Only issue `MESSAGE_WARN_NO_REQUIREMENTS` if there are no containers by kostrykin · Pull Request #1558 · galaxyproject/planemo

kostrykin · 2025-07-22T11:17:28Z

Currently, running planemo shed_lint --tools --ensure_metadata --urls --biocontainers on a tool that defines containerized requirements instead of conda packages yields the warning

.. WARNING: No valid package requirement tags found to infer BioContainer from.

whichs makes the linting fail. Examples of this behavior are, but are not limited to:

This generally happens in the weekly linting workflows employed by many repositories, e.g.:
https://github.com/galaxyproject/tools-iuc/actions/runs/16405860532/workflow#L99-L107

However, the fact that there are no package requirements defined in those tools is a decision by design of those tools. It makes no sense to check the availability of Biocontainers for those tools, does it? Hence, I would consider these lint failures as false positives.

To cope with that, I suggest to suppress the warning if the tool only defines containerized requirements.

mvdbeek · 2025-07-22T12:28:29Z

This is logged as a warning, which I think is the appropriate level for tools that only run containerized. You can chose to ignore particular warnings IIRC, ping @bernt-matthias.

kostrykin · 2025-07-22T12:43:46Z

This is logged as a warning, which I think is the appropriate level for tools that only run containerized.

Yes, but since weekly linting runs with fail-level: warn (see, e.g., here), this causes the whole workflow to fail.

You can chose to ignore particular warnings IIRC, ping @bernt-matthias.

I'd very much appreciate getting to know how to ignore this warning!

bernt-matthias · 2025-07-22T12:57:51Z

You can chose to ignore particular warnings IIRC, ping @bernt-matthias.

Can you try to add requirements_in_conda to the .lint_skip file of the tool. Not 100% sure if this works for linters defined in planemo

Adding a check for defined containers seems also reasonable.

kostrykin · 2025-07-22T14:25:05Z

You can chose to ignore particular warnings IIRC, ping @bernt-matthias.

Can you try to add requirements_in_conda to the .lint_skip file of the tool. Not 100% sure if this works for linters defined in planemo

This gives the error

Unknown linter type(s) ['requirements_in_conda'] in list of linters to be skipped. Known linters ['HelpMissing', 'HelpEmpty', 'HelpPresent', 'HelpTODO', 'HelpInvalidRST', 'HelpValidRST', 'CitationsMissing', 'CitationsNoText', 'CitationsFound', 'CitationsNoValid', 'CommandMissing', 'CommandEmpty', 'CommandTODO', 'CommandInterpreterDeprecated', 'CommandInfo', 'CWLValid', 'CWLInValid', 'CWLVersionMissing', 'CWLVersionUnknown', 'CWLVersionGood', 'CWLDockerMissing', 'CWLDockerGood', 'CWLDescriptionMissing', 'CWLHelpTODO', 'DatatypesCustomConf', 'ValidDatatypes', 'ToolVersionMissing', 'ToolVersionPEP404', 'ToolVersionWhitespace', 'ToolVersionValid', 'ToolNameMissing', 'ToolNameWhitespace', 'ToolNameValid', 'ToolIDMissing', 'ToolIDWhitespace', 'ToolIDValid', 'ToolProfileInvalid', 'ToolProfileLegacy', 'ToolProfileValid', 'RequirementNameMissing', 'RequirementVersionMissing', 'RequirementVersionWhitespace', 'ResourceRequirementExpression', 'BioToolsValid', 'EDAMTermsValid', 'InputsNum', 'InputsMissing', 'InputsMissingDataSource', 'InputsDatasourceTags', 'InputsName', 'InputsNameRedundantArgument', 'InputsNameEmpty', 'InputsNameValid', 'InputsNameDuplicate', 'InputsNameDuplicateOutput', 'InputsTypeChildCombination', 'InputsDataFormat', 'InputsDataOptionsMultiple', 'InputsDataOptionsAttrib', 'InputsDataOptionsFilterAttribFiltersType', 'InputsDataOptionsFiltersType', 'InputsDataOptionsFiltersRef', 'InputsSelectDynamicOptions', 'InputsSelectOptionsDef', 'InputsSelectOptionsDefConditional', 'InputsSelectOptionValueMissing', 'InputsSelectOptionDuplicateValue', 'InputsSelectOptionDuplicateText', 'InputsSelectOptionsMultiple', 'InputsSelectOptionsDefinesOptions', 'InputsSelectOptionsDeprecatedAttr', 'InputsSelectOptionsFromDatasetAndDatatable', 'InputsSelectOptionsMetaFileKey', 'InputsBoolDistinctValues', 'InputsBoolProblematic', 'InputsSelectSingleCheckboxes', 'InputsSelectMandatoryCheckboxes', 'InputsSelectMultipleRadio', 'InputsSelectOptionalRadio', 'ValidatorParamIncompatible', 'ValidatorAttribIncompatible', 'ValidatorHasText', 'ValidatorHasNoText', 'ValidatorExpression', 'ValidatorExpressionFuture', 'ValidatorMinMax', 'ValidatorDatasetMetadataEqualValue', 'ValidatorDatasetMetadataEqualValueOrJson', 'ValidatorMetadataCheckSkip', 'ValidatorTableName', 'ValidatorMetadataName', 'ConditionalParamTypeBool', 'ConditionalParamType', 'ConditionalParamIncompatibleAttributes', 'ConditionalWhenMissing', 'ConditionalOptionMissing', 'ConditionalOptionMissingBoolean', 'OutputsMissing', 'OutputsOutput', 'OutputsNameInvalidCheetah', 'OutputsNameDuplicated', 'OutputsFilterExpression', 'OutputsLabelDuplicatedFilter', 'OutputsLabelDuplicatedNoFilter', 'OutputsCollectionType', 'OutputsNumber', 'OutputsFormatInput', 'OutputsFormat', 'OutputsFormatSourceIncomp', 'StdIOAbsenceLegacy', 'StdIOAbsence', 'StdIORegex', 'TestsMissing', 'TestsMissingDatasource', 'TestsAssertsMultiple', 'TestsAssertsHasNQuant', 'TestsAssertsHasSizeQuant', 'TestsAssertsHasSizeOrValueQuant', 'TestsAssertionValidation', 'TestsCaseValidation', 'TestsExpectNumOutputs', 'TestsParamInInputs', 'TestsOutputName', 'TestsOutputDefined', 'TestsOutputCorresponding', 'TestsOutputCollectionCorresponding', 'TestsOutputCompareAttrib', 'TestsOutputCheckDiscovered', 'TestsOutputCollectionCheckDiscovered', 'TestsOutputCollectionCheckDiscoveredNested', 'TestsOutputFailing', 'TestsExpectNumOutputsFailing', 'TestsHasExpectations', 'TestsNoValid', 'TestsValid', 'XMLOrder', 'XSD']

bernt-matthias

Makes perfect sense to me

mvdbeek · 2025-08-18T09:57:04Z

planemo/linters/biocontainer_registered.py

    conda_targets = tool_source_conda_targets(tool_source)
    if not conda_targets:
-        lint_ctx.warn(MESSAGE_WARN_NO_REQUIREMENTS)
+        _, containers, *_ = tool_source.parse_requirements_and_containers()


This should still check that we have a biocontainer here.

Maybe I'm missing something here. But if this should always check for a Biocontainer, then this PR is pointless (the whole idea of this PR is to only check for Biocontainers in cases where it makes sense to expect a Biocontainer).

Why would it make sense to check for a Biocontainer if the wrapper specifies a custom container image? If I'm not mistaken, this is like producing a warning for every wrapper that uses a custom container image?

Still, if this PR is pointless, I'm still wondering how we are going to suppress the warnings for wrappers that use a custom container image. I think there is no mechanism for this in place yet.

This is a warning that you can choose to ignore (as opposed to errors). The wider Galaxy ecosystem has agreed to bicontainers and caches them on CVMFS, custom images should make the iuc linter fail. You can select the warnings you want to ignore on a per directory basis. You can also ignore the biocontainers linter on a per tool basis. It is a valuable warning.

If I'm not mistaken, this is like producing a warning for every wrapper that uses a custom container image?

yes, that is the purpose of this linter.

@kostrykin can you try to change

planemo/planemo/lint.py

Line 49 in ac2191d

linters.extend(["version_bumped"])

to linters.extend(["version_bumped", "requirements_in_conda", "biocontainer_registered"]).

Then it might be possible to really add these linters to the skip list.

You should also be able to just omit the --biocontainers flag

True, but if you want to use the linter for other tools it could be handy.

@kostrykin can you try to change

planemo/planemo/lint.py

Line 49 in ac2191d

linters.extend(["version_bumped"])

to linters.extend(["version_bumped", "requirements_in_conda", "biocontainer_registered"]).
Then it might be possible to really add these linters to the skip list.

Thanks @bernt-matthias, I tried it locally and it works. I created a PR: #1588

I think the planemo-ci-action does not support installing Planemo from custom branches, does it?

You can try planemo-version https://github.com/galaxyproject/planemo-ci-action/blob/fb7af7555194b70a93637a530cafd869e1f5e6c3/action.yml#L12

bernt-matthias · 2026-01-08T11:43:59Z

Superseded by #1588

Only issue MESSAGE_WARN_NO_REQUIREMENTS if there are no containers

670c0ef

kostrykin mentioned this pull request Jul 22, 2025

Fix weekly linting issues and tests BMCV/galaxy-image-analysis#154

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kostrykin marked this pull request as ready for review July 22, 2025 12:44

bernt-matthias approved these changes Aug 17, 2025

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mvdbeek reviewed Aug 18, 2025

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mvdbeek force-pushed the master branch from 0c408fe to b4c5e39 Compare August 18, 2025 12:27

Merge branch 'galaxyproject:master' into dev/biocontainers

2549aa5

This was referenced Dec 15, 2025

Allow requirements_in_conda and biocontainer_registered in skip_file kostrykin/planemo#2

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Allow requirements_in_conda and biocontainer_registered in skip_file #1588

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bernt-matthias closed this Jan 8, 2026

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kostrykin commented Jul 22, 2025

Uh oh!

mvdbeek commented Jul 22, 2025

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kostrykin commented Jul 22, 2025

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bernt-matthias commented Jul 22, 2025

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kostrykin commented Jul 22, 2025

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bernt-matthias commented Jan 8, 2026

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