Migrate build system to python-build (#3)

* Migrate to `python-build`

* Clean-up setup.py.in

* Fix linux_build.bash

* Update CMakeLists.txt

* Fix linux_build.bash

* Fix linux_build.bash

* Update build

* Update tests

* Fix linux_build.bash

* Update CMake files

* Update CI and RTD integration

* Update build.yml

Author: kostrykin

.github/workflows/build.yml

@@ -44,16 +44,15 @@ jobs:
           export libcarna_version=$(conda list --json |jq -rj '[ .[] | select( .name == "libcarna" ) ][0].version')
           echo "libcarna_version=$libcarna_version" >> "$GITHUB_OUTPUT"
 
-      - name: Build dist
+      - name: Build wheel
         shell: bash
         run: ./linux_build.bash
 
       - name: Upload wheel
         uses: actions/upload-artifact@v4
         with:
           name: dist-${{ inputs.python-version }}
-          path: |
-             dist
+          path: build/dist/libcarna_python-*.whl
 
     outputs:
       libcarna_version: ${{ steps.meta.outputs.libcarna_version }}
@@ -117,9 +116,6 @@ jobs:
         run: |
           eval "$(conda shell.bash hook)"
           conda activate ./.env
-          cd test
-          mkdir test
-          mv results test/results
           python -m unittest -vv
         env:
           LIBCARNA_PYTHON_LOGGING: true

.gitignore

@@ -5,6 +5,7 @@
 /dist
 /LibCarna_Python.egg-info
 /.libcarna-dev
+/test/results/actual
 .ipynb_checkpoints
 *.swp
 *.pyc

.readthedocs.yaml

@@ -20,7 +20,7 @@ build:
   jobs:
     install:
       - bash ./linux_build.bash
-      - pip install dist/libcarna_python-*.whl
+      - pip install build/dist/libcarna_python-*.whl
     pre_build:
       - pip install -r docs/requirements.txt
     build:

CMakeLists.txt

@@ -3,6 +3,10 @@ project( LibCarna-Python )
 set( PYTHON_MODULE_NAME "libcarna" )
 include( FindPackageHandleStandardArgs )
 
+set( MAJOR_VERSION 0 )
+set( MINOR_VERSION 2 )
+set( PATCH_VERSION 0 )
+
 set( CMAKE_CXX_STANDARD 14 )
 set( CMAKE_CXX_STANDARD_REQUIRED ON )
 set( CMAKE_INTERPROCEDURAL_OPTIMIZATION FALSE )
@@ -73,20 +77,31 @@ find_package( Eigen3 REQUIRED )
 include_directories( ${EIGEN3_INCLUDE_DIR} )
 
 # LibCarna
-find_package( LibCarna ${REQUIRED_VERSION_LIBCARNA} REQUIRED COMPONENTS release )
+find_package( LibCarna "3.4.0" REQUIRED COMPONENTS release )
 include_directories( ${LibCarna_INCLUDE_DIR} )
 set( LIBCARNA_VERSION ${FOUND_VERSION} )
 
 ############################################
 
-configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/misc/__init__.py.in
-                ${CMAKE_CURRENT_BINARY_DIR}/${PYTHON_MODULE_NAME}/__init__.py @ONLY )
+configure_file(
+    ${CMAKE_CURRENT_SOURCE_DIR}/misc/__init__.py.in
+    ${CMAKE_CURRENT_BINARY_DIR}/${PYTHON_MODULE_NAME}/__init__.py
+    @ONLY
+)
+
+configure_file(
+    ${CMAKE_CURRENT_SOURCE_DIR}/setup.py.in
+    ${CMAKE_CURRENT_BINARY_DIR}/setup.py
+    @ONLY
+)
 
 file( GLOB PYTHON_AUX_FILES "${CMAKE_CURRENT_SOURCE_DIR}/misc/libcarna/*.py" )
 file( COPY ${PYTHON_AUX_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/${PYTHON_MODULE_NAME}" )
 
 file( GLOB LICENSES "${LibCarna_LICENSE_DIR}/LICENSE*" )
-file( COPY ${LICENSES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/licenses/" )
+file( COPY ${LICENSES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}" )
+file( COPY ${CMAKE_CURRENT_SOURCE_DIR}/README.md DESTINATION "${CMAKE_CURRENT_BINARY_DIR}" )
+file( COPY ${CMAKE_CURRENT_SOURCE_DIR}/LICENSE DESTINATION "${CMAKE_CURRENT_BINARY_DIR}" )
 
 ############################################
 # Project
@@ -165,11 +180,3 @@ install( FILES
     ${CMAKE_CURRENT_BINARY_DIR}/${PYTHON_MODULE_NAME}/__init__.py
     DESTINATION ${INSTALL_LIBRARY_DIR}
 )
-
-############################################
-# Process unit tests
-############################################
-
-if( BUILD_TEST )
-    add_subdirectory( test )
-endif()

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2025 Leonid Kostrykin
+Copyright (c) 2021-2025 Leonid Kostrykin
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

environment.yml

@@ -18,8 +18,9 @@ dependencies:
   - cmake
   - eigen >=3.0.5
   - libxcrypt  # requied for Python 3.10
-  - pyyaml
   - setuptools
+  - python-build
+  - pip
 
   # ---------------------------------------------------------------------------
   # Runtime dependencies (general)

linux_build.bash

@@ -3,36 +3,51 @@ set -ex
 
 # Create or update conda environment
 export ROOT="$PWD"/$(dirname "$0")
-if [ ! -d "$ROOT/.env" ]; then
-    conda env create -f "$ROOT/environment.yml" --prefix "$ROOT/.env"
+if [ ! -d "$ROOT"/.env ]; then
+    conda env create -f "$ROOT"/environment.yml --prefix "$ROOT"/.env
 else
-    conda env update -f "$ROOT/environment.yml" --prefix "$ROOT/.env" --prune
+    conda env update -f "$ROOT"/environment.yml --prefix "$ROOT"/.env --prune
 fi
 
 # Activate conda environment
 eval "$(conda shell.bash hook)"
-conda activate "$ROOT/.env"
+conda activate "$ROOT"/.env
 
-# Setup and check dependencies
-export PYBIND11_PREFIX="$CONDA_PREFIX/share/cmake/pybind11"
-export CMAKE_MODULE_PATH="$CONDA_PREFIX/share/cmake/Modules"
+# Create build directory
+mkdir -p "$ROOT"/build
 
-# Default to not building the test suite
-if [ -z "$LIBCARNA_PYTHON_BUILD_TEST" ]; then
-    export LIBCARNA_PYTHON_BUILD_TEST="OFF"
-else
-    pip install -r test/requirements.txt
+# Build native extension
+cd "$ROOT"/build
+cmake -DCMAKE_BUILD_TYPE=Release \
+    -DPYTHON_EXECUTABLE="$(which python)" \
+    -Dpybind11_DIR="$CONDA_PREFIX/share/cmake/pybind11" \
+    -DCMAKE_MODULE_PATH="$CONDA_PREFIX/share/cmake/Modules" \
+    "$ROOT"
+if [ -z "$LIBCARNA_SKIP_NATIVE" ]; then
+    make VERBOSE=1
 fi
 
-# Build wheel and test
-cd "$ROOT"
-python setup.py bdist_wheel
+# Build wheel
+python -m build --no-isolation
+
+# Install wheel
+rm -rf venv
+python -m venv venv --system-site-package
+source venv/bin/activate
+pip install --no-deps dist/*.whl
+
+# Optionally, run the test suite
+if [ -v LIBCARNA_PYTHON_BUILD_TEST ]; then
+    cd "$ROOT"
+    pip install -r test/requirements.txt
+    python -m unittest
+fi
 
 # Optionally, build the documentation
 if [ -v LIBCARNA_PYTHON_BUILD_DOCS ]; then
+    cd "$ROOT"
     pip install -r docs/requirements.txt
-    export LIBCARNA_PYTHON_PATH="$ROOT/build/make_release"
-    rm -rf $ROOT/docs/build
+    rm -rf docs/build
     sphinx-build -M html docs docs/build
-    cp $ROOT/docs/build/html/examples/*.ipynb $ROOT/examples/
+    cp docs/build/html/examples/*.ipynb examples/
 fi

misc/__init__.py.in

@@ -1,4 +1,4 @@
-version = '@MAJOR_VERSION@.@MINOR_VERSION@.@PATCH_VERSION@'
+version = '@FULL_VERSION@'
 libcarna_version = '@LIBCARNA_VERSION@'
 
 

setup.py

@@ -0,0 +1,55 @@
+from setuptools import setup
+
+
+if __name__ == '__main__':
+    with open('README.md', encoding='utf-8') as io:
+        long_description = io.read()
+
+    setup(
+        name = 'LibCarna-Python',
+        version = '@FULL_VERSION@',
+        description = 'General-purpose real-time 3D visualization',
+        long_description = long_description,
+        long_description_content_type = 'text/markdown',
+        author = 'Leonid Kostrykin',
+        author_email = 'leonid.kostrykin@bioquant.uni-heidelberg.de',
+        url = 'https://github.com/kostrykin/LibCarna-Python',
+        include_package_data = True,
+        license = 'MIT',
+        license_files = [
+            'LICENSE',
+            'LICENSE-Carna',
+            'LICENSE-LibCarna',
+            'LICENSE-Eigen',
+            'LICENSE-GLEW',
+        ],
+        package_dir = {
+            'libcarna': 'libcarna',
+        },
+        packages = ['libcarna'],
+        package_data = {
+            'libcarna': ['*.so'],
+        },
+        classifiers = [
+            'Development Status :: 4 - Beta',
+            'Environment :: GPU',
+            'Operating System :: POSIX :: Linux',
+            'Programming Language :: C++',
+            'Programming Language :: Python',
+            'Topic :: Education',
+            'Topic :: Multimedia :: Graphics :: 3D Rendering',
+            'Topic :: Scientific/Engineering :: Visualization',
+        ],
+        install_requires = [
+            'numpy',
+            'numpngw >=0.1.4, <0.2',
+            'scikit-video >=1.1.11, <1.2',
+            'scipy',
+            'scikit-image',
+            'tifffile',
+            'pooch',
+            'matplotlib',
+            'typing_extensions',  # required for Python 3.10
+        ],
+    )
+