Merge branch 'master' into v0.23.0dev

Author: CPBridge

.github/workflows/run_unit_tests.yml

@@ -27,7 +27,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools
-        pip install -r requirements_test.txt
+        pip install .[test]
         pip install ${{ matrix.dependencies }}
     - name: Lint with flake8
       run: |

.readthedocs.yaml

@@ -24,5 +24,7 @@ formats: all
 # Optionally set the version of Python and requirements required to build your docs
 python:
   install:
-    - requirements: requirements_docs.txt
-    - path: .
+    - method: pip
+      path: .
+      extra_requirements:
+      - docs

docs/development.rst

@@ -61,7 +61,7 @@ Install requirements:
 
 .. code-block:: none
 
-    pip install -r ~/highdicom/requirements_test.txt
+    pip install .[test]
 
 Run tests (including checks for PEP8 compliance):
 
@@ -79,7 +79,7 @@ Install requirements:
 
 .. code-block:: none
 
-    pip install -r ~/highdicom/requirements_docs.txt
+    pip install .[docs]
 
 Build documentation in *HTML* format:
 

pyproject.toml

@@ -0,0 +1,83 @@
+[build-system]
+requires = ["setuptools>=64"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "highdicom"
+dynamic = ["version"]
+description = "High-level DICOM abstractions."
+readme = "README.md"
+requires-python = ">=3.6"
+authors = [
+    { name = "Markus D. Herrmann" },
+]
+maintainers = [
+    { name = "Markus D. Herrmann" },
+    { name = "Christopher P. Bridge" },
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: MacOS",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Multimedia :: Graphics",
+    "Topic :: Scientific/Engineering :: Information Analysis",
+]
+dependencies = [
+    "numpy>=1.19",
+    "pillow-jpls>=1.0",
+    "pillow>=8.3",
+    "pydicom>=2.3.0,!=2.4.0",
+]
+
+[project.optional-dependencies]
+libjpeg = [
+    "pylibjpeg-libjpeg>=1.3",
+    "pylibjpeg-openjpeg>=1.2",
+    "pylibjpeg>=1.4",
+]
+test = [
+    "mypy==0.971",
+    "pytest==7.1.2",
+    "pytest-cov==3.0.0",
+    "pytest-flake8==1.1.1",
+    "numpy-stubs @ git+https://github.com/numpy/numpy-stubs@201115370a0c011d879d69068b60509accc7f750",
+]
+docs = [
+    "sphinx-autodoc-typehints==1.17.0",
+    "sphinx-pyreverse==0.0.17",
+    "sphinx-rtd-theme==1.0.0",
+    "sphinxcontrib-autoprogram==0.1.7",
+    "sphinxcontrib-websupport==1.2.4",
+]
+
+[project.urls]
+homepage = "https://github.com/imagingdatacommons/highdicom"
+documentation = "https://highdicom.readthedocs.io/"
+repository = "https://github.com/ImagingDataCommons/highdicom.git"
+
+[tool.pytest.ini_options]
+addopts = "--doctest-modules"
+testpaths = ["tests"]
+log_cli_level = "INFO"
+
+[tool.mypy]
+warn_unreachable = true
+
+[[tool.mypy.overrides]]
+module = "mypy-pydicom.*"
+ignore_missing_imports = true
+
+[[tool.mypy.overrides]]
+module = "mypy-PIL.*"
+ignore_missing_imports = true

requirements_docs.txt

@@ -5,17 +5,3 @@ test=pytest
 max_line_length = 80
 ignore = E121 E125 W504
 statistics = True
-
-[mypy]
-warn_unreachable = True
-
-[mypy-pydicom.*]
-ignore_missing_imports = True
-
-[mypy-PIL.*]
-ignore_missing_imports = True
-
-[tool:pytest]
-python_files = tests/*.py
-log_cli_level = INFO
-addopts = --doctest-modules

requirements_test.txt

@@ -2719,7 +2719,7 @@ def _check_and_cast_pixel_array(
                     else:
                         segments_overlap = SegmentsOverlapValues.NO
 
-        elif pixel_array.dtype in (np.float_, np.float32, np.float64):
+        elif pixel_array.dtype in (np.float32, np.float64):
             unique_values = np.unique(pixel_array)
             if np.min(unique_values) < 0.0 or np.max(unique_values) > 1.0:
                 raise ValueError(
@@ -2905,7 +2905,7 @@ def _get_segment_pixel_array(
             (0 or 1).
 
         """
-        if pixel_array.dtype in (np.float_, np.float32, np.float64):
+        if pixel_array.dtype in (np.float32, np.float64):
             # Based on the previous checks and casting, if we get here the
             # output is a FRACTIONAL segmentation Floating-point numbers must
             # be mapped to 8-bit integers in the range [0,

setup.cfg

@@ -743,7 +743,7 @@ def fractional_transfer_syntax_uid(request):
         return request.param
 
     @staticmethod
-    @pytest.fixture(params=[np.bool_, np.uint8, np.uint16, np.float_])
+    @pytest.fixture(params=[np.bool_, np.uint8, np.uint16, np.float64])
     def pix_type(request):
         return request.param
 
@@ -1788,7 +1788,7 @@ def test_pixel_types_fractional(
             max_fractional_value=max_fractional_value,
             transfer_syntax_uid=fractional_transfer_syntax_uid
         )
-        if pix_type == np.float_:
+        if pix_type == np.float64:
             assert (
                 instance.SegmentsOverlap ==
                 SegmentsOverlapValues.UNDEFINED.value
@@ -1822,7 +1822,7 @@ def test_pixel_types_fractional(
             max_fractional_value=max_fractional_value,
             transfer_syntax_uid=fractional_transfer_syntax_uid
         )
-        if pix_type == np.float_:
+        if pix_type == np.float64:
             assert (
                 instance.SegmentsOverlap ==
                 SegmentsOverlapValues.UNDEFINED.value
@@ -2315,7 +2315,7 @@ def test_construction_empty_invalid_floats(self):
         with pytest.raises(ValueError):
             Segmentation(
                 source_images=[self._ct_image],  # empty
-                pixel_array=self._ct_pixel_array.astype(np.float_) * 2,
+                pixel_array=self._ct_pixel_array.astype(np.float64) * 2,
                 segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
                 segment_descriptions=(
                     self._segment_descriptions
@@ -2335,7 +2335,7 @@ def test_construction_empty_invalid_floats_binary(self):
         with pytest.raises(ValueError):
             Segmentation(
                 source_images=[self._ct_image],
-                pixel_array=self._ct_pixel_array.astype(np.float_) * 0.5,
+                pixel_array=self._ct_pixel_array.astype(np.float64) * 0.5,
                 segmentation_type=SegmentationTypeValues.BINARY.value,
                 segment_descriptions=(
                     self._segment_descriptions