Increase worflow linting by lldelisle · Pull Request #1463 · galaxyproject/planemo

lldelisle · 2024-06-29T10:32:33Z

I am not sure it is the good way to do it.
For the moment, I cannot make it like for the tools with classes, in order to make it customizable but I think I put everything I thought was missing in the current workflow_lint.
I used sometimes ' and sometimes ". Is this an issue?

lldelisle · 2024-06-29T10:41:39Z

I don't know how to fix:

./planemo/workflow_lint.py:434:1: C901 '_lint_dockstore_workflow_entry' is too complex (15)

lldelisle · 2024-06-29T15:15:34Z

I implemented new linting for the .dockstore.yml. I generate a warning if the workflow has no name or no authors as a consequence the test CmdWorkflowLintTestCase is not passing anymore while it is running with --skip best_practices. Edit: ~~Should I integrate these warnings into the best practices?~~ (I cannot because best practices are for workflow files not .dockstore.yml currently).

lldelisle · 2024-06-29T15:17:31Z

Also I am wondering how many tests I should generate following these changes?

bernt-matthias

Cool. I think adding a test for the --iwc flag would be good.

planemo/commands/cmd_workflow_lint.py

planemo/workflow_lint.py

…hias-bernt

…_practices

lldelisle · 2024-07-01T13:54:19Z

Hi,
Here is a summary of this PR:
I have defined:

2 new linters for directories:
- required_files: check that there is a CHANGELOG.md, a README.md, a .dockstore.yml
- changelog: check that there is a version defined in the CHANGELOG.md
1 new linter for .dockstore.yml
- dockstore_best_practices which requires tests and authors and name
1 new linter for workflow
- release that checks that the release matches what is in the CHANGELOG.md
  All these new linters are enabled when the argument --iwc is set.
  I have improved the linter dockstore with common errors we identified in iwc.

Importantly, the check for a testParameterFiles in .dockstore has been moved to dockstore_best_practices so in a regular run will not raise a warning anymore.

mvdbeek · 2024-07-01T14:35:40Z

You can run black to fix the linting errors

mvdbeek · 2024-07-01T15:44:21Z

And isort to fix the importing ... in fact we should add the same make format that we have for galaxy

lldelisle · 2024-07-01T15:47:52Z

@mvdbeek can you help me with the last test. How to assert that the command raise an InputError? and that the exception message contains a given string? Should I test on result.error rather than result.output?

mvdbeek · 2024-07-01T15:55:32Z

I'm seeing:

"Unknown linter type(s) [''] in list of linters to be skipped. Known linters ['CitationsMissing', 'CitationsNoText', 'CitationsFound', 'CitationsNoValid', 'CommandMissing', 'CommandEmpty', 'CommandTODO', 'CommandInterpreterDeprecated', 'CommandInfo', 'CWLValid', 'CWLInValid', 'CWLVersionMissing', 'CWLVersionUnknown', 'CWLVersionGood', 'CWLDockerMissing', 'CWLDockerGood', 'CWLDescriptionMissing', 'CWLHelpTODO', 'ToolVersionMissing', 'ToolVersionPEP404', 'ToolVersionWhitespace', 'ToolVersionValid', 'ToolNameMissing', 'ToolNameWhitespace', 'ToolNameValid', 'ToolIDMissing', 'ToolIDWhitespace', 'ToolIDValid', 'ToolProfileInvalid', 'ToolProfileLegacy', 'ToolProfileValid', 'RequirementNameMissing', 'RequirementVersionMissing', 'RequirementVersionWhitespace', 'ResourceRequirementExpression', 'HelpMissing', 'HelpEmpty', 'HelpPresent', 'HelpTODO', 'HelpInvalidRST', 'HelpValidRST', 'InputsNum', 'InputsMissing', 'InputsMissingDataSource', 'InputsDatasourceTags', 'InputsName', 'InputsNameRedundantArgument', 'InputsNameEmpty', 'InputsNameValid', 'InputsNameDuplicate', 'InputsNameDuplicateOutput', 'InputsTypeChildCombination', 'InputsDataFormat', 'InputsDataOptionsMultiple', 'InputsDataOptionsA...lidatorDatasetMetadataEqualValueOrJson', 'ValidatorMetadataCheckSkip', 'ValidatorTableName', 'ValidatorMetadataName', 'ConditionalParamTypeBool', 'ConditionalParamType', 'ConditionalParamIncompatibleAttributes', 'ConditionalWhenMissing', 'ConditionalOptionMissing', 'ConditionalOptionMissingBoolean', 'OutputsMissing', 'OutputsOutput', 'OutputsNameInvalidCheetah', 'OutputsNameDuplicated', 'OutputsLabelDuplicatedFilter', 'OutputsLabelDuplicatedNoFilter', 'OutputsCollectionType', 'OutputsNumber', 'OutputsFormatInput', 'OutputsFormat', 'OutputsFormatSourceIncomp', 'StdIOAbsenceLegacy', 'StdIOAbsence', 'StdIORegex', 'TestsMissing', 'TestsMissingDatasource', 'TestsAssertsMultiple', 'TestsAssertsHasNQuant', 'TestsAssertsHasSizeQuant', 'TestsAssertsHasSizeOrValueQuant', 'TestsExpectNumOutputs', 'TestsParamInInputs', 'TestsOutputName', 'TestsOutputDefined', 'TestsOutputCorresponding', 'TestsOutputCollectionCorresponding', 'TestsOutputCompareAttrib', 'TestsOutputCheckDiscovered', 'TestsOutputCollectionCheckDiscovered', 'TestsOutputCollectionCheckDiscoveredNested', 'TestsOutputFailing', 'TestsExpectNumOutputsFailing', 'TestsHasExpectations', 'TestsNoValid', 'TestsValid', 'XMLOrder', 'XSD']\n"

I would think that probably means we're not correctly handing a default argument in the skip linters case ?

lldelisle · 2024-07-01T15:59:39Z

Yes I wanted to tell @bernt-matthias about this. This is a message I get each time I run planemo workflow_lint but surprisingly it still gives a exit code of 0:

(planemo) (base) ldelisle@HP-EliteBook-840-G8-Notebook-PC:~/Documents/mygit/planemo$ planemo workflow_lint tests/data/wf_repos/basic_format2_dockstore --skip best_practices
Unknown linter type(s) ['best_practices'] in list of linters to be skipped. Known linters []
.. CHECK: Tests appear structurally correct for tests/data/wf_repos/basic_format2_dockstore/basic_format2.gxwf.yml
.. CHECK: All tool ids appear to be valid.
(planemo) (base) ldelisle@HP-EliteBook-840-G8-Notebook-PC:~/Documents/mygit/planemo$ echo $?
0

lldelisle · 2024-07-01T16:01:13Z

And even without skip, the message is very confusing for users:

(planemo) (base) ldelisle@HP-EliteBook-840-G8-Notebook-PC:~/Documents/mygit/planemo$ planemo workflow_lint tests/data/wf_repos/basic_wf_iwc_invalid_version/
Unknown linter type(s) [''] in list of linters to be skipped. Known linters []
.. CHECK: Tests appear structurally correct for tests/data/wf_repos/basic_wf_iwc_invalid_version/Super-simple-workflow.ga
.. CHECK: All tool ids appear to be valid.
(planemo) (base) ldelisle@HP-EliteBook-840-G8-Notebook-PC:~/Documents/mygit/planemo$ echo $?
0

But I don't know if this should be solved in this PR or in another PR.

mvdbeek · 2024-07-01T16:01:21Z

That's a different from the one in the test though.

diff --git a/planemo/lint.py b/planemo/lint.py
index 5b85022de4..c5964428aa 100644
--- a/planemo/lint.py
+++ b/planemo/lint.py
@@ -23,7 +23,7 @@ def build_lint_args(ctx, **kwds):
         skip = ctx.global_config.get("lint_skip", "")
         if isinstance(skip, list):
             skip = ",".join(skip)
-    skip_types = [s.strip() for s in skip.split(",")]
+    skip_types = [s.strip() for s in skip.split(",") if s.strip()]

     for skip_file in kwds.get("skip_file", []):
         with open(skip_file) as f:

fixes the odd test output.

lldelisle · 2024-07-01T16:01:42Z

Because this would require a big rearrangement I think and it is more difficult to review.

lldelisle · 2024-07-01T16:02:41Z

fixes the odd test output.

I can integrate this.

planemo/workflow_lint.py

bernt-matthias · 2024-07-01T17:05:35Z

I'm seeing:

"Unknown linter type(s) [''] in list of linters to be skipped. Known linters ['CitationsMissing', 'CitationsNoText', 'CitationsFound', 'CitationsNoValid', 'CommandMissing', 'CommandEmpty', 'CommandTODO', 'CommandInterpreterDeprecated', 'CommandInfo', 'CWLValid', 'CWLInValid', 'CWLVersionMissing', 'CWLVersionUnknown', 'CWLVersionGood', 'CWLDockerMissing', 'CWLDockerGood', 'CWLDescriptionMissing', 'CWLHelpTODO', 'ToolVersionMissing', 'ToolVersionPEP404', 'ToolVersionWhitespace', 'ToolVersionValid', 'ToolNameMissing', 'ToolNameWhitespace', 'ToolNameValid', 'ToolIDMissing', 'ToolIDWhitespace', 'ToolIDValid', 'ToolProfileInvalid', 'ToolProfileLegacy', 'ToolProfileValid', 'RequirementNameMissing', 'RequirementVersionMissing', 'RequirementVersionWhitespace', 'ResourceRequirementExpression', 'HelpMissing', 'HelpEmpty', 'HelpPresent', 'HelpTODO', 'HelpInvalidRST', 'HelpValidRST', 'InputsNum', 'InputsMissing', 'InputsMissingDataSource', 'InputsDatasourceTags', 'InputsName', 'InputsNameRedundantArgument', 'InputsNameEmpty', 'InputsNameValid', 'InputsNameDuplicate', 'InputsNameDuplicateOutput', 'InputsTypeChildCombination', 'InputsDataFormat', 'InputsDataOptionsMultiple', 'InputsDataOptionsA...lidatorDatasetMetadataEqualValueOrJson', 'ValidatorMetadataCheckSkip', 'ValidatorTableName', 'ValidatorMetadataName', 'ConditionalParamTypeBool', 'ConditionalParamType', 'ConditionalParamIncompatibleAttributes', 'ConditionalWhenMissing', 'ConditionalOptionMissing', 'ConditionalOptionMissingBoolean', 'OutputsMissing', 'OutputsOutput', 'OutputsNameInvalidCheetah', 'OutputsNameDuplicated', 'OutputsLabelDuplicatedFilter', 'OutputsLabelDuplicatedNoFilter', 'OutputsCollectionType', 'OutputsNumber', 'OutputsFormatInput', 'OutputsFormat', 'OutputsFormatSourceIncomp', 'StdIOAbsenceLegacy', 'StdIOAbsence', 'StdIORegex', 'TestsMissing', 'TestsMissingDatasource', 'TestsAssertsMultiple', 'TestsAssertsHasNQuant', 'TestsAssertsHasSizeQuant', 'TestsAssertsHasSizeOrValueQuant', 'TestsExpectNumOutputs', 'TestsParamInInputs', 'TestsOutputName', 'TestsOutputDefined', 'TestsOutputCorresponding', 'TestsOutputCollectionCorresponding', 'TestsOutputCompareAttrib', 'TestsOutputCheckDiscovered', 'TestsOutputCollectionCheckDiscovered', 'TestsOutputCollectionCheckDiscoveredNested', 'TestsOutputFailing', 'TestsExpectNumOutputsFailing', 'TestsHasExpectations', 'TestsNoValid', 'TestsValid', 'XMLOrder', 'XSD']\n"

I would think that probably means we're not correctly handing a default argument in the skip linters case ?

Fixed in #1453

bernt-matthias · 2024-07-01T17:10:14Z

This: Known linters [] is a problem... I will submit a fix in a separate PR.

bernt-matthias · 2024-07-01T17:14:54Z

#1465

lldelisle · 2024-07-02T06:44:55Z

The only test failing seems unrelated to this PR.

bernt-matthias · 2024-07-02T06:48:53Z

planemo/workflow_lint.py


+def build_wf_lint_args(ctx, **kwds):
+    lint_args = build_lint_args(ctx, **kwds)
+    lint_args["iwc_grade"] = str(kwds.get("iwc", False))


Suggested change

lint_args["iwc_grade"] = str(kwds.get("iwc", False))

lint_args["iwc_grade"] = kwds.get("iwc", False)

We should just leave this a boolean.

If I keep it as boolean then I get a type violation as lint_args is supposed to be a dict of str -> str

See

planemo/planemo/workflow_lint.py

Line 125 in b9e62ef

ctx: "PlanemoCliContext", paths: Iterable[str], lint_args: Dict[str, Union[str, List[str]]]

Or I change it to : lint_args: Dict[str, Union[str, List[str], bool]] ?

Dict[str, Any] is probably enough, I'll push a commit to your branch.

Thanks, if not I can commit it.

planemo/workflow_lint.py

Co-authored-by: M Bernt <m.bernt@ufz.de>

mvdbeek

This is excellent, thanks everyone!

Lucille Delisle added 2 commits June 29, 2024 12:29

increase worflow linting

64c684c

linting

af6758e

Lucille Delisle added 6 commits June 29, 2024 14:38

restore build_lint_args

1d61ca1

fix cases with no authors in dockstore.yml

dd9b1bb

fix DOCKSTORE_REGISTRY_CONF_VERSION

f7401d8

change name from required to recommanded

d4ae50f

linting

619cae9

fix forgotten consequence of name from required to recommanded

eb86e3b

bernt-matthias reviewed Jul 1, 2024

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planemo/commands/cmd_workflow_lint.py Outdated Show resolved Hide resolved

planemo/workflow_lint.py Outdated Show resolved Hide resolved

planemo/workflow_lint.py Outdated Show resolved Hide resolved

Lucille Delisle added 9 commits July 1, 2024 10:26

put iwc_grade in lint_args as suggested by @bernt-matthias

5516443

remove release/version from WorkflowLintContext as suggested by @matt…

8639d1d

…hias-bernt

fix type of lint_args

5c19e56

remove iwc_grade from WorkflowLintContext and add lint_dockstore_best…

302c504

…_practices

new build_wf_lint_args to match what is happening with tools

1310eb7

fix error on CHANGELOG get version

906c5ca

add tests

39480a8

restore comma

7bb3a50

test --iwc on file

db8f24c

remove path from asserts output

22112e8

run black

147296a

run isort

f5af20f

fix strange output when no --skip

6e8f0ce

mvdbeek reviewed Jul 1, 2024

View reviewed changes

planemo/workflow_lint.py Show resolved Hide resolved

fix final test

f748c11

Lucille Delisle added 3 commits July 1, 2024 22:50

change strategy for iwc on files

0d8dbd6

Merge remote-tracking branch 'upstream/master' into lint_workflow

f88024c

add comma

64f9076

lldelisle changed the title ~~[WIP] increase worflow linting~~ Increase worflow linting Jul 2, 2024

bernt-matthias reviewed Jul 2, 2024

View reviewed changes

nsoranzo and others added 4 commits July 2, 2024 12:15

Add type annotation

bafecff

Apply suggestions from @bernt-matthias

b1eedf4

Co-authored-by: M Bernt <m.bernt@ufz.de>

fix lint_args typing to different places

ecdcf0f

remove unused Union

2f7c139

mvdbeek approved these changes Jul 4, 2024

View reviewed changes

mvdbeek merged commit f47965e into galaxyproject:master Jul 4, 2024

mvdbeek mentioned this pull request Sep 24, 2024

Check lint skip types only for tool linting #1465

Closed

lldelisle deleted the lint_workflow branch September 24, 2024 07:18

lldelisle mentioned this pull request Sep 27, 2024

Improvement of CI galaxyproject/iwc#297

Closed

	lint_args["iwc_grade"] = str(kwds.get("iwc", False))
	lint_args["iwc_grade"] = kwds.get("iwc", False)

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