Pyproject migration

.circleci/config.yml

@@ -22,17 +22,8 @@ jobs:
       - run:
           name: Build manylinux AArch64 wheel
           command: |
-            docker run --rm \
-                -w /root/nrn \
-                -v $PWD:/root/nrn \
-                -v /opt/nrnwheel/mpt:/nrnwheel/mpt \
-                -e NEURON_NIGHTLY_TAG \
-                -e NRN_NIGHTLY_UPLOAD \
-                -e NRN_RELEASE_UPLOAD \
-                -e SETUPTOOLS_SCM_PRETEND_VERSION \
-                -e NRN_BUILD_FOR_UPLOAD=1 \
-                'neuronsimulator/neuron_wheel:latest-gcc9-aarch64' \
-                packaging/python/build_wheels.bash linux << parameters.NRN_PYTHON_VERSION >> coreneuron
+            python3 -m pip install cibuilwheel
+            CIBW_BUILD="cp${NRN_PYTHON_VERSION}*" cibuildwheel
 
       - store_artifacts:
           path: ./wheelhouse

.github/workflows/docs.yml

@@ -59,12 +59,13 @@ jobs:
         working-directory: ${{runner.workspace}}/nrn
         run:  |
           echo "-------- NEURON wheel --------";
-          python setup.py build_ext bdist_wheel;
-          neuron_wheel=dist/NEURON*.whl;
+          python -m pip install cibuildwheel
+          CIBW_BUILD="cp311*" cibuildwheel
+          neuron_wheel=wheelhouse/NEURON*.whl;
           echo "-------- install wheel --------"
           python -m pip install $neuron_wheel;
           echo "-------- now build docs--------";
-          python setup.py docs;
+          python _setup.py docs;
           echo "-------- disable jekyll--------";
           pushd docs/_build;
           touch .nojekyll;

.github/workflows/neuron-ci.yml

@@ -362,8 +362,10 @@ jobs:
                 echo nrn-enable-sanitizer not found, not using it
               fi
           elif [[ "$BUILD_MODE" == "setuptools" ]]; then
-            ./packaging/python/build_wheels.bash CI;
+            python3 -m pip install cibuildwheel
+            CIBW_BUILD="cp311*" cibuildwheel
           fi;
+
           if [[ -z "${nrn_enable_sanitizer_preload_python}" ]]; then
             nrn_enable_sanitizer_preload_python="${PYTHON}"
           fi
@@ -393,7 +395,7 @@ jobs:
           fi;
 
           if [ "$BUILD_MODE" == "setuptools" ]; then
-            neuron_wheel=wheelhouse/NEURON*.whl;
+            neuron_wheel=wheelhouse/*.whl;
             # test with virtual environment
             ./packaging/python/test_wheels.sh $PYTHON $neuron_wheel
             # test with global installation

CMakeLists.txt

@@ -809,14 +809,6 @@ if(NRN_ENABLE_TESTS)
     include(Catch)
   endif()
   include(CTest)
-  if(NRN_ENABLE_PYTHON)
-    # Need this for *all* Python versions we try and run tests with
-    nrn_find_python_module(MODULE pytest ALL REQUIRED)
-    nrn_find_python_module(MODULE pytest_cov ALL)
-    if(NOT PYTEST_COV_FOUND)
-      message(STATUS "pytest-cov package not installed. Python coverage will not be generated.")
-    endif()
-  endif()
   add_dependencies(nrniv_lib copy_share_demo_to_build)
   # Execute neurondemo as part of the build because it lazily calls nrnivmodl. If we don't do this
   # then test_neurondemo.py will run nrnivmodl in a clean build, and report compilation warnings as

azure-pipelines.yml

@@ -32,20 +32,9 @@ stages:
       timeoutInMinutes: 45
       pool:
         vmImage: 'ubuntu-20.04'
-      strategy:
-        matrix:
-          Python38:
-            python.version: '3.8'
-          Python39:
-            python.version: '3.9'
-          Python310:
-            python.version: '3.10'
-          Python311:
-            python.version: '3.11'
-          Python312:
-            python.version: '3.12'
       steps:
 
+      - task: UsePythonVersion@0
       # Secure files documentation:
       #   https://docs.microsoft.com/en-us/azure/devops/pipelines/library/secure-files?view=azure-devops
       #   NOTE: when uploading new secure files, access must be permitted from the Azure pipeline interface (check message there)
@@ -58,19 +47,8 @@ stages:
       # Note that mpt headers must be mounted in the docker imager under `/nrnwheel/mpt`
       # This path is checked by `packaging/python/build_wheels.bash` when run in the image.
       - script: |
-          sudo mkdir -p /opt/nrnwheel/mpt
-          sudo tar -zxf $(mpt_headersSF.secureFilePath) --directory /opt/nrnwheel/mpt
-          docker run --rm \
-            -w /root/nrn \
-            -v $PWD:/root/nrn \
-            -v /opt/nrnwheel/mpt:/nrnwheel/mpt \
-            -e NEURON_NIGHTLY_TAG \
-            -e NRN_NIGHTLY_UPLOAD \
-            -e NRN_RELEASE_UPLOAD \
-            -e SETUPTOOLS_SCM_PRETEND_VERSION \
-            -e NRN_BUILD_FOR_UPLOAD=1 \
-            'neuronsimulator/neuron_wheel:latest-x86_64' \
-            packaging/python/build_wheels.bash linux $(python.version) coreneuron
+          python3 -m pip install cibuildwheel
+          CIBW_BUILD='cp311*' cibuildwheel
         displayName: 'Building ManyLinux Wheel'
 
       - script: |
@@ -86,38 +64,9 @@ stages:
       timeoutInMinutes: 60
       pool:
         vmImage: 'macOS-12'
-      strategy:
-        matrix:
-          Python38:
-            python.version: '3.8'
-            python.org.version: '3.8.9'
-            python.installer.name: 'macosx10.9.pkg'
-          Python39:
-            python.version: '3.9'
-            python.org.version: '3.9.13'
-            python.installer.name: 'macos11.pkg'
-          Python310:
-            python.version: '3.10'
-            python.org.version: '3.10.11'
-            python.installer.name: 'macos11.pkg'
-          Python311:
-            python.version: '3.11'
-            python.org.version: '3.11.7'
-            python.installer.name: 'macos11.pkg'
-          Python312:
-            python.version: '3.12'
-            python.org.version: '3.12.0'
-            python.installer.name: 'macos11.pkg'
 
       steps:
 
-      - script: |
-          installer=python-$(python.org.version)-$(python.installer.name)
-          url=https://www.python.org/ftp/python/$(python.org.version)/$installer
-          curl $url -o $installer
-          sudo installer -pkg $installer -target /
-        displayName: 'Install Python from python.org'
-
       - script: |
           brew install --cask xquartz
           brew install flex bison mpich
@@ -128,6 +77,7 @@ stages:
           brew uninstall --ignore-dependencies libomp || echo "libomp doesn't exist"
         displayName: 'Install OSX System Dependencies'
 
+      - task: UsePythonVersion@0
       # readline has been manually built with ncurses and MACOSX_DEPLOYMENT_TARGET=10.9 and stored as secure file on Azure.
       # See `packaging/python/Dockerfile` for build instructions.
       #
@@ -145,12 +95,15 @@ stages:
       # seems that 10.15 is actually needed for std::filesystem::path.
       - script: |
           export MACOSX_DEPLOYMENT_TARGET=10.15
-          export PATH=/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH
+          export BREW_PREFIX=$(brew --prefix)
+          export PATH=${BREW_PREFIX}/opt/flex/bin:${BREW_PREFIX}/opt/bison/bin:$PATH
           export SDKROOT=$(xcrun --sdk macosx --show-sdk-path)
           export NRN_BUILD_FOR_UPLOAD=1
           sudo mkdir /opt/nrnwheel
           sudo tar -zxf $(readlineSF.secureFilePath) --directory /opt/nrnwheel/
-          packaging/python/build_wheels.bash osx $(python.version) coreneuron
+          export MPI_INCLUDE_HEADERS="${BREW_PREFIX}/opt/openmpi/include;${BREW_PREFIX}/opt/mpich/include"
+          python3 -m pip install cibuildwheel
+          CIBW_BUILD='cp311*' cibuildwheel
         displayName: 'Build MacOS Wheel'
 
       - template: ci/azure-wheel-test-upload.yml