Scheduled NEURON CI #1245
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name: Scheduled NEURON CI | |
on: | |
push: | |
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 [[ $(date +%u) == 1 ]] | |
then | |
# If it's a Monday, test the latest release (and latest released wheels) in addition | |
tag_name="${{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}} | |
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 12 runner | |
- { vm: macos-12, flavour: macOS } | |
# GitHub Actions MacOS 11 runner | |
- { vm: macos-11, flavour: macOS } | |
# CentOS7 Docker image | |
- { vm: ubuntu-latest, container: "centos:7", flavour: redhat } | |
# CentOS Stream 8 Docker image | |
- { vm: ubuntu-latest, container: "quay.io/centos/centos:stream8", 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 | |
# 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 | |
# 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 |