hatch

.github/workflows/build-test-publish.yml

@@ -13,12 +13,14 @@ jobs:
           python-version: "3.11"
       - name: "Build pure Python wheels"
         run: |
-          python -m pip wheel -w dist -e src/
+          python -m pip install hatch
+          cd src
+          hatch build
 
       - uses: actions/upload-artifact@v4
         with:
           name: wheel
-          path: ./dist/itk_dreg-*.whl
+          path: ./src/dist/itk_dreg-*.whl
 
   pytest:
     name: "Test with PyTest"
@@ -36,26 +38,21 @@ jobs:
 
       - name: "Install Dependencies"
         shell: bash
+        working-directory: src
         run: |
-          python -m pip install flit
-          cd src
-          flit install --deps develop
-
-      - name: Download Python Wheel Artifact
-        uses: actions/download-artifact@v4
-        with:
-          name: wheel
+          python -m pip install -e '.[test]'
 
-      - name: "Install itk_dreg from Wheel Artifact"
+      - name: "Install itk-dreg from source"
+        working-directory: src
         run: |
           wheel_name_full=`(find . -name "itk_dreg-*.whl")`
-          python -m pip uninstall -y itk_dreg
-          python -m pip install ${wheel_name_full}
+          python -m pip install -e '.[test]'
 
       - name: "Run Tests"
         shell: bash
+        working-directory: src
         run: |
-          pytest ./test -vvv -s -k "not localcluster and not serialize_pairwise_result"
+          pytest -vvv -s -k "not localcluster and not serialize_pairwise_result"
 
   publish:
     needs:

src/itk_dreg/__init__.py

@@ -1,5 +1,5 @@
 """
-ITK-DREG Distributed registration framework.
+itk-dreg distributed registration framework.
 """
 
-__version__ = "0.0.1"
+__version__ = "0.1.0"

src/pyproject.toml

@@ -1,10 +1,13 @@
 [build-system]
-requires = ["flit_core >=3.2,<4"]
-build-backend = "flit_core.buildapi"
+requires = ["hatchling"]
+build-backend = "hatchling.build"
 
 [project]
-name = "itk_dreg"
-authors = [{name = "InsightSoftwareConsortium", email = "matt.mccormick@kitware.com"}]
+name = "itk-dreg"
+authors = [
+    {name = "Matt McCormick", email = "matt.mccormick@kitware.com"},
+    {name = "Tom Birdsong", email = "tom.birdsong@kitware.com"}
+]
 license = {file = "LICENSE"}
 classifiers = [
     "License :: OSI Approved :: Apache Software License",
@@ -26,23 +29,25 @@ classifiers = [
     "Operating System :: MacOS"
 ]
 requires-python = ">=3.9"
-dynamic = ["version", "description"]
+dynamic = ["version"]
 readme = "../README.md"
-keywords = ['ITK','InsightToolkit']
+keywords = ['itk','InsightToolkit','registration', 'brain','distributed', 'dask']
 
 dependencies = [
     'dask[distributed] >=2023.10.0',
-    'itk >=5.4rc02',
+    'itk >=5.4rc04',
     'numpy'
 ]
 
 [project.urls]
-Home = "https://github.com/InsightSoftwareConsortium/itk-dreg"
+Home = "https://itk-dreg.readthedocs.io/"
+Source = "https://github.com/InsightSoftwareConsortium/itk-dreg"
+Issues = "https://github.com/InsightSoftwareConsortium/issues"
 
 [project.optional-dependencies]
 test = [
-    'itk-elastix>=0.19.1',
-    'itk-ioomezarrngff>=0.2.1',
+    'itk-elastix>=0.19.2',
+    'itk-ioomezarrngff>=0.3rc1',
     'nbmake',
     'pytest',
     'scipy>=1.11.3'
@@ -60,7 +65,7 @@ doc = [
 ]
 
 impl = [
-    'itk-elastix>=0.19.0',
+    'itk-elastix>=0.19.2',
     'scipy>=1.11.3'
 ]
 
@@ -77,6 +82,25 @@ notebook = [
     'graphviz',
 ]
 
-[tool.ruff]
+[tool.ruff.lint]
 extend-ignore = ["E501"]
 
+[tool.hatch.version]
+path = "itk_dreg/__init__.py"
+
+[tool.hatch.envs.default]
+dependencies = [
+    'itk-elastix>=0.19.2',
+    'scipy>=1.11.3',
+    'itk-ioomezarrngff>=0.3rc1',
+    'nbmake',
+    'pytest',
+]
+
+[tool.hatch.envs.default.scripts]
+test = [
+    "pytest -vvv -s"
+]
+
+[tool.black]
+line-length = 88

test/elastix/test_elx_import.py → src/test/elastix/test_elx_import.py

@@ -12,6 +12,4 @@
 
 
 def test_loadmodule():
-    import itk_dreg.elastix
-    import itk_dreg.elastix.util
-    import itk_dreg.elastix.register
+    pass

test/elastix/test_elx_integration.py → src/test/elastix/test_elx_integration.py

@@ -7,9 +7,7 @@
 import itk
 import numpy as np
 import dask
-import dask.array as da
 
-sys.path.append('./src')
 import itk_dreg.itk
 from itk_dreg.register import register_images
 
@@ -30,41 +28,47 @@
 https://github.com/InsightSoftwareConsortium/ITKElastix/issues/255
 """
 
+
 def test_run_dreg():
-    dask.config.set(scheduler='single-threaded')
+    dask.config.set(scheduler="single-threaded")
+
+    fixed_arr = np.ones([100] * 3)
+    moving_arr = np.random.random_sample([50] * 3).astype(np.float32)
 
-    fixed_arr = np.ones([100]*3)
-    moving_arr = np.random.random_sample([50]*3).astype(np.float32)
-
     register_method = ElastixDRegBlockPairRegistrationMethod()
     reduce_method = dreg_mock.CountingReduceResultsMethod()
-    
+
     registration_result = None
     registration_schedule = None
 
     with tempfile.TemporaryDirectory() as testdir:
-        FIXED_FILEPATH = f'{testdir}/fixed_image.mha'
-        MOVING_FILEPATH = f'{testdir}/moving_image.mha'
+        FIXED_FILEPATH = f"{testdir}/fixed_image.mha"
+        MOVING_FILEPATH = f"{testdir}/moving_image.mha"
         fixed_image = itk.image_view_from_array(fixed_arr)
         itk.imwrite(fixed_image, FIXED_FILEPATH, compression=False)
-        fixed_cb = lambda : itk_dreg.itk.make_reader(FIXED_FILEPATH)
+
+        def fixed_cb():
+            return itk_dreg.itk.make_reader(FIXED_FILEPATH)
+
         moving_image = itk.image_view_from_array(moving_arr)
-        moving_image.SetSpacing([2]*3)
+        moving_image.SetSpacing([2] * 3)
         itk.imwrite(moving_image, MOVING_FILEPATH, compression=False)
-        moving_cb = lambda : itk_dreg.itk.make_reader(MOVING_FILEPATH)
+
+        def moving_cb():
+            return itk_dreg.itk.make_reader(MOVING_FILEPATH)
 
         parameter_object = itk.ParameterObject.New()
         parameter_object.AddParameterMap(
-            parameter_object.GetDefaultParameterMap('rigid')
+            parameter_object.GetDefaultParameterMap("rigid")
         )
 
         registration_schedule = register_images(
-            fixed_chunk_size=(10,20,100),
-            initial_transform=itk.TranslationTransform[itk.D,3].New(),
+            fixed_chunk_size=(10, 20, 100),
+            initial_transform=itk.TranslationTransform[itk.D, 3].New(),
             moving_reader_ctor=moving_cb,
             fixed_reader_ctor=fixed_cb,
             reduce_method=reduce_method,
-            overlap_factors=[0.1]*3,
+            overlap_factors=[0.1] * 3,
             block_registration_method=register_method,
             elx_parameter_object_serial=parameter_object_to_list(parameter_object),
             itk_transform_types=[itk.Euler3DTransform[itk.D]],
@@ -76,4 +80,3 @@ def test_run_dreg():
 
     assert reduce_method.num_calls == 1
     assert registration_result.status.shape == registration_schedule.fixed_da.numblocks
-

test/elastix/test_elx_serialize.py → src/test/elastix/test_elx_serialize.py

@@ -1,34 +1,42 @@
-from unittest.mock import DEFAULT
 import itk
-itk.auto_progress(2)
 
 import pickle
-import dask.distributed.protocol
 
 import itk_dreg.elastix.serialize
 
+itk.auto_progress(2)
+
+
 def validate_parameter_maps(m1, m2):
     assert all([k in m2.keys() for k in m1.keys()])
     assert all([k in m1.keys() for k in m2.keys()])
     for key in m1.keys():
         assert m1[key] == m2[key]
 
+
 def validate_parameter_objects(p1, p2):
     assert p1.GetNumberOfParameterMaps() == p2.GetNumberOfParameterMaps()
     for map_index in range(p1.GetNumberOfParameterMaps()):
-        validate_parameter_maps(p1.GetParameterMap(map_index), p2.GetParameterMap(map_index))
+        validate_parameter_maps(
+            p1.GetParameterMap(map_index), p2.GetParameterMap(map_index)
+        )
+
 
 def test_serialize_elx_parameter_object():
-    DEFAULT_PARAMETER_MAPS = ['rigid']
+    DEFAULT_PARAMETER_MAPS = ["rigid"]
     parameter_object = itk.ParameterObject.New()
     parameter_object.AddParameterMap(
         itk.ParameterObject.GetDefaultParameterMap(DEFAULT_PARAMETER_MAPS[0])
     )
 
-    parameter_list = itk_dreg.elastix.serialize.parameter_object_to_list(parameter_object)
+    parameter_list = itk_dreg.elastix.serialize.parameter_object_to_list(
+        parameter_object
+    )
     pickled_parameter_list = pickle.dumps(parameter_list)
     unpickled_parameter_list = pickle.loads(pickled_parameter_list)
-    unpickled_parameter_object = itk_dreg.elastix.serialize.list_to_parameter_object(unpickled_parameter_list)
+    unpickled_parameter_object = itk_dreg.elastix.serialize.list_to_parameter_object(
+        unpickled_parameter_list
+    )
     validate_parameter_objects(unpickled_parameter_object, parameter_object)
 
     # TODO: https://github.com/InsightSoftwareConsortium/ITKElastix/issues/257
@@ -43,7 +51,7 @@ def test_serialize_elx_parameter_object():
 
     # Validate baseline is unchanged
     assert parameter_object.GetNumberOfParameterMaps() == 1
-    validate_parameter_maps(parameter_object.GetParameterMap(0),
-                            itk.ParameterObject.GetDefaultParameterMap(DEFAULT_PARAMETER_MAPS[0]))
-
-
+    validate_parameter_maps(
+        parameter_object.GetParameterMap(0),
+        itk.ParameterObject.GetDefaultParameterMap(DEFAULT_PARAMETER_MAPS[0]),
+    )