Update scikit-build

Author: eleftherioszisis

.github/workflows/check-sdist.yml

@@ -24,7 +24,7 @@ jobs:
 
       - name: Build a source tarball
         run:
-          python setup.py sdist
+          python -m build --sdist
 
       - name: Test tarball
         run: |

.github/workflows/publish-sdist-wheels.yml

@@ -28,10 +28,10 @@ jobs:
         with:
           submodules: 'true'
 
-      - name: Install Python
-        uses: actions/setup-python@v5
+      - uses: actions/setup-python@v5
+        name: Install Python 3.9
         with:
-          python-version: '3.11'
+          python-version: '3.9'
 
       - name: Install cibuildwheel
         run: |
@@ -164,14 +164,18 @@ jobs:
         with:
           submodules: 'true'
 
-      - name: Set up Python
+      - name: Set up Python 3.9
         uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: 3.9
+
+      - name: Install Dependencies
+        run:
+          python -m pip install build
 
       - name: Build a source tarball
         run:
-          python setup.py sdist
+          python -m build --sdist
 
       - name: Test tarball
         run: |

3rdparty/HighFive

@@ -1,6 +1,7 @@
-cmake_minimum_required(VERSION 3.2)
+cmake_minimum_required(VERSION 3.15)
 #allow using of HDF5_ROOT for building with a custom HDF5 version
 cmake_policy(SET CMP0074 NEW)
+
 project(MorphIO VERSION 2.0.0)
 
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/bin)
@@ -42,6 +43,9 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
 if (EXTERNAL_HIGHFIVE)
   find_package(HighFive REQUIRED)
 endif()
+
+set(PYBIND11_NEWPYTHON ON)
+
 if (EXTERNAL_PYBIND11)
   find_package(pybind11 REQUIRED CONFIG)
 endif()

CMakeLists.txt

@@ -1,10 +1,8 @@
 [build-system]
 requires = [
-    "scikit-build-core",
-    "setuptools_scm>=8",
-    "cmake>=3.14",
-    "ninja",
-    "pybind11",
+    "scikit-build-core>=0.10,<1",
+    # use h5py's hdf5 install on Windows so we don't have to redistribute hdf5
+    'h5py; platform_system == "Windows"'
 ]
 build-backend = "scikit_build_core.build"
 
@@ -25,50 +23,46 @@ classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "License :: OSI Approved :: Apache Software License v2.0",
 ]
+keywords = [
+  "computational neuroscience",
+  "morphology",
+  "neuron",
+  "neurolucida",
+  "neuromorphology",
+]
 dynamic = ["version"]
-#dependencies = [
-#    "blueetl-core>=0.1.0",
-#]
 
-[tool.setuptools_scm]
-#
-#    install_requires=install_requires,
-#    extras_require={
-#        'docs': ['sphinx-bluebrain-theme'],
-#    },
-#    url='https://github.com/BlueBrain/MorphIO/',
-#    ext_modules=[CMakeExtension('morphio._morphio'),
-#                 ],
-#    cmdclass={'build_ext': CMakeBuild,
-#              },
-#    packages=[],
-#    license="LGPLv3",
-#    zip_safe=False,
-#    use_scm_version=True,
-#    setup_requires=[
-#        'setuptools_scm',
-#    ],
-#    python_requires=">=3.8",
-#)
+[project.optional-dependencies]
+docs = ["sphinx-bluebrain-theme"]
+
+[project.urls]
+Homepage = "https://github.com/BlueBrain/MorphIO"
+Repository = "https://github.com/BlueBrain/MorphIO.git"
+Documentation = "https://morphio.readthedocs.io/"
+Tracker = "https://github.com/BlueBrain/MorphIO/issues"
 
 [tool.scikit-build]
-cmake.targets = ["_morphio"]
+build.targets = ["_morphio"]
 metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
 wheel.packages = [ 'morphio', 'morphio.mut', 'morphio.vasculature' ]
 cmake.args = [
     "-DHIGHFIVE_EXAMPLES=OFF",
     "-DHIGHFIVE_UNIT_TESTS=OFF",
-    '-DMORPHIO_TESTS=OFF',
+    "-DMORPHIO_TESTS=OFF",
+    "-DMorphIO_CXX_WARNINGS=OFF",
+    "-GNinja",
     ]
 #sdist.include = ["src/some_generated_file.txt"]
 #sdist.exclude = [".github"]
 
+[tool.setuptools_scm]
+local_scheme = "no-local-version"
+
 [tool.pytest.ini_options]
 testpaths = ["tests"]
 
-#'-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=' + extdir,
-#'-DMORPHIO_VERSION_STRING=' + self.distribution.get_version(),
-#'-DPYTHON_EXECUTABLE=' + sys.executable,

binds/python/pybind11

@@ -19,7 +19,7 @@ def test_doc_exists():
         morphio.mut.Soma,
     ]
     for cls in classes:
-        public_methods = (method for method in dir(cls) if not method[:2] == '__')
+        public_methods = (method for method in dir(cls) if not method.startswith("_"))
         for method in public_methods:
             assert getattr(cls, method).__doc__, \
                 'Public method {} of class {} is not documented !'.format(method, cls)