41% <35.41%> (ø)
janis_core/utils/__init__.py	65.82% <62.50%> (-0.38%)	:arrow_down:
janis_core/tool/documentation.py	84.37% <71.42%> (-10.37%)	:arrow_down:
... and 41 more

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[illusional]

@junyk, every individual component in this mega PR has been reviewed, and I don't see much point going through line-by-line - it's too big. So I'll just merge it 👍 .

Edit: tests need to pass, I've pushed changes to fix the tests:

• Remove bad janis-bioinformatics debug test
• Lazily import janis_assistant for TestSuiteRunner, so we can test the "evaluate output" functions.

[janis-bot]

Test Succeeded for group 5fdaf0c3c6e6f1c06e0091ec Run 5fdaf0c3c6e6f1c06e0091ed: Test Succeeded Run 5fdaf0c3c6e6f1c06e0091ee: Test Succeeded