Merge pull request #11 from nipype/develop

debugged unittests

Author: tclose

.github/workflows/tests.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.7", "3.11"]
+        python-version: ["3.8", "3.11"]
       fail-fast: false
     runs-on: ${{ matrix.os }}
     defaults:

.gitignore

@@ -1,4 +1,4 @@
-.venv
+.venv*
 /.project
 /.pydevproject
 *.pyc

example-specs/task/ants_n4_bias_field_correction.yaml

@@ -164,6 +164,8 @@ tests:
     dimension: '3'
     input_image:
     bspline_fitting_distance: '300'
+    save_bias: 'False'
+    copy_header: 'False'
     shrink_factor: '3'
     n_iterations: '[50,50,30,20]'
   imports: &id001
@@ -186,6 +188,10 @@ tests:
   # dict[str, str] - values to provide to inputs fields in the task initialisation
   # (if not specified, will try to choose a sensible value)
     convergence_threshold: 1e-6
+    n_iterations: '[50,50,30,20]'
+    input_image:
+    save_bias: 'False'
+    copy_header: 'False'
   imports:
   # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item
   # consisting of 'module', 'name', and optionally 'alias' keys
@@ -205,6 +211,10 @@ tests:
   # dict[str, str] - values to provide to inputs fields in the task initialisation
   # (if not specified, will try to choose a sensible value)
     bspline_order: '5'
+    bspline_fitting_distance: 10
+    save_bias: 'False'
+    copy_header: 'False'
+    input_image:
   imports:
   # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item
   # consisting of 'module', 'name', and optionally 'alias' keys
@@ -225,6 +235,7 @@ tests:
   # (if not specified, will try to choose a sensible value)
     input_image:
     save_bias: 'True'
+    copy_header: 'False'
     dimension: '3'
   imports:
   # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item
@@ -247,6 +258,8 @@ tests:
     input_image:
     dimension: '3'
     histogram_sharpening: (0.12, 0.02, 200)
+    save_bias: 'False'
+    copy_header: 'False'
   imports:
   # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item
   # consisting of 'module', 'name', and optionally 'alias' keys
@@ -274,6 +287,8 @@ doctests:
     bspline_fitting_distance: '300'
     shrink_factor: '3'
     n_iterations: '[50,50,30,20]'
+    save_bias: 'False'
+    copy_header: 'False'
   imports: *id001
   # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item
   # consisting of 'module', 'name', and optionally 'alias' keys
@@ -286,6 +301,9 @@ doctests:
   # If the field is of file-format type and the value is None, then the
   # '.mock()' method of the corresponding class is used instead.
     convergence_threshold: 1e-6
+    n_iterations: '[50,50,30,20]'
+    save_bias: 'False'
+    copy_header: 'False'
   imports:
   # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item
   # consisting of 'module', 'name', and optionally 'alias' keys
@@ -298,6 +316,8 @@ doctests:
   # If the field is of file-format type and the value is None, then the
   # '.mock()' method of the corresponding class is used instead.
     bspline_order: '5'
+    save_bias: 'False'
+    copy_header: 'False'
   imports:
   # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item
   # consisting of 'module', 'name', and optionally 'alias' keys
@@ -311,6 +331,7 @@ doctests:
   # '.mock()' method of the corresponding class is used instead.
     input_image:
     save_bias: 'True'
+    copy_header: 'False'
     dimension: '3'
   imports:
   # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item
@@ -324,6 +345,8 @@ doctests:
   # If the field is of file-format type and the value is None, then the
   # '.mock()' method of the corresponding class is used instead.
     input_image:
+    save_bias: 'False'
+    copy_header: 'False'
     dimension: '3'
     histogram_sharpening: (0.12, 0.02, 200)
   imports:

nipype2pydra/utils.py

@@ -8,6 +8,11 @@
 from pathlib import Path
 from fileformats.core import FileSet
 
+try:
+    from typing import GenericAlias
+except ImportError:
+    from typing import _GenericAlias as GenericAlias
+
 from importlib import import_module
 
 
@@ -70,7 +75,7 @@ def add_to_sys_path(path: Path):
 def is_fileset(tp: type):
     return (
         inspect.isclass(tp)
-        and type(tp) is not ty.GenericAlias
+        and type(tp) is not GenericAlias
         and issubclass(tp, FileSet)
     )
 

pyproject.toml

@@ -60,6 +60,7 @@ test = [
     "pytest >=6.2.5",
     "pytest-env>=0.6.2",
     "pytest-cov>=2.12.1",
+    "fileformats-medimage-extras",
 ]
 docs = [
     "packaging",

tests/test_task.py

@@ -2,7 +2,6 @@
 import yaml
 from conftest import show_cli_trace
 import pytest
-import shutil
 import logging
 from nipype2pydra.cli import task as task_cli
 from nipype2pydra.utils import add_to_sys_path
@@ -18,7 +17,6 @@
     "trait_modified",
     "environ",
     "output_type",
-    "crop_list",
 ]
 
 
@@ -48,7 +46,7 @@ def test_task_conversion(task_spec_file, cli_runner, work_dir, gen_test_conftest
         pydra_module = import_module(output_module_path)
     pydra_task = getattr(pydra_module, task_spec["task_name"])
     nipype_interface = getattr(
-        import_module(task_spec["nipype_module"]), task_spec["task_name"]
+        import_module(task_spec["nipype_module"]), task_spec["nipype_name"]
     )
 
     nipype_trait_names = nipype_interface.input_spec().all_trait_names()