updated specification syntax to match latest workflow-src branch of n…

…ipype2pydra

nipype-auto-conv/generate

@@ -1,81 +1,3 @@
-#!/usr/bin/env python3
-import sys
-import os.path
-from warnings import warn
-from pathlib import Path
-import shutil
-from importlib import import_module
-import yaml
-from tqdm import tqdm
-import nipype
-import nipype2pydra.utils
-from nipype2pydra.task import get_converter
-
-
-SPECS_DIR = Path(__file__).parent / "specs"
-PKG_ROOT = Path(__file__).parent.parent
-PKG_NAME = "freesurfer"
-
-if ".dev" in nipype.__version__:
-    raise RuntimeError(
-        f"Cannot use a development version of Nipype {nipype.__version__}"
-    )
-
-if ".dev" in nipype2pydra.__version__:
-    warn(
-        f"using development version of nipype2pydra ({nipype2pydra.__version__}), "
-        f"development component will be dropped in {PKG_NAME} package version"
-    )
-
-# Insert specs dir into path so we can load callables modules
-sys.path.insert(0, str(SPECS_DIR))
-
-auto_init = f"# Auto-generated by {__file__}, do not edit as it will be overwritten\n\n"
-
-auto_dir = PKG_ROOT / "pydra" / "tasks" / PKG_NAME / "auto"
-if auto_dir.exists():
-    shutil.rmtree(auto_dir)
-
-all_interfaces = []
-for fspath in tqdm(
-    sorted(SPECS_DIR.glob("**/*.yaml")), "converting interfaces from Nipype to Pydra"
-):
-    with open(fspath) as f:
-        spec = yaml.load(f, Loader=yaml.SafeLoader)
-
-    rel_pkg_path = str(fspath.parent.relative_to(SPECS_DIR)).replace(os.path.sep, ".")
-    if rel_pkg_path == ".":
-        rel_pkg_path = fspath.stem
-    else:
-        rel_pkg_path += "." + fspath.stem
-
-    callables = import_module(rel_pkg_path + "_callables")
-
-    module_name = nipype2pydra.utils.to_snake_case(spec["task_name"])
-
-    converter = get_converter(
-        output_module=f"pydra.tasks.{PKG_NAME}.auto.{module_name}",
-        callables_module=callables,  # type: ignore
-        **spec,
-    )
-    converter.generate(PKG_ROOT)
-    auto_init += f"from .{module_name} import {converter.task_name}\n"
-    all_interfaces.append(converter.task_name)
-
-
-with open(PKG_ROOT / "pydra" / "tasks" / PKG_NAME / "auto" / "_version.py", "w") as f:
-    f.write(
-        f"""# Auto-generated by {__file__}, do not edit as it will be overwritten
-
-nipype_version = "{nipype.__version__.split('.dev')[0]}"
-nipype2pydra_version = "{nipype2pydra.__version__.split('.dev')[0]}"
-post_release = (nipype_version + nipype2pydra_version).replace(".", "")
-"""
-    )
-
-auto_init += (
-    "\n\n__all__ = [\n" + "\n".join(f'    "{i}",' for i in all_interfaces) + "\n]\n"
-)
-
-with open(PKG_ROOT / "pydra" / "tasks" / PKG_NAME / "auto" / "__init__.py", "w") as f:
-    f.write(auto_init)
+#!/usr/bin/env bash
+conv_dir=$(dirname $0)
+nipype2pydra convert $conv_dir/specs $conv_dir/..

nipype-auto-conv/requirements.txt

@@ -1,12 +1,2 @@
-black
-attrs>=22.1.0
 nipype
-tqdm
-pydra
-PyYAML>=6.0
-fileformats >=0.8
-fileformats-medimage >=0.4
-fileformats-datascience >= 0.1
-fileformats-medimage-freesurfer
-traits
 nipype2pydra

nipype-auto-conv/specs/package.yaml

@@ -0,0 +1,8 @@
+# name of the package to generate, e.g. pydra.tasks.mriqc
+name: pydra.tasks.freesurfer
+# name of the nipype package to generate from (e.g. mriqc)
+nipype_name: nipype.interfaces.freesurfer
+# The name of the global struct/dict that contains workflow inputs that are to be converted to inputs of the function along with the type of the struct, either "dict" or "class"
+config_params: null
+# Mappings between nipype packages and their pydra equivalents. Regular expressions are supported
+import_translations: null