Merge pull request #16 from tclose/unitests

Added NIfTI unittest

Author: tclose

.github/workflows/pythonpackage.yml

@@ -52,9 +52,20 @@ jobs:
     strategy:
       matrix:
         python-version: [3.7, 3.8, 3.9]
-
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
     - uses: actions/checkout@v2
+    - name: Install Minconda
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-activate-base: true
+        activate-environment: ""
+    - name: Install MRtrix via Conda
+      run: |
+        conda install -c mrtrix3 mrtrix3
+        mrconvert --version
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:

conftest.py

@@ -0,0 +1,22 @@
+import os
+import tempfile
+from pathlib import Path
+import pytest
+
+
+@pytest.fixture
+def work_dir():
+    return Path(tempfile.mkdtemp())
+
+
+# For debugging in IDE's don't catch raised exceptions and let the IDE
+# break at it
+if os.getenv("_PYTEST_RAISE", "0") != "0":
+
+    @pytest.hookimpl(tryfirst=True)
+    def pytest_exception_interact(call):
+        raise call.excinfo.value
+
+    @pytest.hookimpl(tryfirst=True)
+    def pytest_internalerror(excinfo):
+        raise excinfo.value

pydra/tasks/mrtrix3/tests/test_utils.py

@@ -1,17 +1,42 @@
+from pathlib import Path
 import pytest
 from pydra.tasks.mrtrix3.utils import MRConvert
-from medimages4tests.dicom.mri.dwi.siemens.skyra.syngo_d13c import sample_image
+from medimages4tests.dicom.mri.dwi.siemens.skyra.syngo_d13c import (
+    sample_image as sample_dwi_dicom,
+)
+from medimages4tests.nifti import sample_image as sample_nifti
 
 
 @pytest.fixture
-def dicom_dataset():
-    return sample_image()
+def dwi_dicom_dataset():
+    return sample_dwi_dicom()
 
 
-def test_mrconvert(dicom_dataset):
+@pytest.fixture
+def nifti_dataset(work_dir):
+    return sample_nifti(work_dir / "nifti", compressed=True)
+
+
+def test_mrconvert_default_out_file(nifti_dataset):
+
+    task = MRConvert(in_file=nifti_dataset, axes=[0, 1, 2, -1])
+
+    result = task()
+
+    assert Path(result.output.out_file).exists()
+
+
+@pytest.mark.xfail(
+    reason=(
+        "Cannot pass input to input field with 'output_file_template' "
+        "https://github.com/nipype/pydra/pull/585 (or equivalent) is merged "
+        "into main branch"
+    )
+)
+def test_mrconvert_explicit_out_file(dwi_dicom_dataset):
 
-    task = MRConvert(in_file=dicom_dataset, out_file="test.nii.gz")
+    task = MRConvert(in_file=dwi_dicom_dataset, out_file="test.nii.gz")
 
     result = task()
 
-    assert result.output.out_file.exists()
+    assert Path(result.output.out_file).exists()

setup.cfg

@@ -20,7 +20,7 @@ classifiers =
 [options]
 python_requires = >=3.7
 install_requires =
-    pydra >= 0.6.2
+    pydra >= 0.19
 packages = find_namespace:
 
 [options.packages.find]
@@ -44,7 +44,7 @@ test =
     pytest-env
     pytest-xdist
     pytest-rerunfailures
-    medimages4tests
+    medimages4tests >= 0.2
     codecov
 tests =
     %(test)s