starting to debug generic script for task conversions

Author: tclose

nipype2pydra/cli.py

@@ -23,6 +23,13 @@ def cli():
 )
 @click.argument("spec-file", type=click.File())
 @click.argument("out-file", type=click.File(mode="w"))
+@click.option(
+    "-c",
+    "--callables",
+    type=click.File(),
+    default=None,
+    help="a Python file containing callable functions required in the command interface",
+)
 @click.option(
     "-i",
     "--interface_name",
@@ -33,14 +40,14 @@ def cli():
         "provided all interfaces defined in the spec are converted"
     ),
 )
-def task(spec_file, out_file, interface_name):
+def task(spec_file, out_file, interface_name, callables):
 
     spec = yaml.safe_load(spec_file)
 
     if interface_name:
         spec = {n: v for n, v in spec.items() if n in interface_name}
 
-    converter = TaskConverter(spec)
+    converter = TaskConverter(spec, callables)
     code = converter.generate()
     out_file.write(code)
 

nipype2pydra/task.py

@@ -2,6 +2,7 @@
 from pathlib import Path
 import typing as ty
 import inspect
+import sys
 from importlib import import_module
 from copy import copy
 import black
@@ -57,7 +58,7 @@ class TaskConverter:
         ("\'MultiOutputFile\'", "specs.MultiOutputFile"),
     ]
 
-    def __init__(self, interface_spec, callables):
+    def __init__(self, interface_spec, callables_file):
         self.interface_spec = copy(interface_spec)
         if self.interface_spec.get("output_requirements") is None:
             self.interface_spec["output_requirements"] = []
@@ -84,6 +85,10 @@ def __init__(self, interface_spec, callables):
         self.cmd = nipype_interface._cmd
         self.nipype_input_spec = nipype_interface.input_spec()
         self.nipype_output_spec = nipype_interface.output_spec()
+        sys.path.append(str(Path(callables_file).resolve().parent))
+        self.callables_module = import_module(Path(callables_file).stem)
+        sys.path.pop()
+# import callablescallables
 
     def pydra_specs(self, write=False, dirname=None):
         """creating pydra input/output spec from nipype specs
@@ -398,7 +403,7 @@ def function_callables(self):
         fun_names = list(set(self.interface_spec["output_callables"].values()))
         fun_names.sort()
         for fun_nm in fun_names:
-            fun = getattr(callables, fun_nm)
+            fun = getattr(self.callables_module, fun_nm)
             fun_str += inspect.getsource(fun) + "\n"
         return fun_str