Merge pull request #842 from nipype/subclass-or-union

generalize is_fileset_or_union utility to is_subclass_or_union

Author: tclose

pydra/environments/docker.py

@@ -15,7 +15,7 @@ class Docker(base.Container):
     def execute(self, job: "Job[shell.Task]") -> dict[str, ty.Any]:
         docker_img = f"{self.image}:{self.tag}"
         # mounting all input locations
-        mounts, values = self.get_bindings(job=job, root=self.root)
+        mounts, arg_values = self.get_bindings(job=job, root=self.root)
 
         docker_args = [
             "docker",
@@ -32,7 +32,7 @@ def execute(self, job: "Job[shell.Task]") -> dict[str, ty.Any]:
 
         job.cache_dir.mkdir(exist_ok=True)
         values = base.execute(
-            docker_args + [docker_img] + job.task._command_args(values=values),
+            docker_args + [docker_img] + job.task._command_args(values=arg_values),
         )
         output = dict(zip(keys, values))
         if output["return_code"]:

pydra/utils/typing.py

@@ -527,7 +527,7 @@ def check_union(tp, pattern_args):
                         except TypeError as e:
                             reasons.append(e)
                         else:
-                            reasons = None
+                            reasons = []
                             break
                     if self.match_any_of_union and len(reasons) < len(tp_args):
                         # Just need one of the union args to match
@@ -1122,16 +1122,42 @@ def is_fileset_or_union(type_: type, allow_none: bool | None = None) -> bool:
     is_fileset : bool
         whether the type is a FileSet or a Union containing a FileSet
     """
+    return is_subclass_or_union(type_, core.FileSet, allow_none=allow_none)
+
+
+def is_subclass_or_union(
+    type_: type, reference: type, allow_none: bool | None = None
+) -> bool:
+    """Check if the type is a subclass of given reference or a Union containing
+    that reference type
+
+    Parameters
+    ----------
+    type_ : type
+        the type to check
+    reference : type
+        the reference type to check whether the type is a sub-class of or not
+    allow_none : bool, optional
+        whether to allow None as a valid type, by default None. If None, then None
+        is not allowed at the outer layer, but is allowed within a Union
+
+    Returns
+    -------
+    bool
+        whether the type is a FileSet or a Union containing a FileSet
+    """
     if type_ is None and allow_none:
         return True
     if is_union(type_):
         return any(
-            is_fileset_or_union(t, allow_none=allow_none or allow_none is None)
+            is_subclass_or_union(
+                t, reference, allow_none=allow_none or allow_none is None
+            )
             for t in ty.get_args(type_)
         )
     elif not inspect.isclass(type_):
         return False
-    return issubclass(type_, core.FileSet)
+    return issubclass(type_, reference)
 
 
 def is_type(*args: ty.Any) -> bool:

pyproject.toml

@@ -57,7 +57,7 @@ doc = [
     "packaging",
     "pandas",
     "pandoc",
-    "pydra-mrtrix3 >=3.0.4a17",
+    "pydra-tasks-mrtrix3 >=3.1.0a1",
     "scipy",
     "sphinx",
     "sphinx-argparse",
@@ -100,7 +100,7 @@ tutorial = [
     "openneuro-py",
     "pandas",
     "psutil",
-    "pydra-mrtrix3 >=3.0.4a17",
+    "pydra-tasks-mrtrix3 >=3.1.0a1",
     "scipy",
     "sh",
 ]