debugging interface conversions

Author: tclose

.gitignore

@@ -22,4 +22,4 @@ __pycache__
 /outputs
 /test-data
 /nipype2pydra/_version.py
-
+/required-fileformats/**/_version.py

nipype2pydra/interface/base.py

@@ -683,23 +683,23 @@ def pydra_fld_output(self, field, name):
             pydra_metadata["callable"] = self.outputs.callables[name]
         return (pydra_type, pydra_metadata)
 
-    def function_callables(self):
-        if not self.outputs.callables:
-            return ""
-        if not self.callables_module:
-            raise Exception(
-                "callables module must be provided if output_callables are set in the spec file"
-            )
-        fun_str = ""
-        if list(set(self.outputs.callables.values())):
-            fun_str = inspect.getsource(self.callables_module)
-        # fun_names.sort()
-        # for fun_nm in fun_names:
-        #     fun = getattr(self.callables_module, fun_nm)
-        #     fun_str += inspect.getsource(fun) + "\n"
-        # list_outputs = getattr(self.callables_module, "_list_outputs")
-        # fun_str += inspect.getsource(list_outputs) + "\n"
-        return fun_str
+    # def function_callables(self):
+    #     if not self.outputs.callables:
+    #         return ""
+    #     if not self.callables_module:
+    #         raise Exception(
+    #             "callables module must be provided if output_callables are set in the spec file"
+    #         )
+    #     fun_str = ""
+    #     if list(set(self.outputs.callables.values())):
+    #         fun_str = inspect.getsource(self.callables_module)
+    #     # fun_names.sort()
+    #     # for fun_nm in fun_names:
+    #     #     fun = getattr(self.callables_module, fun_nm)
+    #     #     fun_str += inspect.getsource(fun) + "\n"
+    #     # list_outputs = getattr(self.callables_module, "_list_outputs")
+    #     # fun_str += inspect.getsource(list_outputs) + "\n"
+    #     return fun_str
 
     def pydra_type_converter(self, field, spec_type, name):
         """converting types to types used in pydra"""

nipype2pydra/interface/python.py

@@ -18,10 +18,13 @@ def type2str(type_):
         return type_
     if type_ is ty.Any:
         return "ty.Any"
-    elif hasattr(type_, "__name__"):
-        return type_.__name__
+    if origin := ty.get_origin(type_):
+        return f"{type2str(origin)}[{', '.join(type2str(arg) for arg in ty.get_args(type_))}]"
+    module_name = "ty." if type_.__module__ == "typing" else ""
+    if hasattr(type_, "__name__"):
+        return module_name + type_.__name__
     elif hasattr(type_, "__qualname__"):
-        return type_.__qualname__
+        return module_name + type_.__qualname__
     else:
         return str(type_).replace("typing.", "ty.")
 
@@ -151,7 +154,9 @@ def generate_code(self, input_fields, nonstd_types, output_fields) -> ty.Tuple[
         assert method_body, "Neither `run_interface` and `list_outputs` are defined"
 
         spec_str = "@python.define\n"
-        spec_str += f"class {self.task_name}(python.Task['{self.task_name}.Outputs']):\n"
+        spec_str += (
+            f"class {self.task_name}(python.Task['{self.task_name}.Outputs']):\n"
+        )
         spec_str += '    """\n'
         spec_str += self.create_doctests(
             input_fields=input_fields, nonstd_types=nonstd_types
@@ -181,14 +186,13 @@ def generate_code(self, input_fields, nonstd_types, output_fields) -> ty.Tuple[
         if any(t is not ty.Any for t in output_types):
             spec_str += " -> "
             if len(output_types) > 1:
-                spec_str += "tuples[" + ", ".join(output_types) + "]"
+                spec_str += "tuple[" + ", ".join(output_types) + "]"
             else:
                 spec_str += output_types[0]
         spec_str += ":\n"
         spec_str += "    " + method_body.replace("\n", "\n    ") + "\n"
         spec_str += "\n        return {}".format(", ".join(output_names))
 
-
         for m in sorted(self.used.methods, key=attrgetter("__name__")):
             if m.__name__ not in self.included_methods:
                 spec_str += "\n\n" + self.process_method(

nipype2pydra/interface/shell.py

@@ -107,7 +107,11 @@ def generate_code(self, input_fields, nonstd_types, output_fields) -> str:
                 name, _, __, mdata = inpt
             if "xor" in mdata:
                 xor_sets.add(frozenset(list(mdata["xor"]) + [name]))
-            if mdata.get("position", None) == 0:
+            pos = mdata.get("position", None)
+            if isinstance(pos, str):
+                # convert string reprs (I think a mistake) to ints
+                pos = mdata["position"] = int(pos)
+            if pos == 0:
                 has_zero_pos = True
 
         # Increment positions if there is a zero position
@@ -164,6 +168,8 @@ def generate_code(self, input_fields, nonstd_types, output_fields) -> str:
             output_fields_str += (
                 f"        {name}: {type_to_str(type_)} = shell.out({', '.join(args)})\n"
             )
+        if not output_fields_str:
+            output_fields_str = "        pass\n"
 
         spec_str = (
             self.init_code

nipype2pydra/interface/tests/test_interface.py

@@ -24,11 +24,35 @@
     "ants-interfaces-ai",
     "ants-interfaces-measure_image_similarity",
     "ants-interfaces-threshold_image",
-    "fsl-interfaces-prob_track_x2",
-    "fsl-interfaces-flameo",
-    "fsl-interfaces-make_dyadic_vectors",
+    "fsl-interfaces-copy_geom",
+    "fsl-interfaces-flirt",
+    "fsl-interfaces-mcflirt",
+    "fsl-interfaces-filmgls",
+    "fsl-interfaces-topup",
+    "fsl-interfaces-slice",
+    "fsl-interfaces-apply_topup",
+    "fsl-interfaces-tract_skeleton",
+    "fsl-interfaces-smooth_estimate",
+    "fsl-interfaces-apply_xfm",
     "fsl-interfaces-dual_regression",
-    "fsl-interfaces-epi_de_warp",
+    "fsl-interfaces-eddy",
+    "fsl-interfaces-split",
+    "freesurfer-interfaces-logan",
+    "freesurfer-interfaces-mrtm1",
+    "freesurfer-interfaces-mrtm2",
+    "freesurfer-interfaces-concatenate_lta",
+    "freesurfer-interfaces-one_sample_t_test",
+    "freesurfer-interfaces-concatenate",
+    "freesurfer-interfaces-mris_preproc_recon_all",
+    "freesurfer-interfaces-recon_all",
+    "freesurfer-interfaces-glm_fit",
+    "freesurfer-interfaces-mri_convert",
+    "freesurfer-interfaces-parcellation_stats",
+    "freesurfer-interfaces-mp_rto_mni305",
+    "afni-interfaces-qwarp_plus_minus",
+    "afni-interfaces-qwarp",
+    "afni-interfaces-align_epi_anat_py",
+    "afni-interfaces-fwh_mx",
 ]
 
 XFAIL_INTERFACES_IN_COMBINED = [
@@ -48,10 +72,10 @@
     params=[
         str(p.relative_to(EXAMPLE_INTERFACES_DIR)).replace("/", "-")[:-5]
         for p in (EXAMPLE_INTERFACES_DIR).glob("**/interfaces/*.yaml")
-        if (
-            str(p.relative_to(EXAMPLE_INTERFACES_DIR)).replace("/", "-")[:-5]
-            not in XFAIL_INTERFACES
-        )
+        # if (
+        #     str(p.relative_to(EXAMPLE_INTERFACES_DIR)).replace("/", "-")[:-5]
+        #     not in XFAIL_INTERFACES
+        # )
     ]
 )
 def interface_spec_file(request):
@@ -63,57 +87,56 @@ def interface_spec_file(request):
 def test_interface_convert(
     interface_spec_file, cli_runner, work_dir, gen_test_conftest
 ):
-    # Clear UsedSymbol caches
+    # Clear UsedSymbol caches from previous tests
     clear_caches()
 
-    try:
-        with open(interface_spec_file) as f:
-            interface_spec = yaml.safe_load(f)
-        pkg_root = work_dir / "src"
-        pkg_root.mkdir()
-        # shutil.copyfile(gen_test_conftest, pkg_root / "conftest.py")
-
-        pkg_converter = PackageConverter(
-            name="nipype2pydratest."
-            + "_".join(
-                interface_spec["nipype_module"].split(".")
-                + [interface_spec["task_name"]]
-            ),
-            nipype_name=interface_spec["nipype_module"],
-            interface_only=True,
-        )
+    with open(interface_spec_file) as f:
+        interface_spec = yaml.safe_load(f)
+    pkg_root = work_dir / "src"
+    pkg_root.mkdir()
+    # shutil.copyfile(gen_test_conftest, pkg_root / "conftest.py")
+
+    pkg_converter = PackageConverter(
+        name="nipype2pydratest."
+        + "_".join(
+            interface_spec["nipype_module"].split(".") + [interface_spec["task_name"]]
+        ),
+        nipype_name=interface_spec["nipype_module"],
+        interface_only=True,
+    )
 
-        converter = pkg_converter.add_interface_from_spec(
-            spec=interface_spec,
-            # callables_file=interface_spec_file.parent
-            # / (interface_spec_file.stem + "_callables.py"),
-        )
+    converter = pkg_converter.add_interface_from_spec(
+        spec=interface_spec,
+        # callables_file=interface_spec_file.parent
+        # / (interface_spec_file.stem + "_callables.py"),
+    )
 
-        converter.write(pkg_root)
-
-        nipype_ports = []
-        intra_pkg_modules = defaultdict(set)
-
-        for _, klass in converter.used.imported_classes:
-            address = full_address(klass)
-            if address in pkg_converter.nipype_port_converters:
-                nipype_ports.append(pkg_converter.nipype_port_converters[address])
-        for _, func in converter.used.imported_funcs:
-            if full_address(func) not in list(pkg_converter.workflows):
-                intra_pkg_modules[func.__module__].add(func)
-
-        already_converted = set()
-        for converter in tqdm(
-            nipype_ports, "Porting interfaces from the core nipype package"
-        ):
-            converter.write(
-                pkg_root,
-                already_converted=already_converted,
-            )
+    converter.write(pkg_root)
+
+    nipype_ports = []
+    intra_pkg_modules = defaultdict(set)
+
+    for _, klass in converter.used.imported_classes:
+        address = full_address(klass)
+        if address in pkg_converter.nipype_port_converters:
+            nipype_ports.append(pkg_converter.nipype_port_converters[address])
+    for _, func in converter.used.imported_funcs:
+        if full_address(func) not in list(pkg_converter.workflows):
+            intra_pkg_modules[func.__module__].add(func)
+
+    already_converted = set()
+    for converter in tqdm(
+        nipype_ports, "Porting interfaces from the core nipype package"
+    ):
+        converter.write(
+            pkg_root,
+            already_converted=already_converted,
+        )
 
-        # Write any additional functions in other modules in the package
-        pkg_converter.write_intra_pkg_modules(pkg_root, intra_pkg_modules)
+    # Write any additional functions in other modules in the package
+    pkg_converter.write_intra_pkg_modules(pkg_root, intra_pkg_modules)
 
+    try:
         with add_to_sys_path(pkg_root):
             try:
                 pydra_module = import_module(converter.output_module)
@@ -202,7 +225,13 @@ def test_interface_convert(
 
         # assert result.value == 0
     except Exception:
-        task_name = interface_spec_file.parent.name + "-" + interface_spec_file.stem
+        task_name = "-".join(
+            [
+                interface_spec_file.parent.parent.name,
+                interface_spec_file.parent.name,
+                interface_spec_file.stem,
+            ]
+        )
         if task_name in XFAIL_INTERFACES or task_name in XFAIL_INTERFACES_IN_COMBINED:
             msg = f"Test for '{task_name}' is expected to fail:\n{format_exc()}"
             if task_name in XFAIL_INTERFACES_IN_COMBINED:

nipype2pydra/package.py

@@ -732,9 +732,7 @@ def nipype_port_converters(self) -> ty.Dict[str, interface.BaseInterfaceConverte
                 + "."
                 + to_snake_case(task_name)
             )
-            converter = interface.get_converter(
-                output_module=output_module, callables_module=callables_file, **spec
-            )
+            converter = interface.get_converter(output_module=output_module, **spec)
             converter.package = self
             converters[converter.full_address] = converter
 

required-fileformats/afni/fileformats/medimage_afni/_version.py

@@ -1,8 +1,13 @@
-# file generated by setuptools_scm
+# file generated by setuptools-scm
 # don't change, don't track in version control
+
+__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+
 TYPE_CHECKING = False
 if TYPE_CHECKING:
-    from typing import Tuple, Union
+    from typing import Tuple
+    from typing import Union
+
     VERSION_TUPLE = Tuple[Union[int, str], ...]
 else:
     VERSION_TUPLE = object
@@ -12,5 +17,5 @@
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.2.3.dev42+gb9e3ee9.d20240226'
-__version_tuple__ = version_tuple = (0, 2, 3, 'dev42', 'gb9e3ee9.d20240226')
+__version__ = version = '0.4.5.dev37+gfb38d6c.d20250731'
+__version_tuple__ = version_tuple = (0, 4, 5, 'dev37', 'gfb38d6c.d20250731')

required-fileformats/ants/fileformats/medimage_ants/_version.py

@@ -1,8 +1,13 @@
-# file generated by setuptools_scm
+# file generated by setuptools-scm
 # don't change, don't track in version control
+
+__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+
 TYPE_CHECKING = False
 if TYPE_CHECKING:
-    from typing import Tuple, Union
+    from typing import Tuple
+    from typing import Union
+
     VERSION_TUPLE = Tuple[Union[int, str], ...]
 else:
     VERSION_TUPLE = object
@@ -12,5 +17,5 @@
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.2.3.dev42+gb9e3ee9.d20240226'
-__version_tuple__ = version_tuple = (0, 2, 3, 'dev42', 'gb9e3ee9.d20240226')
+__version__ = version = '0.4.5.dev37+gfb38d6c.d20250731'
+__version_tuple__ = version_tuple = (0, 4, 5, 'dev37', 'gfb38d6c.d20250731')

required-fileformats/brainsuite/fileformats/medimage_brainsuite/_version.py

@@ -1,8 +1,13 @@
-# file generated by setuptools_scm
+# file generated by setuptools-scm
 # don't change, don't track in version control
+
+__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+
 TYPE_CHECKING = False
 if TYPE_CHECKING:
-    from typing import Tuple, Union
+    from typing import Tuple
+    from typing import Union
+
     VERSION_TUPLE = Tuple[Union[int, str], ...]
 else:
     VERSION_TUPLE = object
@@ -12,5 +17,5 @@
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.2.3.dev42+gb9e3ee9.d20240226'
-__version_tuple__ = version_tuple = (0, 2, 3, 'dev42', 'gb9e3ee9.d20240226')
+__version__ = version = '0.4.5.dev37+gfb38d6c.d20250731'
+__version_tuple__ = version_tuple = (0, 4, 5, 'dev37', 'gfb38d6c.d20250731')

required-fileformats/bru2nii/fileformats/medimage_bru2nii/_version.py

@@ -1,8 +1,13 @@
-# file generated by setuptools_scm
+# file generated by setuptools-scm
 # don't change, don't track in version control
+
+__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+
 TYPE_CHECKING = False
 if TYPE_CHECKING:
-    from typing import Tuple, Union
+    from typing import Tuple
+    from typing import Union
+
     VERSION_TUPLE = Tuple[Union[int, str], ...]
 else:
     VERSION_TUPLE = object
@@ -12,5 +17,5 @@
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.2.3.dev42+gb9e3ee9.d20240226'
-__version_tuple__ = version_tuple = (0, 2, 3, 'dev42', 'gb9e3ee9.d20240226')
+__version__ = version = '0.4.5.dev37+gfb38d6c.d20250731'
+__version_tuple__ = version_tuple = (0, 4, 5, 'dev37', 'gfb38d6c.d20250731')