pydra layout

Author: thewtex

.github/workflows/build-test.yml

@@ -32,7 +32,7 @@ jobs:
     - name: Test with pytest
       run: |
         pip install -r requirements-dev.txt
-        pytest tests.py -v --doctest-modules --junitxml=junit/test-results-${{ matrix.os }}-${{ matrix.python-version }}.xml
+        pytest tests/ -v --cov=simtk --doctest-modules --junitxml=junit/test-results-${{ matrix.os }}-${{ matrix.python-version }}.xml
     - name: Upload pytest test results
       uses: actions/upload-artifact@v2
       with:

.gitignore

@@ -1,3 +1,4 @@
 .coverage
 coverage.xml
 .benchmarks
+benchmark*svg

simtk/pydra.py

@@ -0,0 +1,15 @@
+"""simtk pydra tasks and workflows."""
+
+# __all__ = [
+        # 'load_image_task'
+        # ]
+
+# import numpy as np
+# from pydra import mark
+# import itk
+
+# from simtk import load_image
+
+# load_image_annotated = mark.annotate({'filename': str, 'nphases': int,
+    # 'norientations': int, 'spacing': np.ndarray, 'return': itk.VectorImage })(load_image)
+# load_image_task = mark.task(load_image_annotated)()

tests/test_pydra.py

@@ -0,0 +1,22 @@
+from pathlib import Path
+import os
+import sys
+
+import itk
+import numpy as np
+
+script_dir = Path(__file__).resolve().parent
+data_dir = (script_dir / '..' / 'data').resolve()
+if not (data_dir / 'input' / 'Cell_3phase.tif').exists():
+    print('Testing data not available.')
+    sys.exit(1)
+package_dir = (script_dir / '..').resolve()
+sys.path.insert(0, str(package_dir))
+
+test_psf_file = str(data_dir / 'input' / 'PSF_3phase.tif')
+
+import simtk.pydra
+
+def test_import_simtk_pydra():
+    assert 'simtk' in simtk.pydra.__doc__
+    assert 'pydra' in simtk.pydra.__doc__

tests.py renamed to tests/test_simtk.py

@@ -6,21 +6,23 @@
 import numpy as np
 
 script_dir = Path(__file__).resolve().parent
-data_dir = (script_dir / 'data').resolve()
+data_dir = (script_dir / '..' / 'data').resolve()
 if not (data_dir / 'input' / 'Cell_3phase.tif').exists():
     print('Testing data not available.')
     sys.exit(1)
+package_dir = (script_dir / '..').resolve()
+sys.path.insert(0, str(package_dir))
 
 test_psf_file = str(data_dir / 'input' / 'PSF_3phase.tif')
 
-import simtk
+from simtk import load_image
 
 def test_package():
     import simtk
     assert hasattr(simtk, '__version__')
 
 def test_load_image(benchmark):
-    image = benchmark(simtk.load_image, test_psf_file, spacing=[0.11, 0.11, 0.1])
+    image = benchmark(load_image, test_psf_file, spacing=[0.11, 0.11, 0.1])
 
     baseline = str(data_dir / 'baseline' / 'load_image.nrrd')
     baseline_image = itk.imread(baseline)