Add tests for python 3.9 to 3.12

.github/workflows/simulation_test.yml

@@ -18,24 +18,40 @@ on:
         description: 'libsonata branch to use'
         required: false
 
-
 env:
   NEURON_COMMIT_ID: '13654b3'
-  NEURON_BRANCH: ${{ inputs.LIBSONATA_REPORT_BRANCH || 'master' }}
+  NEURON_BRANCH: ${{ inputs.NEURON_BRANCH || 'master' }}
   LIBSONATA_REPORT_BRANCH: ${{ inputs.LIBSONATA_REPORT_BRANCH || '1.2.3' }}
   LIBSONATA_BRANCH: ${{ inputs.LIBSONATA_BRANCH || 'v0.1.26' }}
 
 jobs:
   simulation:
-    runs-on: ubuntu-22.04
+    runs-on: ${{ matrix.os }}
 
+    strategy:
+      matrix:
+        os: [ubuntu-22.04]
+        python-version: ['3.9', '3.10', '3.11', '3.12']
     steps:
+    - name: Setup Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
     - name: Checkout neurodamus repository
       uses: actions/checkout@v4
       with:
         ref: ${{ github.event.pull_request.head.sha }}
         fetch-depth: 0
 
+    - name: Cache pip
+      uses: actions/cache@v3
+      with:
+        path: ~/.cache/pip
+        key: ${{ matrix.os }}-pip-${{ matrix.python-version }}-v1
+        restore-keys: |
+          ${{ matrix.os }}-pip-
+
     - name: Get HEAD commit message and look for branches
       run: |
         COMMIT_MESSAGE=$(git log -1 --pretty=%B)
@@ -44,11 +60,13 @@ jobs:
         if [[ ! -z $NEURON_BRANCH ]]; then echo "NEURON_BRANCH=$NEURON_BRANCH" >> $GITHUB_ENV; fi
         LIBSONATA_REPORT_BRANCH=$(echo $COMMIT_MESSAGE | grep -Po 'LIBSONATA_REPORT_BRANCH=\K[0-9a-zA-Z/_.\-]*' || true)
         if [[ ! -z $LIBSONATA_REPORT_BRANCH ]]; then echo "LIBSONATA_REPORT_BRANCH=$LIBSONATA_REPORT_BRANCH" >> $GITHUB_ENV; fi
+        LIBSONATA_BRANCH=$(echo $COMMIT_MESSAGE | grep -Po 'LIBSONATA_BRANCH=\K[0-9a-zA-Z/_.\-]*' || true)
+        if [[ ! -z $LIBSONATA_BRANCH ]]; then echo "LIBSONATA_BRANCH=$LIBSONATA_BRANCH" >> $GITHUB_ENV; fi
 
-    - name: Install hdf5-mpich
+    - name: Install system dependencies
       run: |
         sudo apt-get update
-        sudo apt-get install mpich libmpich-dev libhdf5-mpich-dev hdf5-tools
+        sudo apt-get install -y mpich libmpich-dev libhdf5-mpich-dev hdf5-tools flex libfl-dev bison ninja-build
 
     - name: Cache python virtual env
       id: cache-venv
@@ -57,12 +75,19 @@ jobs:
         cache-name: cache-venv
       with:
         path: venv
-        key: build-libsonata-${{ env.LIBSONATA_BRANCH }} # todo: add python version
+        key: ${{ matrix.os }}-libsonata-${{ env.LIBSONATA_BRANCH }}-py${{ matrix.python-version }}
 
-    - name: Install libsonata
+    - name: Upgrade pip and install base Python packages
       if: steps.cache-venv.outputs.cache-hit != 'true'
       run: |
         python -m venv venv
+        . ./venv/bin/activate
+        python -m pip install --upgrade pip setuptools
+        pip install cython numpy wheel pkgconfig
+
+    - name: Install libsonata
+      if: steps.cache-venv.outputs.cache-hit != 'true'
+      run: |
         . ./venv/bin/activate
         CC=mpicc CXX=mpic++ pip install git+https://github.com/BlueBrain/libsonata
 
@@ -73,7 +98,7 @@ jobs:
         cache-name: cache-libsonatareport
       with:
         path: libsonatareport
-        key: build-libsonatareport-${{ env.LIBSONATA_REPORT_BRANCH }}
+        key: ${{ matrix.os }}-libsonatareport-${{ env.LIBSONATA_REPORT_BRANCH }}-py${{ matrix.python-version }}
 
     - name: Install libsonatareport
       if: steps.cache-libsonatareport.outputs.cache-hit != 'true'
@@ -92,25 +117,35 @@ jobs:
         cache-name: cache-neuron
       with:
         path: nrn
-        key: build-neuron-${{ env.NEURON_BRANCH }}-${{ env.NEURON_COMMIT_ID }}
+        key: ${{ matrix.os }}-neuron-${{ env.NEURON_BRANCH }}-${{ env.NEURON_COMMIT_ID }}-py${{ matrix.python-version }}
 
     - name: Install NEURON
       if: steps.cache-neuron.outputs.cache-hit != 'true'
       run: |
         export SONATAREPORT_DIR=$(pwd)/libsonatareport/build/install
         sudo apt-get install flex libfl-dev bison ninja-build
-        . ./venv/bin/activate
-        git clone --branch=${{ env.NEURON_BRANCH }} https://github.com/neuronsimulator/nrn.git
-        cd nrn
         if [[ ${{ env.NEURON_BRANCH }} == 'master' ]]; then
+          git clone --branch=${{ env.NEURON_BRANCH }} https://github.com/neuronsimulator/nrn.git
+          cd nrn
           git checkout ${{ env.NEURON_COMMIT_ID }}
+          cd ..
+        else
+          git clone --branch=${{ env.NEURON_BRANCH }} https://github.com/neuronsimulator/nrn.git --depth=1
         fi
-        python -m pip install --upgrade pip -r nrn_requirements.txt
-        mkdir build && cd build
-        cmake -G Ninja -DPYTHON_EXECUTABLE=$(which python) -DCMAKE_INSTALL_PREFIX=$(pwd)/install -DNRN_ENABLE_MPI=ON -DNRN_ENABLE_INTERVIEWS=OFF \
-          -DNRN_ENABLE_CORENEURON=ON -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCORENRN_ENABLE_REPORTING=ON -DCMAKE_PREFIX_PATH=$SONATAREPORT_DIR ..
-        cmake --build . --parallel
-        cmake --build . --target install
+        . ./venv/bin/activate
+        python -m pip install --upgrade pip -r nrn/nrn_requirements.txt
+        cmake -B nrn/build -S nrn -G Ninja \
+          -DPYTHON_EXECUTABLE=$(which python) \
+          -DCMAKE_INSTALL_PREFIX=$(pwd)/nrn/build/install \
+          -DNRN_ENABLE_MPI=ON \
+          -DNRN_ENABLE_INTERVIEWS=OFF \
+          -DNRN_ENABLE_CORENEURON=ON \
+          -DCMAKE_C_COMPILER=gcc \
+          -DCMAKE_CXX_COMPILER=g++ \
+          -DCORENRN_ENABLE_REPORTING=ON \
+          -DCMAKE_PREFIX_PATH=$SONATAREPORT_DIR
+        cmake --build nrn/build --parallel
+        cmake --build nrn/build --target install
 
     - name: Install mpi4py
       if: steps.cache-venv.outputs.cache-hit != 'true'
@@ -144,6 +179,9 @@ jobs:
     - name: Example run
       run: |
         . ./venv/bin/activate
+        if [ ${{ matrix.python-version }} == 3.9 ]; then
+          export RDMAV_FORK_SAFE=1
+        fi;
         export PYTHONPATH=$(pwd)/nrn/build/lib/python:$PYTHONPATH
         cp neurodamus/data/hoc/* tests/share/hoc/
         export HOC_LIBRARY_PATH=$(pwd)/tests/share/hoc