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build-neuron.yml
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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}}
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 }
# 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 --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