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Add template rst files for readthedocs #57

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Add template rst files for readthedocs

Add template rst files for readthedocs #57

Workflow file for this run

.github/workflows/docker-slurm.yaml at 4b4433f
name: ExascaleSandboxTests
on:
push:
branches: [ develop, main ]
pull_request:
branches: [ develop, main ]
workflow_dispatch:
env:
REGISTRY_IMAGE: ghcr.io/noaa-gsl/exascaleworkflowsandbox/spack-stack-gnu-openmpi
AWS_REGION: us-east-2
jobs:
lint-check:
runs-on: ubuntu-latest
steps:
-
name: Checkout repository
uses: actions/checkout@v4
-
name: Format Check
run: |
pip install flake8 black isort
flake8 src tests
black src tests --check --diff
isort src tests --check --diff --profile black
build-spack-stack-arm64:
runs-on: LinuxARM64-4core-16G-150Gb
timeout-minutes: 360
permissions:
packages: write
contents: read
id-token: write
steps:
-
# Beta ARM runners do not have Docker installed
name: Install Docker
run: |
# Uninstall incompatible packages
for pkg in docker.io containerd runc; do sudo apt-get remove $pkg; done
# Add Docker's official GPG key:
sudo apt-get update
sudo apt-get install ca-certificates curl
sudo install -m 0755 -d /etc/apt/keyrings
sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg -o /etc/apt/keyrings/docker.asc
sudo chmod a+r /etc/apt/keyrings/docker.asc
# Add the repository to Apt sources:
echo \
"deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/ubuntu \
$(. /etc/os-release && echo "$VERSION_CODENAME") stable" | \
sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
sudo apt-get update -y
# Install docker packages
sudo apt-get install -y docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin
# Allow runner use to run docker without sudo
sudo usermod -aG docker $USER
sudo apt-get install acl
sudo setfacl --modify user:$USER:rw /var/run/docker.sock
-
name: Test Docker Installation
run: docker run hello-world
-
name: Install AWS CLI
run: sudo apt install -y awscli
-
name: Checkout repository
uses: actions/checkout@v4
-
name: Configure AWS credentials
uses: aws-actions/configure-aws-credentials@v4
with:
aws-region: ${{ env.AWS_REGION }}
role-to-assume: arn:aws:iam::${{ secrets.AWS_ACCOUNT_ID }}:role/${{ secrets.AWS_GITHUB_ROLE }}
role-duration-seconds: 21600 # 6 hours
role-session-name: chiltepin-github-actions
-
name: Test authentication
run: |
aws sts get-caller-identity
-
name: Docker meta
id: meta
uses: docker/metadata-action@v5
with:
images: ${{ env.REGISTRY_IMAGE }}
tags: |
type=raw,value=latest
flavor: |
latest=true
prefix=
suffix=
-
name: Set up Docker Buildx
uses: docker/setup-buildx-action@v3
-
name: Login to GHCR
uses: docker/login-action@v3
with:
registry: ghcr.io
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}
logout: false
-
name: Prune pre-loaded GHA docker images
run: |
docker images
docker image prune -a -f
docker images
-
name: Create spack-stack Dockerfile and mirror
run: |
cd docker/spack-stack
cat mirrors.in.yaml | envsubst > mirrors.yaml
./create_dockerfile.sh
-
name: Build spack-stack and push by digest
id: build
uses: docker/build-push-action@v5
with:
context: ./docker/spack-stack
file: ./docker/spack-stack/Dockerfile
platforms: linux/arm64
secret-files: "mirrors=./docker/spack-stack/mirrors.yaml"
secrets: |
"access_key_id=${{ env.AWS_ACCESS_KEY_ID }}"
"secret_access_key=${{ env.AWS_SECRET_ACCESS_KEY }}"
"session_token=${{ env.AWS_SESSION_TOKEN }}"
labels: ${{ steps.meta.outputs.labels }}
cache-from: type=registry,ref=ghcr.io/noaa-gsl/exascaleworkflowsandbox/spack-stack-gnu-openmpi-cache-arm64:cache
cache-to: type=registry,ref=ghcr.io/noaa-gsl/exascaleworkflowsandbox/spack-stack-gnu-openmpi-cache-arm64:cache,mode=max
outputs: type=image,name=${{ env.REGISTRY_IMAGE }},push-by-digest=true,name-canonical=true,push=true
-
name: Export digest
run: |
mkdir -p /tmp/digests
digest="${{ steps.build.outputs.digest }}"
touch "/tmp/digests/${digest#sha256:}"
-
name: Upload digest
uses: actions/upload-artifact@v4
with:
name: digests-linux-arm64
path: /tmp/digests/*
if-no-files-found: error
retention-days: 1
build-spack-stack-amd64:
runs-on: ubuntu2204-4c-16g-150ssd
timeout-minutes: 360
permissions:
packages: write
contents: read
id-token: write
steps:
-
name: Checkout repository
uses: actions/checkout@v4
-
name: Configure AWS credentials
uses: aws-actions/configure-aws-credentials@v4
with:
aws-region: ${{ env.AWS_REGION }}
role-to-assume: arn:aws:iam::${{ secrets.AWS_ACCOUNT_ID }}:role/${{ secrets.AWS_GITHUB_ROLE }}
role-duration-seconds: 21600 # 6 hours
role-session-name: chiltepin-github-actions
-
name: Test authentication
run: |
aws sts get-caller-identity
-
name: Docker meta
id: meta
uses: docker/metadata-action@v5
with:
images: ${{ env.REGISTRY_IMAGE }}
tags: |
type=raw,value=latest
flavor: |
latest=true
prefix=
suffix=
-
name: Set up Docker Buildx
uses: docker/setup-buildx-action@v3
-
name: Login to GHCR
uses: docker/login-action@v3
with:
registry: ghcr.io
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}
logout: false
-
name: Prune pre-loaded GHA docker images
run: |
docker images
docker image prune -a -f
docker images
-
name: Create spack-stack Dockerfile and mirror
run: |
cd docker/spack-stack
cat mirrors.in.yaml | envsubst > mirrors.yaml
./create_dockerfile.sh
-
name: Build spack-stack and push by digest
id: build
uses: docker/build-push-action@v5
with:
context: ./docker/spack-stack
file: ./docker/spack-stack/Dockerfile
platforms: linux/amd64
secret-files: "mirrors=./docker/spack-stack/mirrors.yaml"
secrets: |
"access_key_id=${{ env.AWS_ACCESS_KEY_ID }}"
"secret_access_key=${{ env.AWS_SECRET_ACCESS_KEY }}"
"session_token=${{ env.AWS_SESSION_TOKEN }}"
labels: ${{ steps.meta.outputs.labels }}
cache-from: type=registry,ref=ghcr.io/noaa-gsl/exascaleworkflowsandbox/spack-stack-gnu-openmpi-cache-amd64:cache
cache-to: type=registry,ref=ghcr.io/noaa-gsl/exascaleworkflowsandbox/spack-stack-gnu-openmpi-cache-amd64:cache,mode=max
outputs: type=image,name=${{ env.REGISTRY_IMAGE }},push-by-digest=true,name-canonical=true,push=true
-
name: Export digest
run: |
mkdir -p /tmp/digests
digest="${{ steps.build.outputs.digest }}"
touch "/tmp/digests/${digest#sha256:}"
-
name: Upload digest
uses: actions/upload-artifact@v4
with:
name: digests-linux-amd64
path: /tmp/digests/*
if-no-files-found: error
retention-days: 1
merge-spack-stack:
runs-on: ubuntu-latest
needs:
- build-spack-stack-amd64
- build-spack-stack-arm64
steps:
-
name: Checkout repository
uses: actions/checkout@v4
-
name: Download digests
uses: actions/download-artifact@v4
with:
path: /tmp/digests
pattern: digests-*
merge-multiple: true
-
name: Set up Docker Buildx
uses: docker/setup-buildx-action@v3
-
name: Docker meta
id: meta
uses: docker/metadata-action@v5
with:
images: ${{ env.REGISTRY_IMAGE }}
tags: |
type=raw,value=latest
flavor: |
latest=true
prefix=
suffix=
-
name: Login to GHCR
uses: docker/login-action@v3
with:
registry: ghcr.io
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}
logout: false
-
name: Create manifest list and push
working-directory: /tmp/digests
run: |
docker buildx imagetools create $(jq -cr '.tags | map("-t " + .) | join(" ")' <<< "$DOCKER_METADATA_OUTPUT_JSON") \
$(printf '${{ env.REGISTRY_IMAGE }}@sha256:%s ' *)
-
name: Inspect image
run: |
docker buildx imagetools inspect ${{ env.REGISTRY_IMAGE }}:${{ steps.meta.outputs.version }}
build-and-test-chiltepin:
needs:
- merge-spack-stack
runs-on: ubuntu2204-16c-64g-600ssd
timeout-minutes: 360
permissions:
packages: write
contents: read
pull-requests: write
steps:
-
name: Checkout repository
uses: actions/checkout@v4
-
name: Set up QEMU
uses: docker/setup-qemu-action@v3
-
name: Set up Docker Buildx
uses: docker/setup-buildx-action@v3
-
name: Login to GHCR
uses: docker/login-action@v3
with:
registry: ghcr.io
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}
logout: false
-
name: Prune pre-loaded GHA docker images
run: |
docker images
docker image prune -a -f
docker images
-
name: Build frontend
uses: docker/build-push-action@v5
with:
context: ./docker
file: ./docker/frontend/Dockerfile
push: false
load: true
tags: ghcr.io/noaa-gsl/exascaleworkflowsandbox/frontend:latest
cache-from: type=registry,ref=ghcr.io/noaa-gsl/exascaleworkflowsandbox/frontend:cache
cache-to: type=registry,ref=ghcr.io/noaa-gsl/exascaleworkflowsandbox/frontend:cache,mode=max
-
name: Build master
uses: docker/build-push-action@v5
with:
context: ./docker
file: ./docker/master/Dockerfile
push: false
load: true
tags: ghcr.io/noaa-gsl/exascaleworkflowsandbox/master:latest
cache-from: type=registry,ref=ghcr.io/noaa-gsl/exascaleworkflowsandbox/master:cache
cache-to: type=registry,ref=ghcr.io/noaa-gsl/exascaleworkflowsandbox/master:cache,mode=max
-
name: Build node
uses: docker/build-push-action@v5
with:
context: ./docker
file: ./docker/node/Dockerfile
push: false
load: true
tags: ghcr.io/noaa-gsl/exascaleworkflowsandbox/node:latest
cache-from: type=registry,ref=ghcr.io/noaa-gsl/exascaleworkflowsandbox/node:cache
cache-to: type=registry,ref=ghcr.io/noaa-gsl/exascaleworkflowsandbox/node:cache,mode=max
-
name: Start Slurm cluster containers
run: |
cd docker
export DOCKER_CLIENT_TIMEOUT=600
export COMPOSE_HTTP_TIMEOUT=600
docker compose version
docker compose config
docker images
docker ps -a
docker compose -f docker-compose.yml up -d --no-build
-
name: Copy test files to work directory
run: |
docker exec frontend bash -l -c "mkdir -p work; cd work ; cp -r ../chiltepin/* ."
-
name: Install chiltepin package
run: docker exec frontend bash -l -c "cd work ; pip install -e ."
-
name: Run test suite
run: |
docker exec frontend bash -l -c "cd work/tests ; PYTHONPATH=.. pytest -s -v --assert=plain --config=config.yaml --platform=docker"
-
name: Debug session
if: ${{ failure() }}
uses: mxschmitt/action-tmate@v3
timeout-minutes: 60
with:
limit-access-to-actor: true
-
name: Shut down Slurm cluster containers
run: |
cd docker
export DOCKER_CLIENT_TIMEOUT=600
export COMPOSE_HTTP_TIMEOUT=600
docker compose -f docker-compose.yml down
-
name: Push frontend
uses: docker/build-push-action@v5
with:
context: ./docker
file: ./docker/frontend/Dockerfile
push: true
platforms: linux/amd64,linux/arm64
tags: ghcr.io/noaa-gsl/exascaleworkflowsandbox/frontend:latest
cache-from: type=registry,ref=ghcr.io/noaa-gsl/exascaleworkflowsandbox/frontend:cache
cache-to: type=registry,ref=ghcr.io/noaa-gsl/exascaleworkflowsandbox/frontend:cache,mode=max
-
name: Push master
uses: docker/build-push-action@v5
with:
context: ./docker
file: ./docker/master/Dockerfile
push: true
platforms: linux/amd64,linux/arm64
tags: ghcr.io/noaa-gsl/exascaleworkflowsandbox/master:latest
cache-from: type=registry,ref=ghcr.io/noaa-gsl/exascaleworkflowsandbox/master:cache
cache-to: type=registry,ref=ghcr.io/noaa-gsl/exascaleworkflowsandbox/master:cache,mode=max
-
name: Push node
uses: docker/build-push-action@v5
with:
context: ./docker
file: ./docker/node/Dockerfile
push: true
platforms: linux/amd64,linux/arm64
tags: ghcr.io/noaa-gsl/exascaleworkflowsandbox/node:latest
cache-from: type=registry,ref=ghcr.io/noaa-gsl/exascaleworkflowsandbox/node:cache
cache-to: type=registry,ref=ghcr.io/noaa-gsl/exascaleworkflowsandbox/node:cache,mode=max
-
name: Add Test-MPAS-App label
run: |
curl \
-X POST \
-H "Accept: application/vnd.github+json" \
-H "Authorization: Bearer ${{ secrets.LABEL_PR }}" \
-H "X-GitHub-Api-Version: 2022-11-28" \
https://api.github.com/repos/${{ github.repository }}/issues/${{ github.event.number }}/labels \
-d '{"labels":["Test-MPAS-App"]}'