Pin Python to 3.12 on Fedora latest #1724
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| name: Scheduled NEURON CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| schedule: | |
| # Run at 2am every day | |
| - cron: '0 2 * * *' | |
| workflow_dispatch: | |
| inputs: | |
| azure_drop_url: | |
| description: 'Azure drop (artifacts) url' | |
| neuron_branch: | |
| description: 'NEURON branch to test' | |
| default: '' | |
| defaults: | |
| run: | |
| shell: bash | |
| jobs: | |
| # This allows us to dynamically vary the number of branches we run on on | |
| # different days. | |
| provide_version_matrix: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: check Azure drop url exists -> ${{ github.event.inputs.azure_drop_url }} | |
| if: github.event_name == 'workflow_dispatch' && github.event.inputs.azure_drop_url | |
| run: | | |
| curl -sfSI -X GET '${{ github.event.inputs.azure_drop_url }}' | |
| - name: Get latest release information | |
| id: get_latest_release | |
| uses: joutvhu/get-release@v1 | |
| env: | |
| GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} | |
| with: | |
| debug: true | |
| latest: true | |
| prerelease: true | |
| repo: "nrn" | |
| - name: Construct matrix of branch/tag names and wheel versions to test | |
| id: provide_versions | |
| run: | | |
| if [[ '${{github.event.inputs.neuron_branch}}' == "" ]] | |
| then | |
| # If we're not told to test a specific branch, test the default branch with neuron-nightly wheels | |
| values="{\"branch_or_tag\": \"\", \"default_wheel\": \"neuron-nightly\"}" | |
| if [[ $(date +%u) == 1 ]] || [[ ${{ github.event_name }} == 'pull_request' ]] || [[ ${{ github.event_name }} == 'push' ]] | |
| then | |
| # If it's a Monday, test the latest release (and latest released wheels) in addition | |
| # Also test it on any PR, and any push to a PR | |
| tag_name="${{steps.get_latest_release.outputs.tag_name}}" | |
| values="${values}, {\"branch_or_tag\": \"${tag_name}\", \"default_wheel\": \"neuron==${tag_name}\"}" | |
| fi | |
| echo "matrix=[${values}]" >> $GITHUB_OUTPUT | |
| else | |
| # Test the given branch with no wheels by default. If an Azure URL is given, those wheels will be used. | |
| echo "matrix=[{\"branch_or_tag\": \"${{github.event.inputs.neuron_branch}}\", \"default_wheel\": \"\"}]" >> $GITHUB_OUTPUT | |
| fi | |
| outputs: | |
| matrix: ${{ steps.provide_versions.outputs.matrix }} | |
| ci: | |
| timeout-minutes: 45 | |
| needs: provide_version_matrix | |
| runs-on: ${{ matrix.os.vm }} | |
| container: ${{ matrix.os.container }} | |
| name: ${{matrix.os.container || matrix.os.vm}} ${{matrix.branch_or_tag_and_default_wheel.branch_or_tag}} ${{matrix.branch_or_tag_and_default_wheel.default_wheel}} | |
| env: | |
| SDK_ROOT: $(xcrun --sdk macosx --show-sdk-path) | |
| OS_FLAVOUR: ${{matrix.os.flavour}} | |
| # version of Python we will build NEURON with on MacOS | |
| MACOSX_PY_VERSION: 3.12 | |
| UNPRIVILEGED_USER: runner # User created+used inside Docker containers | |
| # Extra software collections to be installed and enabled on CentOS7 | |
| SOFTWARE_COLLECTIONS_centos_7: devtoolset-9 rh-git218 rh-python38 | |
| strategy: | |
| matrix: | |
| os: | |
| # GitHub Actions MacOS 13 runner | |
| - { vm: macos-13, flavour: macOS } | |
| # GitHub Actions MacOS 12 runner | |
| - { vm: macos-12, flavour: macOS } | |
| # Alma Linux 8 Docker image | |
| - { vm: ubuntu-latest, container: "almalinux:8.10", flavour: redhat } | |
| # CentOS Stream 9 Docker image | |
| - { vm: ubuntu-latest, container: "quay.io/centos/centos:stream9", flavour: redhat } | |
| # Fedora 37 Docker image | |
| - { vm: ubuntu-latest, container: "fedora:37", flavour: redhat } | |
| # Fedora Latest (38, at time of writing) Docker image | |
| - { vm: ubuntu-latest, container: "fedora:latest", flavour: redhat } | |
| # Ubuntu 20.04 Docker image | |
| - { vm: ubuntu-latest, container: "ubuntu:20.04", flavour: debian } | |
| # Ubuntu Latest (22.04, at time of writing) Docker image | |
| - { vm: ubuntu-latest, container: "ubuntu:latest", flavour: debian } | |
| # Debian Bullseye (11) Docker image | |
| - { vm: ubuntu-latest, container: "debian:bullseye", flavour: debian } | |
| # At the time of writing, Debian Bookworm (12) Docker image | |
| - { vm: ubuntu-latest, container: "debian:stable", flavour: debian } | |
| branch_or_tag_and_default_wheel: ${{ fromJson(needs.provide_version_matrix.outputs.matrix) }} | |
| fail-fast: false | |
| steps: | |
| # Checkout the dedicated repository that steers the CI build | |
| - uses: actions/checkout@v3 | |
| # Install required packages using the system package manager. This | |
| # includes installing or updating the git client to a sufficiently | |
| # new version that the checkout of the main nrn repository does *not* | |
| # fall back to using the REST API, which clobbers submodule information | |
| # and breaks the build. | |
| - name: Install ${{matrix.os.flavour}} packages | |
| run: | | |
| OS_CONTAINER="${{matrix.os.container}}" | |
| # only the part after the last slash | |
| OS_CONTAINER="${OS_CONTAINER##*/}" | |
| # replace : and . with _ | |
| OS_CONTAINER="${OS_CONTAINER//[:.]/_}" | |
| CONTAINER_SCRIPT="scripts/install_${{matrix.os.flavour}}_${OS_CONTAINER}.sh" | |
| # pass this on to the next steps too, for convenience | |
| echo "OS_CONTAINER=${OS_CONTAINER}" >> "${GITHUB_ENV}" | |
| # (container+flavour)-specific script runs first because it must be | |
| # able to enable repositories that make the flavour-specific script | |
| # work. | |
| if [ -f "${CONTAINER_SCRIPT}" ]; then source "${CONTAINER_SCRIPT}"; fi | |
| if [ -f "${FLAVOUR_SCRIPT}" ]; then source "${FLAVOUR_SCRIPT}"; fi | |
| env: | |
| FLAVOUR_SCRIPT: scripts/install_${{matrix.os.flavour}}.sh | |
| - if: ${{matrix.os.flavour}} == 'macOS' || ${{matrix.os.container}} == 'fedora:latest' | |
| name: Set up Python@${{ env.MACOSX_PY_VERSION }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.MACOSX_PY_VERSION }} | |
| # Checkout the repository; do this before the privilege step so that we | |
| # can chown the result there | |
| - name: Checkout NEURON | |
| working-directory: ${{github.workspace}} | |
| run: | | |
| branch_or_tag="${{matrix.branch_or_tag_and_default_wheel.branch_or_tag}}" | |
| echo "branch_or_tag=${branch_or_tag}" | |
| if [ -n "${branch_or_tag}" ]; then BRANCH_OPT="--branch=${branch_or_tag}"; fi | |
| git clone --depth=1 --single-branch ${BRANCH_OPT} ${{github.server_url}}/${{github.repository_owner}}/nrn | |
| # Init submodules for testing purposes | |
| cd nrn && git submodule update --init --recursive | |
| # When we run in Ubuntu/Fedora/Debian containers from Docker Hub then we | |
| # are root. This is different from when we use the GitHub Actions images | |
| # directly, and leads to errors from MPI later. If we run inside Docker, | |
| # create a regular user to run as. | |
| - name: Setup unprivileged user | |
| # If we run in a native GitHub Actions container, without Docker, this | |
| # isn't needed | |
| if: matrix.os.container | |
| run: | | |
| useradd --create-home ${UNPRIVILEGED_USER} | |
| chown -R ${UNPRIVILEGED_USER}:${UNPRIVILEGED_USER} ${GITHUB_WORKSPACE} | |
| # Put all the remaining steps in one job that runs as an unprivileged user | |
| - name: Build and test NEURON | |
| working-directory: ${{github.workspace}}/nrn | |
| run: ../wrappers/runUnprivileged.sh ../scripts/buildNeuron.sh | |
| env: | |
| INSTALL_DIR : ${{github.workspace}}/nrn/install | |
| # Download specific wheels from Azure via workflow dispatch | |
| - name: Download Azure drop (artifacts) -> ${{ github.event.inputs.azure_drop_url }} | |
| if: github.event.inputs.azure_drop_url | |
| working-directory: ${{github.workspace}} | |
| run: ./scripts/getAzureDrop.sh '${{ github.event.inputs.azure_drop_url }}' | |
| # Test the wheels. If an Azure URL was given, those wheels are used. Otherwise: | |
| # - default branch (master): neuron-nightly | |
| # - latest release (tag X.Y): neuron==X.Y | |
| # - feature branch: wheels only tested if a URL is given | |
| - name: Test (nightly) NEURON wheel | |
| if: github.event.inputs.azure_drop_url || matrix.branch_or_tag_and_default_wheel.default_wheel | |
| working-directory: ${{github.workspace}}/nrn | |
| run: ../wrappers/runUnprivileged.sh ../scripts/testNeuronWheel.sh | |
| env: | |
| NRN_PACKAGE: ${{matrix.branch_or_tag_and_default_wheel.default_wheel}} | |
| NEURON_BRANCH_OR_TAG: ${{matrix.branch_or_tag}} | |
| # This step will set up an SSH connection on tmate.io for live debugging | |
| # of non-Docker runs that failed. | |
| - name: live debug session on failure | |
| if: failure() && !matrix.os.container | |
| uses: mxschmitt/action-tmate@v3 |