Merge pull request #16 from nipype/latest-nipype-conv

Set up nipype2pydra converter templates

.gitignore

@@ -131,11 +131,18 @@ dmypy.json
 # Pycharm
 .idea
 
+# Vim
+.*.sw[op]
+
 # VS Code
 .vscode
 
 # Mac garbarge
 .DS_store
 
+# Generated files
+/pydra/tasks/ants/_version.py
+/related-packages/fileformats/fileformats/medimage_ants/_version.py
+/related-packages/fileformats-extras/fileformats/extras/medimage_ants/_version.py
 /pydra/tasks/ants/auto
 /pydra/tasks/ants/_version.py

README.rst

@@ -1,11 +1,11 @@
-===============================
+===========================
 Pydra task package for ants
-===============================
+===========================
 
-.. image:: https://github.com/nipype/pydra-ants/actions/workflows/pythonpackage.yaml/badge.svg
-   :target: https://github.com/nipype/pydra-ants/actions/workflows/pythonpackage.yaml
-.. .. image:: https://codecov.io/gh/nipype/pydra-ants/branch/main/graph/badge.svg?token=UIS0OGPST7
-..    :target: https://codecov.io/gh/nipype/pydra-ants
+.. image:: https://github.com/nipype/pydra-ants/actions/workflows/ci-cd.yaml/badge.svg
+   :target: https://github.com/nipype/pydra-ants/actions/workflows/ci-cd.yaml
+.. image:: https://codecov.io/gh/nipype/pydra-ants/branch/main/graph/badge.svg?token=UIS0OGPST7
+   :target: https://codecov.io/gh/nipype/pydra-ants
 .. image:: https://img.shields.io/pypi/pyversions/pydra-ants.svg
    :target: https://pypi.python.org/pypi/pydra-ants/
    :alt: Supported Python versions
@@ -27,7 +27,7 @@ Automatically generated tasks can be found in the `pydra.tasks.ants.auto` packag
 These packages should be treated with extreme caution as they likely do not pass testing.
 Generated tasks that have been edited and pass testing are imported into one or more of the
 `pydra.tasks.ants.v*` packages, corresponding to the version of the ants toolkit
-they are designed for. 
+they are designed for.
 
 Tests
 -----
@@ -71,14 +71,22 @@ Contributing to this package
 Developer installation
 ~~~~~~~~~~~~~~~~~~~~~~
 
+Install the `fileformats <https://arcanaframework.github.io/fileformats/>`__ packages
+corresponding to AFNI specific file formats
+
+
+.. code-block::
+
+   $ pip install -e ./related-packages/fileformats[dev]
+   $ pip install -e ./related-packages/fileformats-extras[dev]
 
 Install repo in developer mode from the source directory and install pre-commit to
 ensure consistent code-style and quality.
 
 .. code-block::
 
    $ pip install -e .[test,dev]
-$ pre-commit install
+   $ pre-commit install
 
 Next install the requirements for running the auto-conversion script and generate the
 Pydra task interfaces from their Nipype counterparts
@@ -93,7 +101,8 @@ The run the conversion script to convert Nipype interfaces to Pydra
 
    $ nipype-auto-conv/generate
 
-## Methodology
+Methodology
+~~~~~~~~~~~
 
 The development of this package is expected to have two phases
 
@@ -149,6 +158,6 @@ in the ``inputs > types`` and ``outputs > types`` dicts of the YAML spec.
 
 If the required file-type is not found implemented within fileformats, please see the `fileformats
 docs <https://arcanaframework.github.io/fileformats/developer.html>`__ for instructions on how to define
-new fileformat types, and see 
+new fileformat types, and see
 `fileformats-medimage-extras <https://github.com/ArcanaFramework/fileformats-medimage-extras/blob/6c2dabe91e95687eebc2639bb6f034cf9595ecfc/fileformats/extras/medimage/nifti.py#L30-L48>`__
 for an example on how to implement methods to generate sample data for them.

nipype-auto-conv/generate

@@ -5,10 +5,11 @@ from warnings import warn
 from pathlib import Path
 import shutil
 from importlib import import_module
+from tqdm import tqdm
 import yaml
 import nipype
 import nipype2pydra.utils
-from nipype2pydra.task import TaskConverter
+from nipype2pydra.task import get_converter
 
 
 SPECS_DIR = Path(__file__).parent / "specs"
@@ -35,7 +36,10 @@ auto_dir = PKG_ROOT / "pydra" / "tasks" / PKG_NAME / "auto"
 if auto_dir.exists():
     shutil.rmtree(auto_dir)
 
-for fspath in sorted(SPECS_DIR.glob("**/*.yaml")):
+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)
 
@@ -49,13 +53,14 @@ for fspath in sorted(SPECS_DIR.glob("**/*.yaml")):
 
     module_name = nipype2pydra.utils.to_snake_case(spec["task_name"])
 
-    converter = TaskConverter(
+    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:
@@ -68,5 +73,9 @@ 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)

nipype-auto-conv/requirements.txt

@@ -2,10 +2,11 @@ black
 attrs>=22.1.0
 nipype
 pydra
+tqdm
 PyYAML>=6.0
 fileformats >=0.8
 fileformats-medimage >=0.4
 fileformats-datascience >= 0.1
 fileformats-medimage-ants
 traits
-nipype2pydra
+nipype2pydra

nipype-auto-conv/specs/affine_initializer.yaml

@@ -5,17 +5,17 @@
 #
 # Docs
 # ----
-# 
+#
 #     Initialize an affine transform (as in antsBrainExtraction.sh)
-# 
+#
 #     >>> from nipype.interfaces.ants import AffineInitializer
 #     >>> init = AffineInitializer()
 #     >>> init.inputs.fixed_image = 'fixed1.nii'
 #     >>> init.inputs.moving_image = 'moving1.nii'
 #     >>> init.cmdline
 #     'antsAffineInitializer 3 fixed1.nii moving1.nii transform.mat 15.000000 0.100000 0 10'
-# 
-#     
+#
+#
 task_name: AffineInitializer
 nipype_name: AffineInitializer
 nipype_module: nipype.interfaces.ants.utils
@@ -34,9 +34,12 @@ inputs:
     # type=file|default=<undefined>: reference image
     moving_image: medimage/nifti1
     # type=file|default=<undefined>: moving image
-    out_file: generic/file
+    out_file: Path
     # type=file: output transform file
     # type=file|default='transform.mat': output transform file
+  callable_defaults:
+  # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py`
+  # to set as the `default` method of input fields
   metadata:
   # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1)
 outputs:
@@ -88,15 +91,15 @@ tests:
     environ:
     # type=dict|default={}: Environment variables
   imports:
-  # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item
+  # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item
   # consisting of 'module', 'name', and optionally 'alias' keys
   expected_outputs:
   # dict[str, str] - expected values for selected outputs, noting that tests will typically
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true
@@ -110,15 +113,15 @@ tests:
     moving_image:
     # type=file|default=<undefined>: moving image
   imports:
-  # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item
+  # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item
   # consisting of 'module', 'name', and optionally 'alias' keys
   expected_outputs:
   # dict[str, str] - expected values for selected outputs, noting that tests will typically
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true
@@ -131,12 +134,12 @@ doctests:
   # dict[str, str] - name-value pairs for inputs to be provided to the doctest.
   # If the field is of file-format type and the value is None, then the
   # '.mock()' method of the corresponding class is used instead.
-    fixed_image:
+    fixed_image: '"fixed1.nii"'
     # type=file|default=<undefined>: reference image
-    moving_image:
+    moving_image: '"moving1.nii"'
     # type=file|default=<undefined>: moving image
   imports:
-  # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item
+  # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item
   # consisting of 'module', 'name', and optionally 'alias' keys
   directive:
   # str - any doctest directive to place on the cmdline call, e.g. # doctest: +ELLIPSIS

nipype-auto-conv/specs/affine_initializer_callables.py

@@ -1 +1,20 @@
-"""Module to put any functions that are referred to in AffineInitializer.yaml"""
+"""Module to put any functions that are referred to in the "callables" section of AffineInitializer.yaml"""
+
+import os
+
+
+def out_file_callable(output_dir, inputs, stdout, stderr):
+    outputs = _list_outputs(
+        output_dir=output_dir, inputs=inputs, stdout=stdout, stderr=stderr
+    )
+    return outputs["out_file"]
+
+
+# Original source at L885 of <nipype-install>/interfaces/base/core.py
+def _gen_filename(name, inputs=None, stdout=None, stderr=None, output_dir=None):
+    raise NotImplementedError
+
+
+# Original source at L834 of <nipype-install>/interfaces/ants/utils.py
+def _list_outputs(inputs=None, stdout=None, stderr=None, output_dir=None):
+    return {"out_file": os.path.abspath(inputs.out_file)}

nipype-auto-conv/specs/ai.yaml

@@ -5,9 +5,9 @@
 #
 # Docs
 # ----
-# 
+#
 #     Calculate the optimal linear transform parameters for aligning two images.
-# 
+#
 #     Examples
 #     --------
 #     >>> AI(
@@ -17,16 +17,16 @@
 #     ... ).cmdline
 #     'antsAI -c [10,1e-06,10] -d 3 -m Mattes[structural.nii,epi.nii,32,Regular,1]
 #     -o initialization.mat -p 0 -s [20,0.12] -t Affine[0.1] -v 0'
-# 
+#
 #     >>> AI(fixed_image='structural.nii',
 #     ...    moving_image='epi.nii',
 #     ...    metric=('Mattes', 32, 'Regular', 1),
 #     ...    search_grid=(12, (1, 1, 1)),
 #     ... ).cmdline
 #     'antsAI -c [10,1e-06,10] -d 3 -m Mattes[structural.nii,epi.nii,32,Regular,1]
 #     -o initialization.mat -p 0 -s [20,0.12] -g [12.0,1x1x1] -t Affine[0.1] -v 0'
-# 
-#     
+#
+#
 task_name: AI
 nipype_name: AI
 nipype_module: nipype.interfaces.ants.utils
@@ -43,15 +43,18 @@ inputs:
   # passed to the field in the automatically generated unittests.
     fixed_image: generic/file
     # type=file|default=<undefined>: Image to which the moving_image should be transformed
-    moving_image: generic/file
-    # type=file|default=<undefined>: Image that will be transformed to fixed_image
     fixed_image_mask: generic/file
     # type=file|default=<undefined>: fixed mage mask
+    moving_image: generic/file
+    # type=file|default=<undefined>: Image that will be transformed to fixed_image
     moving_image_mask: generic/file
     # type=file|default=<undefined>: moving mage mask
-    output_transform: generic/file
+    output_transform: Path
     # type=file: output file name
     # type=file|default='initialization.mat': output file name
+  callable_defaults:
+  # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py`
+  # to set as the `default` method of input fields
   metadata:
   # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1)
 outputs:
@@ -113,15 +116,15 @@ tests:
     environ:
     # type=dict|default={}: Environment variables
   imports:
-  # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item
+  # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item
   # consisting of 'module', 'name', and optionally 'alias' keys
   expected_outputs:
   # dict[str, str] - expected values for selected outputs, noting that tests will typically
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true

nipype-auto-conv/specs/ai_callables.py

@@ -1 +1,18 @@
-"""Module to put any functions that are referred to in AI.yaml"""
+"""Module to put any functions that are referred to in the "callables" section of AI.yaml"""
+
+
+def output_transform_callable(output_dir, inputs, stdout, stderr):
+    outputs = _list_outputs(
+        output_dir=output_dir, inputs=inputs, stdout=stdout, stderr=stderr
+    )
+    return outputs["output_transform"]
+
+
+# Original source at L885 of <nipype-install>/interfaces/base/core.py
+def _gen_filename(name, inputs=None, stdout=None, stderr=None, output_dir=None):
+    raise NotImplementedError
+
+
+# Original source at L539 of <nipype-install>/interfaces/ants/utils.py
+def _list_outputs(inputs=None, stdout=None, stderr=None, output_dir=None):
+    return getattr(self, "_output")