Summary
Commit ce4f3c1 ("Migrate lint.py to normalized models, merge best practices") changed the public signatures of gxformat2.lint.lint_format2 and gxformat2.lint.lint_ga in ways that silently broke downstream callers — Planemo in particular.
Before
def lint_ga(lint_context, workflow_dict, path=None): ...
def lint_format2(lint_context, workflow_dict, path=None): ...
After ce4f3c1
def lint_ga(lint_context, nnw: NormalizedNativeWorkflow, raw_dict: dict | None = None): ...
def lint_format2(lint_context, nf2: NormalizedFormat2, raw_dict: dict | None = None): ...
Second positional argument switched from a raw dict to a normalized pydantic model, and the path= keyword argument was removed.
Downstream impact
planemo/workflow_lint.py:166-167:
lint_func = lint_format2 if workflow_class == "GalaxyWorkflow" else lint_ga
lint_func(lint_context, workflow_dict, path=path)
Planemo passes a raw dict and a path= kwarg. Both fail against the new signature — TypeError for path=, AttributeError deeper in the call chain for the dict.
Proposed fix
Make the entry points polymorphic and tolerate the legacy kwargs:
def lint_ga(lint_context, nnw, raw_dict=None, path=None):
if isinstance(nnw, dict):
if raw_dict is None:
raw_dict = nnw
nnw = ensure_native(nnw)
...(Same for lint_format2.) Keeps existing model-based callers working, restores Planemo. path= is accepted and ignored.
Being addressed on branch abstraction_applications as part of the linting overhaul.
Minor secondary issue
gxformat2.lint uses str.format(**kwds) for one template; galaxy.tool_util.lint.LintContext (the context Planemo actually passes) uses %-style formatting. Placeholders like {value} survive unformatted when the galaxy context is used. Best avoided by using f-strings.
Summary
Commit
ce4f3c1("Migrate lint.py to normalized models, merge best practices") changed the public signatures ofgxformat2.lint.lint_format2andgxformat2.lint.lint_gain ways that silently broke downstream callers — Planemo in particular.Before
After
ce4f3c1Second positional argument switched from a raw
dictto a normalized pydantic model, and thepath=keyword argument was removed.Downstream impact
planemo/workflow_lint.py:166-167:Planemo passes a raw dict and a
path=kwarg. Both fail against the new signature —TypeErrorforpath=,AttributeErrordeeper in the call chain for the dict.Proposed fix
Make the entry points polymorphic and tolerate the legacy kwargs:
(Same for
lint_format2.) Keeps existing model-based callers working, restores Planemo.path=is accepted and ignored.Being addressed on branch
abstraction_applicationsas part of the linting overhaul.Minor secondary issue
gxformat2.lintusesstr.format(**kwds)for one template;galaxy.tool_util.lint.LintContext(the context Planemo actually passes) uses%-style formatting. Placeholders like{value}survive unformatted when the galaxy context is used. Best avoided by using f-strings.