Use pyproject.toml instead of setup.py (#1168)

manthey · web-flow · commit 5d6b29e87659 · 2025-06-02T14:00:30.000-04:00
* Make some imports lazy * Switch from setup.py to pure pyproject.toml. Many thanks to @barrettMCW for showing how this could be done with Cython. * Find python headers
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -67,7 +67,7 @@ jobs:
   py39:
     working_directory: ~/project
     machine:
-      image: ubuntu-2204:current
+      image: ubuntu-2404:current
     steps:
       - checkout
       - upgradepython:
@@ -93,7 +93,7 @@ jobs:
   py310:
     working_directory: ~/project
     machine:
-      image: ubuntu-2204:current
+      image: ubuntu-2404:current
     steps:
       - checkout
       - upgradepython:
@@ -119,7 +119,7 @@ jobs:
   py311:
     working_directory: ~/project
     machine:
-      image: ubuntu-2204:current
+      image: ubuntu-2404:current
     steps:
       - checkout
       - upgradepython:
@@ -145,7 +145,7 @@ jobs:
   py312:
     working_directory: ~/project
     machine:
-      image: ubuntu-2204:current
+      image: ubuntu-2404:current
     steps:
       - checkout
       - upgradepython:
@@ -171,7 +171,7 @@ jobs:
   py313:
     working_directory: ~/project
     machine:
-      image: ubuntu-2204:current
+      image: ubuntu-2404:current
     steps:
       - checkout
       - upgradepython:
@@ -213,7 +213,7 @@ jobs:
   docker:
     working_directory: ~/project
     machine:
-      image: ubuntu-2204:current
+      image: ubuntu-2404:current
     steps:
       - checkout
       - run:
@@ -245,7 +245,7 @@ jobs:
   publish_docker:
     working_directory: ~/project
     machine:
-      image: ubuntu-2204:current
+      image: ubuntu-2404:current
     steps:
       - checkout
       - attach_workspace:
@@ -266,7 +266,7 @@ jobs:
   wheels:
     working_directory: ~/project
     machine:
-      image: ubuntu-2204:current
+      image: ubuntu-2404:current
     steps:
       - checkout
       # - setup_remote_docker
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,9 +1,8 @@
-cmake_minimum_required(VERSION 3.6.2)
+cmake_minimum_required(VERSION 3.15...3.26)
 
-project(histomicstk)
+project(histomicstk LANGUAGES CXX)
 
-find_package(PythonInterp REQUIRED)
-find_package(PythonExtensions REQUIRED)
+find_package(Python3 REQUIRED COMPONENTS Interpreter Development.Module NumPy)
 
 add_subdirectory(histomicstk/features)
 add_subdirectory(histomicstk/segmentation/label)
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -69,7 +69,7 @@ Ready to contribute? Here's how to set up ``HistomicsTK`` for local development.
    $ mkvirtualenv HistomicsTK
    $ cd HistomicsTK/
    $ python -m pip install setuptools-scm Cython>=0.25.2 scikit-build>=0.8.1 cmake>=0.6.0 numpy>=1.12.1
-   $ python setup.py develop
+   $ python -m pip install .
 
 Of course, any type of virtual python environment will do. These instructions are equally applicable inside ``conda`` environments.
 
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -4,7 +4,6 @@ include LICENSE
 include NOTICE
 include *.rst
 global-include CMakeLists.txt
-include setup.py
 include pyproject.toml
 include requirements-dev.txt
 graft histomicstk
diff --git a/build_wheels.sh b/build_wheels.sh
@@ -10,5 +10,5 @@ docker create --name wheels dsarchive/histomicstk_wheels
 docker cp wheels:/io/wheels .
 docker rm wheels
 
-python -m pip install scikit-build
-python setup.py sdist
+python -m pip install scikit-build build
+python -m build
diff --git a/histomicstk/features/CMakeLists.txt b/histomicstk/features/CMakeLists.txt
@@ -1,9 +1,18 @@
-find_package(Cython REQUIRED)
-find_package(NumPy REQUIRED)
+find_package(Python COMPONENTS Interpreter Development.Module NumPy REQUIRED)
 
-add_cython_target(_compute_marginal_glcm_probs_cython CXX)
-add_library(_compute_marginal_glcm_probs_cython MODULE ${_compute_marginal_glcm_probs_cython})
-python_extension_module(_compute_marginal_glcm_probs_cython)
-target_include_directories(_compute_marginal_glcm_probs_cython PRIVATE ${NumPy_INCLUDE_DIR})
+add_custom_command(
+  OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_compute_marginal_glcm_probs_cython.cpp
+  COMMENT
+    "Making ${CMAKE_CURRENT_BINARY_DIR}/_compute_marginal_glcm_probs_cython.cpp from ${CMAKE_CURRENT_SOURCE_DIR}/_compute_marginal_glcm_probs_cython.pyx"
+  COMMAND Python::Interpreter -m cython --cplus -o "${CMAKE_CURRENT_BINARY_DIR}/_compute_marginal_glcm_probs_cython.cpp"
+          "${CMAKE_CURRENT_SOURCE_DIR}/_compute_marginal_glcm_probs_cython.pyx"
+  DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/_compute_marginal_glcm_probs_cython.pyx"
+  VERBATIM)
 
-install(TARGETS _compute_marginal_glcm_probs_cython LIBRARY DESTINATION histomicstk/features)
+python_add_library(_compute_marginal_glcm_probs_cython MODULE
+                   "${CMAKE_CURRENT_BINARY_DIR}/_compute_marginal_glcm_probs_cython.cpp"
+                   WITH_SOABI)
+
+target_link_libraries(_compute_marginal_glcm_probs_cython PRIVATE Python::Module Python::NumPy)
+
+install(TARGETS _compute_marginal_glcm_probs_cython DESTINATION histomicstk/features)
diff --git a/histomicstk/segmentation/label/CMakeLists.txt b/histomicstk/segmentation/label/CMakeLists.txt
@@ -1,10 +1,18 @@
-find_package(Cython REQUIRED)
-find_package(NumPy REQUIRED)
+find_package(Python COMPONENTS Interpreter Development.Module NumPy REQUIRED)
 
-add_cython_target(_trace_object_boundaries_cython CXX)
-add_library(_trace_object_boundaries_cython MODULE ${_trace_object_boundaries_cython})
-python_extension_module(_trace_object_boundaries_cython)
-message("NUMPY_INCLUDE_DIRS:${NumPy_INCLUDE_DIR}")
-target_include_directories(_trace_object_boundaries_cython PRIVATE ${NumPy_INCLUDE_DIR})
+add_custom_command(
+  OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_trace_object_boundaries_cython.cpp
+  COMMENT
+    "Making ${CMAKE_CURRENT_BINARY_DIR}/_trace_object_boundaries_cython.cpp from ${CMAKE_CURRENT_SOURCE_DIR}/_trace_object_boundaries_cython.pyx"
+  COMMAND Python::Interpreter -m cython --cplus -o "${CMAKE_CURRENT_BINARY_DIR}/_trace_object_boundaries_cython.cpp"
+          "${CMAKE_CURRENT_SOURCE_DIR}/_trace_object_boundaries_cython.pyx"
+  DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/_trace_object_boundaries_cython.pyx"
+  VERBATIM)
 
-install(TARGETS _trace_object_boundaries_cython LIBRARY DESTINATION histomicstk/segmentation/label)
+python_add_library(_trace_object_boundaries_cython MODULE
+                   "${CMAKE_CURRENT_BINARY_DIR}/_trace_object_boundaries_cython.cpp"
+                   WITH_SOABI)
+
+target_link_libraries(_trace_object_boundaries_cython PRIVATE Python::Module Python::NumPy)
+
+install(TARGETS _trace_object_boundaries_cython DESTINATION histomicstk/segmentation/label)
diff --git a/histomicstk/segmentation/nuclear/CMakeLists.txt b/histomicstk/segmentation/nuclear/CMakeLists.txt
@@ -1,9 +1,18 @@
-find_package(Cython REQUIRED)
-find_package(NumPy REQUIRED)
+find_package(Python COMPONENTS Interpreter Development.Module NumPy REQUIRED)
 
-add_cython_target(_max_clustering_cython CXX)
-add_library(_max_clustering_cython MODULE ${_max_clustering_cython})
-python_extension_module(_max_clustering_cython)
-target_include_directories(_max_clustering_cython PRIVATE ${NumPy_INCLUDE_DIR})
+add_custom_command(
+  OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_max_clustering_cython.cpp
+  COMMENT
+    "Making ${CMAKE_CURRENT_BINARY_DIR}/_max_clustering_cython.cpp from ${CMAKE_CURRENT_SOURCE_DIR}/_max_clustering_cython.pyx"
+  COMMAND Python::Interpreter -m cython --cplus -o "${CMAKE_CURRENT_BINARY_DIR}/_max_clustering_cython.cpp"
+          "${CMAKE_CURRENT_SOURCE_DIR}/_max_clustering_cython.pyx"
+  DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/_max_clustering_cython.pyx"
+  VERBATIM)
 
-install(TARGETS _max_clustering_cython LIBRARY DESTINATION histomicstk/segmentation/nuclear)
+python_add_library(_max_clustering_cython MODULE
+                   "${CMAKE_CURRENT_BINARY_DIR}/_max_clustering_cython.cpp"
+                   WITH_SOABI)
+
+target_link_libraries(_max_clustering_cython PRIVATE Python::Module Python::NumPy)
+
+install(TARGETS _max_clustering_cython DESTINATION histomicstk/segmentation/nuclear)
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,8 +1,71 @@
 [build-system]
-requires = ["setuptools", "wheel", "scikit-build", "cmake", "ninja", "numpy", "cython", "setuptools-scm"]
+requires = ["scikit-build-core>=0.7", "setuptools-scm", "cython>=0.29", "numpy"]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "histomicstk"
+description = "A Python toolkit for Histopathology Image Analysis"
+readme = "README.rst"
+authors = [
+    {name = "Kitware, Inc.", email = "developers@digitalslidearchive.net"}
+]
+urls = {Homepage = "https://github.com/DigitalSlideArchive/HistomicsTK"}
+license = {text = "Apache Software License 2.0"}
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+]
+keywords = ["histomicstk"]
+requires-python = ">=3.9"
+dependencies = [
+    "girder-client",
+    "nimfa",
+    "numpy",
+    "scipy",
+    "Pillow",
+    "pandas",
+    "scikit-image",
+    "scikit-learn",
+    "imageio",
+    "shapely",
+    "sqlalchemy",
+    "matplotlib",
+    "pyvips",
+    "dask[dataframe]<2024.11.0",
+    "distributed",
+    "large-image[sources];sys.platform=='linux'",
+    "large-image[common];sys.platform!='linux'",
+    "large-image-converter;sys.platform=='linux'",
+    "girder-slicer-cli-web",
+    "ctk-cli",
+    "opencv-python-headless",
+]
+dynamic = ["version"]
+
+[project.scripts]
+histomicstk = "histomicstk.cli.__main__:main"
+
+[tool.scikit-build]
+wheel.packages = ["histomicstk"]
+sdist.exclude = ["*.git*"]
+cmake.build-type = "Release"
+
+[tool.setuptools_scm]
+local_scheme = "no-local-version"
+fallback_version = "0.0.0"
+
+[tool.setuptools.package-data]
+"*" = ["*.pyx", "*.pxd"]
 
 [tool.codespell]
-# Ref: https://github.com/codespell-project/codespell#using-a-config-file
 skip = '.git*,*.pdf,*.svg,.pre-commit-config.yaml'
 check-hidden = true
 ignore-regex = '(^\s*"image/\S+": ".*)'
diff --git a/setup.py b/setup.py
