improved package structure

.github/workflows/lint.yml

@@ -0,0 +1,27 @@
+name: Lint
+
+on: [ pull_request ]
+
+env:
+  MODULE_NAME: imops
+
+jobs:
+  lint:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Check python code style
+        run: |
+          pip install -r requirements-linters.txt
+          flake8 .
+          isort --check .
+          black --check .
+      - name: Check Cython code style
+        run: |
+          pip install cython-lint
+          cython-lint imops/src

.github/workflows/tests.yml

@@ -43,17 +43,6 @@ jobs:
           echo $MODULE_PARENT
           echo "MODULE_PARENT=$(echo $MODULE_PARENT)" >> $GITHUB_ENV
 
-      - name: Check python code style
-        run: |
-          pip install -r requirements-linters.txt
-          flake8 .
-          isort --check .
-          black --check .
-      - name: Check Cython code style
-        run: |
-          pip install cython-lint
-          cython-lint imops/src
-
       - name: Test with pytest
         run: |
           pytest tests -m "not nonumba" --junitxml=reports/junit-${{ matrix.python-version }}.xml --cov="$MODULE_PARENT/$MODULE_NAME" --cov-report=xml --cov-branch

.gitignore

@@ -10,3 +10,4 @@ imops/src/_fast*.pyx
 dist/
 *.so
 .vscode/
+.idea/

MANIFEST.in

@@ -1,6 +1,6 @@
 include *.md
 include requirements.txt
 include pyproject.toml
-include _build_utils.py
 recursive-include imops *.py
 recursive-include imops/cpp *.h *.hpp *.cpp
+exclude tests/*

_build_utils.py → imops/_build_utils.py

@@ -66,7 +66,7 @@ def get_ext_modules():
     modules = ['backprojection', 'measure', 'morphology', 'numeric', 'radon', 'zoom', 'convex_hull']
     modules_to_link_against_numpy_core_math_lib = ['numeric']
 
-    src_dir = Path(__file__).parent / name / 'src'
+    src_dir = Path(__file__).parent / 'src'
     for module in modules:
         # Cython extension and .pyx source file names must be the same to compile
         # https://stackoverflow.com/questions/8024805/cython-compiled-c-extension-importerror-dynamic-module-does-not-define-init-fu

imops/compat.py

@@ -9,6 +9,13 @@
     from numpy import VisibleDeprecationWarning
 
 try:
-    from scipy.ndimage._morphology import _ni_support
+    from scipy.ndimage._morphology._ni_support import _normalize_sequence as normalize_sequence
 except ImportError:
-    from scipy.ndimage.morphology import _ni_support
+    from scipy.ndimage.morphology._ni_support import _normalize_sequence as normalize_sequence
+
+try:
+    from scipy.spatial import QhullError
+except ImportError:
+    from scipy.spatial.qhull import QhullError
+
+from scipy.ndimage._nd_image import euclidean_feature_transform  # noqa

imops/morphology.py

@@ -4,15 +4,7 @@
 import numpy as np
 from edt import edt
 from scipy.ndimage import distance_transform_edt as scipy_distance_transform_edt, generate_binary_structure
-from scipy.ndimage._nd_image import euclidean_feature_transform
 from scipy.spatial import ConvexHull
-
-
-try:
-    from scipy.spatial import QhullError
-except ImportError:
-    from scipy.spatial.qhull import QhullError  # Old scipy has another structure
-
 from skimage.morphology import (
     binary_closing as scipy_binary_closing,
     binary_dilation as scipy_binary_dilation,
@@ -23,7 +15,7 @@
 
 from .backend import BackendLike, Cython, Scipy, resolve_backend
 from .box import add_margin, box_to_shape, mask_to_box, shape_to_box
-from .compat import _ni_support
+from .compat import QhullError, euclidean_feature_transform, normalize_sequence
 from .crop import crop_to_box
 from .pad import restore_crop
 from .src._convex_hull import _grid_points_in_poly, _left_right_bounds, _offset_unique
@@ -499,7 +491,7 @@ def distance_transform_edt(
     if image.dtype != bool:
         image = np.atleast_1d(np.where(image, 1, 0))
     if sampling is not None:
-        sampling = _ni_support._normalize_sequence(sampling, image.ndim)
+        sampling = normalize_sequence(sampling, image.ndim)
         sampling = np.asarray(sampling, dtype=np.float64)
         if not sampling.flags.contiguous:
             sampling = sampling.copy()

pyproject.toml

@@ -4,17 +4,17 @@ build-backend = 'setuptools.build_meta'
 
 [project]
 name = 'imops'
-dynamic = ['version']
+dynamic = ['dependencies', 'version']
 description = 'Efficient parallelizable algorithms for multidimensional arrays to speed up your data pipelines'
 readme = 'README.md'
 requires-python = '>=3.7'
 license = { file = 'LICENSE' }
 keywords = ['image processing', 'fast', 'ndarray', 'data pipelines']
 authors = [
-    {name = 'maxme1', email = '[email protected]'},
-    {name = 'vovaf709', email = '[email protected]'},
-    {name = 'talgat', email = '[email protected]'},
-    {name = 'alexeybelkov', email='[email protected]'}
+    { name = 'maxme1', email = '[email protected]' },
+    { name = 'vovaf709', email = '[email protected]' },
+    { name = 'talgat', email = '[email protected]' },
+    { name = 'alexeybelkov', email = '[email protected]' }
 ]
 classifiers = [
     'Development Status :: 5 - Production/Stable',
@@ -51,23 +51,21 @@ line_length = 120
 lines_after_imports = 2
 profile = 'black'
 combine_as_imports = true
-skip_glob=['.asv/*', '.eggs/*']
+skip_glob = ['.asv/*', '.eggs/*']
 
 [tool.cython-lint]
 max-line-length = 120
 
-[tool.setuptools]
-py-modules = ['_build_utils']
-
 [tool.setuptools.cmdclass]
-build_py = "_build_utils.PyprojectBuild"
+build_py = "imops._build_utils.PyprojectBuild"
 
 [tool.setuptools.packages.find]
 include = ['imops']
+exclude = ['tests']
 
 [tool.setuptools.package-data]
 imops = ['py.typed']
 
 [tool.setuptools.dynamic]
-version = {attr = 'imops.__version__.__version__'}
+version = { attr = 'imops.__version__.__version__' }
 dependencies = { file = ['requirements.txt'] }

setup.py

@@ -23,13 +23,14 @@
     long_description = file.read()
 version = runpy.run_path(root / name / '__version__.py')['__version__']
 
-scope = {'__file__': __file__}
-exec((root / '_build_utils.py').read_text(), scope)
+build_utils = root / name / '_build_utils.py'
+scope = {'__file__': str(build_utils)}
+exec(build_utils.read_text(), scope)
 ext_modules = scope['get_ext_modules']()
 
 setup(
     name=name,
-    packages=find_packages(include=(name,)),
+    packages=find_packages(include=(name,), exclude=('tests', 'tests.*')),
     include_package_data=True,
     version=version,
     description='Efficient parallelizable algorithms for multidimensional arrays to speed up your data pipelines',
@@ -51,8 +52,8 @@
     extras_require={'numba': ['numba'], 'all': ['numba']},
     setup_requires=[
         'setuptools<69.0.0',
-        'Cython>=3.0.0,<4.0.0',
         'numpy<3.0.0',
+        'Cython>=3.0.0,<4.0.0',
         'pybind11',
     ],
     ext_modules=ext_modules,