planemo.linters package
planemo.linters.biocontainer_registered module
Ensure a best-practice BioContainer is registered for a tool.
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class planemo.linters.biocontainer_registered.BiocontainerCheck(targets, name)[source]
Bases: NamedTuple
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name: str | None
Alias for field number 1
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targets: List[CondaTarget]
Alias for field number 0
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class planemo.linters.biocontainer_registered.BiocontainerMissing[source]
Bases: Linter
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classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]
should add at most one message to the lint context
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class planemo.linters.biocontainer_registered.BiocontainerRequirementsMissing[source]
Bases: Linter
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classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]
should add at most one message to the lint context
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class planemo.linters.biocontainer_registered.BiocontainerValid[source]
Bases: Linter
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classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]
should add at most one message to the lint context
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planemo.linters.biocontainer_registered.mulled_container_name(namespace: str, targets: List[CondaTarget]) → str | None[source]
planemo.linters.conda_requirements module
Ensure requirements are matched in best-practice Conda channels.
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class planemo.linters.conda_requirements.CondaCheck(target, best_hit, exact)[source]
Bases: NamedTuple
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best_hit: Any | None
Alias for field number 1
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exact: bool | None
Alias for field number 2
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target: CondaTarget
Alias for field number 0
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class planemo.linters.conda_requirements.CondaRequirementInexact[source]
Bases: Linter
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classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]
should add at most one message to the lint context
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class planemo.linters.conda_requirements.CondaRequirementMissing[source]
Bases: Linter
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classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]
should add at most one message to the lint context
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class planemo.linters.conda_requirements.CondaRequirementValid[source]
Bases: Linter
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classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]
should add at most one message to the lint context
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class planemo.linters.conda_requirements.CondaRequirementsMissing[source]
Bases: Linter
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classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]
should add at most one message to the lint context
planemo.linters.doi module
Lint DOI citations in Galaxy tools.
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class planemo.linters.doi.DoiCheck(citation, publication_id, doiless_publication_id, status_code, error)[source]
Bases: NamedTuple
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citation: Any
Alias for field number 0
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doiless_publication_id: str
Alias for field number 2
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error: str | None
Alias for field number 4
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publication_id: str
Alias for field number 1
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status_code: int | None
Alias for field number 3
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class planemo.linters.doi.DoiEmpty[source]
Bases: Linter
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classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]
should add at most one message to the lint context
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class planemo.linters.doi.DoiInvalid[source]
Bases: Linter
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classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]
should add at most one message to the lint context
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class planemo.linters.doi.DoiPrefix[source]
Bases: Linter
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classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]
should add at most one message to the lint context
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class planemo.linters.doi.DoiUnexpectedResponse[source]
Bases: Linter
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classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]
should add at most one message to the lint context
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class planemo.linters.doi.DoiValid[source]
Bases: Linter
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classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]
should add at most one message to the lint context
planemo.linters.urls module
Lint Galaxy tool help text URLs.
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class planemo.linters.urls.URLCheck(url, help_node, error)[source]
Bases: NamedTuple
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error: str | None
Alias for field number 2
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help_node: Any
Alias for field number 1
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url: str
Alias for field number 0
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class planemo.linters.urls.URLInaccessible[source]
Bases: Linter
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classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]
should add at most one message to the lint context
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class planemo.linters.urls.URLValid[source]
Bases: Linter
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classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]
should add at most one message to the lint context
planemo.linters.xsd module
Tool linting module that lints Galaxy tool against experimental XSD.
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planemo.linters.xsd.lint_tool_xsd(tool_xml, lint_ctx)[source]
Write a temp file out and lint it.