cwl v1.3.0-dev1 native loop support #1779
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Huzzah!
You'll also need to add a dump of the v1.3.0-dev1 schema to https://github.com/common-workflow-language/cwltool/tree/cwl-v1.3/cwltool/schemas
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #1779 +/- ##
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- Coverage 83.84% 83.76% -0.08%
==========================================
Files 46 46
Lines 8244 8262 +18
Branches 2190 2199 +9
==========================================
+ Hits 6912 6921 +9
- Misses 855 861 +6
- Partials 477 480 +3 ☔ View full report in Codecov by Sentry. |
| "The `cwltool:Loop` clause is not compatible with the `when` directive." | ||
| ) | ||
| if "loopWhen" not in r: | ||
| raise SourceLine( |
cwltool/update.py
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| ) | ||
| cls = cast(str, r["class"]) | ||
| if cls in rewrite: | ||
| r["class"] = rewrite[cls] |
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With the fix in common-workflow-language/schema_salad#846 this passes unit tests for me. |
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I didn't think you meant to close this PR @tetron 🙂 |
github seems to have done it automatically |
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Ok, unit tests passing, there's an issue with some conformance tests, and then we need to make codecov happy, but it is progress at least. |
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@tetron I think those may be due to recent changes to Did you see my email about the cofest? |
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Ok! So we're just down to the test coverage check. |
schema-salad catches that before the updater runs
Keep the cwltool:Loop tests as "loop_ext"
I can't mark the individual line because the formatter insists on reformatting the line in a way that flake8 no longer recognizes the annotation.
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I keep fiddling with this but I think we should just override the codecov check because at least one of the lines it is complaining about appears to be almost impossible to trigger in normal usage because it is an exception handler and "normal" exceptions get routed another way, so it only engages if a very truly unexpected case happens. Possibly we could mock something but I'm pretty sure at this point the cost/benefit of trying to make codecov happy for these corner cases is very bad. I haven't yet managed to determine if there's a way to tell codecov to ignore certain lines. |
This commit converts the logic introduced to handle the
cwltool:Looprequirement extension to handle the newloopconstruct introduced in the CWL v1.3 spec.A proper method in the
upgrade.pymodule handles the automatic conversion from the old requirement to the new format.The existing
test_loop.pyfile is still useful to verify the correctness of the conversion process.See also common-workflow-language/cwl-v1.3#5