Revert "Remove CI to build faster"

This reverts commit bea2ceb.

.circleci/config.yml

@@ -0,0 +1,106 @@
+version: 2.1
+
+orbs:
+  python: circleci/[email protected]
+
+jobs:
+  manylinux2014-aarch64:
+
+    parameters:
+      NRN_PYTHON_VERSION:
+        type: string
+      NRN_NIGHTLY_UPLOAD:
+        type: string
+
+    machine:
+      image: default
+
+    resource_class: arm.medium
+
+    steps:
+      - checkout
+      - 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
+
+      - store_artifacts:
+          path: ./wheelhouse
+          destination: artifacts
+
+      - run:
+          name: Test manylinux AArch64 wheel
+          command: |
+
+            # install mpi dependencies
+            sudo apt update
+            sudo apt install -y mpich openmpi-bin libopenmpi-dev libmpich-dev
+
+            # choose available python versions from pyenv
+            pyenv_py_ver=""
+            case << parameters.NRN_PYTHON_VERSION >> in
+              38) pyenv_py_ver="3.8" ;;
+              39) pyenv_py_ver="3.9" ;;
+              310) pyenv_py_ver="3.10" ;;
+              311) pyenv_py_ver="3.11" ;;
+              312) pyenv_py_ver="3.12" ;;
+              *) echo "Error: pyenv python version not specified or not supported." && exit 1;;
+            esac
+
+            env PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install $pyenv_py_ver --force
+            pyenv global $pyenv_py_ver
+            export PYTHON_EXE=$(which python)
+
+            # test wheel
+            packaging/python/test_wheels.sh $PYTHON_EXE $(ls -t wheelhouse/*.whl)
+
+      - run:
+          name: Upload nightly wheel to pypi.org
+          command: |
+            if [ "<< parameters.NRN_NIGHTLY_UPLOAD >>" == "true" ]; then
+              python -m pip install --upgrade pip
+              python -m pip install twine
+              python -m twine upload --verbose --skip-existing -u $TWINE_USERNAME -p $TWINE_PASSWORD  wheelhouse/*.whl
+            else
+              echo "Skipping pypi.org upload!"
+            fi
+
+workflows:
+
+  build-workflow:
+    jobs:
+      - manylinux2014-aarch64:
+          filters:
+            branches:
+              only:
+                - /release\/.*/
+                - /circleci\/.*/
+          matrix:
+            parameters:
+              NRN_PYTHON_VERSION: ["312"]
+              NRN_NIGHTLY_UPLOAD: ["false"]
+
+  nightly:
+    triggers:
+      - schedule:
+          cron: "0 0 * * *"
+          filters:
+            branches:
+              only:
+                - master
+    jobs:
+      - manylinux2014-aarch64:
+          matrix:
+            parameters:
+              NRN_PYTHON_VERSION: ["38", "39", "310", "311", "312"]
+              NRN_NIGHTLY_UPLOAD: ["true"]

.github/workflows/coverage.yml

@@ -0,0 +1,193 @@
+name: NEURON Code Coverage
+
+concurrency:
+  # Don't cancel on master, creating a PR when a push workflow is already going will cancel the push workflow in favour of the PR workflow
+  group: ${{ github.workflow }}-${{ github.ref == 'refs/heads/master' && github.run_id || github.event.number && github.head_ref || github.ref_name }}
+  cancel-in-progress: true
+
+on:
+  merge_group:
+  push:
+    branches:
+      - master
+      - release/**
+  pull_request:
+    branches:
+      - master
+      - release/**
+# TODO : https://github.com/neuronsimulator/nrn/issues/1063
+#    paths-ignore:
+#      - '**.md'
+#      - '**.rst'
+#      - 'docs/**'
+
+env:
+  PY_MIN_VERSION: '3.8'
+  PY_MID_VERSION: '3.10'
+  PY_MAX_VERSION: '3.12'
+
+jobs:
+  coverage:
+    runs-on: ubuntu-22.04
+
+    name: Code Coverage
+
+    timeout-minutes: 60
+
+    env:
+      DISPLAY: ${{ ':0' }}
+      MUSIC_INSTALL_DIR: /opt/MUSIC
+      MUSIC_VERSION: 1.2.0
+
+    steps:
+
+      - name: Install apt packages
+        run: |
+          sudo apt-get install xfonts-100dpi build-essential doxygen lcov libboost-all-dev libopenmpi-dev libmpich-dev libx11-dev libxcomposite-dev mpich openmpi-bin gpg ninja-build flex bison libfl-dev
+        shell: bash
+
+      - name: Setup Caliper profiler
+        run: |
+          git clone https://github.com/LLNL/Caliper.git
+          cd Caliper
+          mkdir build && cd build
+          cmake ..
+          make && sudo make install
+
+      - name: Setup MUSIC@${{ env.MUSIC_VERSION }}
+        run: |
+          python3 -m venv music-venv
+          source music-venv/bin/activate
+          python3 -m pip install 'mpi4py<4' cython numpy setuptools
+          sudo mkdir -p $MUSIC_INSTALL_DIR
+          sudo chown -R $USER $MUSIC_INSTALL_DIR
+          curl -L -o MUSIC.zip https://github.com/INCF/MUSIC/archive/refs/tags/${MUSIC_VERSION}.zip
+          unzip MUSIC.zip && mv MUSIC-* MUSIC && cd MUSIC
+          ./autogen.sh
+          ./configure --with-python-sys-prefix --prefix=$MUSIC_INSTALL_DIR --disable-anysource
+          make -j install
+          deactivate
+        working-directory: ${{runner.temp}}
+
+      - name: Setup Xvfb
+        run: |
+          sudo apt-get install xvfb
+          sudo /usr/bin/Xvfb $DISPLAY -screen 0 1600x1200x24 -noreset -nolock -shmem &  # run in bg
+
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 2
+
+      - name: Clone nmodl
+        working-directory: ${{runner.workspace}}/nrn
+        run: |
+            git submodule update --init --recursive --force --depth 1 -- external/nmodl
+
+      - name: Set up Python@${{ env.PY_MIN_VERSION }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PY_MIN_VERSION }}
+
+      - name: Install Python@${{ env.PY_MIN_VERSION }} dependencies
+        working-directory: ${{runner.workspace}}/nrn
+        run: |
+          python -m pip install --upgrade -r external/nmodl/requirements.txt
+          python -m pip install --upgrade -r ci_requirements.txt
+          python -m pip install --upgrade pip -r nrn_requirements.txt
+
+      - name: Set up Python@${{ env.PY_MID_VERSION }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PY_MID_VERSION }}
+
+      - name: Set up Python@${{ env.PY_MAX_VERSION }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PY_MAX_VERSION }}
+
+      - name: Install Python@${{ env.PY_MAX_VERSION }} dependencies
+        working-directory: ${{runner.workspace}}/nrn
+        run: |
+          python -m pip install --upgrade -r external/nmodl/requirements.txt
+          python -m pip install --upgrade -r ci_requirements.txt
+          python -m pip install --upgrade pip -r nrn_requirements.txt
+
+
+      - name: Build & Test
+        id: build-test
+        shell: bash
+        working-directory: ${{runner.workspace}}/nrn
+        run:  |
+          export SHELL="/bin/bash"
+
+          # Compiler setup
+          export CC=gcc
+          export CXX=g++
+
+          # Python setup
+          export PYTHON_MIN=$(which $PYTHON_MIN_NAME);
+          export PYTHON_MID=$(which $PYTHON_MID_NAME);
+          export PYTHON_MAX=$(which $PYTHON_MAX_NAME);
+
+          mkdir build && cd build;
+
+          # CMake options & flags
+          cmake_args=(-G Ninja \
+                      -DCMAKE_BUILD_TYPE=Debug \
+                      -DCMAKE_C_COMPILER="$CC" \
+                      -DCMAKE_CXX_COMPILER="$CXX" \
+                      -DNRN_ENABLE_BACKTRACE=ON \
+                      -DNRN_ENABLE_CORENEURON=ON \
+                      -DNRN_ENABLE_COVERAGE=ON \
+                      -DNRN_ENABLE_INTERVIEWS=ON \
+                      -DNRN_ENABLE_MPI=ON \
+                      -DNRN_ENABLE_PERFORMANCE_TESTS=OFF \
+                      -DNRN_ENABLE_PROFILING=ON \
+                      -DNRN_ENABLE_PYTHON=ON \
+                      -DNRN_ENABLE_PYTHON_DYNAMIC=ON \
+                      -DNRN_PYTHON_DYNAMIC="${PYTHON_MIN};${PYTHON_MAX}" \
+                      -DNRN_PYTHON_EXTRA_FOR_TESTS=${PYTHON_MID} \
+                      -DNRN_ENABLE_TESTS=ON \
+                      -DNRN_ENABLE_MUSIC=ON \
+                      -DCMAKE_PREFIX_PATH="${MUSIC_INSTALL_DIR}" \
+                      -DMUSIC_ROOT="${MUSIC_INSTALL_DIR}")
+          cmake .. "${cmake_args[@]}"
+          # Coverage
+          # The Linux runners apparently have 2 cores, but jobs were being killed when we did not specify this explicitly.
+          # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
+          # By default we get a modern version of CMake that understands --parallel.
+          cmake --build . --parallel 2
+          cmake --build . --target cover_baseline
+          xvfb-run ctest --rerun-failed --output-on-failure;
+          for python in "${PYTHON_MIN}" "${PYTHON_MAX}"
+          do
+            echo "Using ${python}"
+            NEURONHOME="${PWD}/share/nrn" \
+              PYTHONPATH="${PWD}/lib/python:${PYTHONPATH}" \
+              PATH="${PWD}/bin:${PATH}" \
+              LD_LIBRARY_PATH="${PWD}/lib:${LD_LIBRARY_PATH}" \
+              DYLD_LIBRARY_PATH="${PWD}/lib:${DYLD_LIBRARY_PATH}" \
+              "${python}" -c "from neuron import h; import neuron; neuron.test();neuron.test_rxd();"
+          done
+          cmake --build . --target cover_collect
+          cmake --build . --target cover_combine
+        env:
+          MATRIX_EVAL: "CC=gcc CXX=g++"
+          PYTHON_MIN_NAME: "python${{ env.PY_MIN_VERSION }}"
+          PYTHON_MID_NAME: "python${{ env.PY_MID_VERSION }}"
+          PYTHON_MAX_NAME: "python${{ env.PY_MAX_VERSION }}"
+
+      # This step will set up an SSH connection on tmate.io for live debugging.
+      # To enable it, you have to:
+      #   * add 'live-debug-coverage' to your PR title
+      #   * push something to your PR branch (note that just re-running the pipeline disregards the title update)
+      - name: live debug session on failure (manual steps required, check `.github/coverage.yml`)
+        if: failure() && contains(github.event.pull_request.title, 'live-debug-coverage')
+        uses: mxschmitt/action-tmate@v3
+
+      - uses: codecov/codecov-action@v4
+        with:
+          directory: ./build
+          fail_ci_if_error: true
+          verbose: true
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/docs.yml

@@ -0,0 +1,80 @@
+name: NEURON Documentation
+
+concurrency:
+  # Don't cancel on master, creating a PR when a push workflow is already going will cancel the push workflow in favour of the PR workflow
+  group: ${{ github.workflow }}-${{ github.ref == 'refs/heads/master' && github.run_id || github.event.number && github.head_ref || github.ref_name }}
+  cancel-in-progress: true
+
+on:
+  merge_group:
+  push:
+    branches:
+      - master
+      - release/**
+  pull_request:
+    branches:
+      - master
+      - release/**
+
+env:
+  DEFAULT_PY_VERSION: '3.12'
+
+jobs:
+  documentation:
+    runs-on: ubuntu-20.04
+
+    name: Documentation
+
+    timeout-minutes: 25
+
+    steps:
+
+      - name: Install apt packages
+        run: |
+          sudo apt-get update --fix-missing
+          sudo apt-get install build-essential libopenmpi-dev libmpich-dev libx11-dev libxcomposite-dev mpich openmpi-bin
+          sudo apt-get install ffmpeg doxygen pandoc
+        shell: bash
+
+      - name: Set up Python@${{ env.DEFAULT_PY_VERSION }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.DEFAULT_PY_VERSION }}
+
+      - uses: actions/checkout@v4
+
+      - name: Install Python dependencies
+        working-directory: ${{runner.workspace}}/nrn
+        run: |
+          python -m pip install --upgrade pip -r nrn_requirements.txt
+
+      - name: Install Python documentation dependencies
+        working-directory: ${{runner.workspace}}/nrn
+        run: |
+          python -m pip install --upgrade -r docs/docs_requirements.txt
+
+      - name: Documentation
+        id: documentation
+        shell: bash
+        working-directory: ${{runner.workspace}}/nrn
+        run:  |
+          echo "-------- NEURON wheel --------";
+          python setup.py build_ext bdist_wheel;
+          neuron_wheel=dist/NEURON*.whl;
+          echo "-------- install wheel --------"
+          python -m pip install $neuron_wheel;
+          echo "-------- now build docs--------";
+          python setup.py docs;
+          echo "-------- disable jekyll--------";
+          pushd docs/_build;
+          touch .nojekyll;
+          echo "-------- OK to deploy! --------";
+          echo "OK_TO_DEPLOY_DOCS=true" >> $GITHUB_ENV
+
+      # This step will set up an SSH connection on tmate.io for live debugging.
+      # To enable it, you have to:
+      #   * add 'live-debug-docs' to your PR title
+      #   * push something to your PR branch (note that just re-running the pipeline disregards the title update)
+      - name: live debug session on failure (manual steps required, check `.github/docs.yml`)
+        if: failure() && contains(github.event.pull_request.title, 'live-debug-docs')
+        uses: mxschmitt/action-tmate@v3