Guide Notebooks Regression - EC2 #109
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| name: Guide Notebooks Regression - EC2 | |
| run-name: Guide Notebooks Regression - EC2 | |
| on: [push] | |
| jobs: | |
| start_ec2_runner: | |
| runs-on: ubuntu-latest | |
| env: | |
| AWS_KEY_ID: ${{ secrets.AWS_KEY_ID }} | |
| AWS_KEY_SECRET: ${{ secrets.AWS_KEY_SECRET }} | |
| AWS_GH_RUNNER_KEY: ${{ secrets.AWS_GH_RUNNER_KEY }} | |
| GH_TOKEN: ${{ secrets.GH_TOKEN }} | |
| AWS_INSTANCE_TYPE: ${{ vars.AWS_INSTANCE_TYPE }} | |
| AWS_IMAGE_ID: ${{ vars.AWS_IMAGE_ID }} | |
| AWS_SECURITY_GROUP: ${{ vars.AWS_SECURITY_GROUP }} | |
| outputs: | |
| EC2_INSTANCE_ID: ${{ steps.create_instance.outputs.EC2_INSTANCE_ID }} | |
| RUNNER_LABEL: ${{ steps.create_instance.outputs.EC2_PUBLIC_DNS }} | |
| steps: | |
| - name: configure_aws | |
| run: | | |
| set -xe | |
| sudo apt update | |
| sudo apt install -y awscli jq | |
| mkdir ${HOME}/.aws | |
| echo "[default]" > ${HOME}/.aws/credentials | |
| echo "aws_access_key_id = ${AWS_KEY_ID}" >> ${HOME}/.aws/credentials | |
| echo "aws_secret_access_key = ${AWS_KEY_SECRET}" >> ${HOME}/.aws/credentials | |
| echo "region = us-east-1" >> ${HOME}/.aws/credentials | |
| cat ${HOME}/.aws/credentials | |
| - name: create_instance | |
| id: create_instance | |
| run: | | |
| set -xe | |
| output=$(aws ec2 run-instances \ | |
| --instance-type ${AWS_INSTANCE_TYPE} \ | |
| --image-id ${AWS_IMAGE_ID} \ | |
| --security-group-ids ${AWS_SECURITY_GROUP} \ | |
| --count 1) | |
| EC2_INSTANCE_ID=$(echo ${output} | jq -r ".Instances[0].InstanceId") | |
| EC2_PUBLIC_DNS='' | |
| while [ -z ${EC2_PUBLIC_DNS} ]; do | |
| EC2_PUBLIC_DNS=$(aws ec2 describe-instances \ | |
| --instance-ids ${EC2_INSTANCE_ID} \ | |
| | jq -r ".Reservations[0].Instances[0].PublicDnsName") | |
| sleep 1 | |
| done | |
| echo "EC2_INSTANCE_ID=${EC2_INSTANCE_ID}" >> "$GITHUB_OUTPUT" | |
| echo "EC2_PUBLIC_DNS=${EC2_PUBLIC_DNS}" >> "$GITHUB_OUTPUT" | |
| - name: register_runner | |
| id: register_runner | |
| run: | | |
| set -xe | |
| echo ${AWS_GH_RUNNER_KEY} > ${HOME}/.ssh/gh_runner | |
| chmod 600 ${HOME}/.ssh/gh_runner | |
| echo ${GH_TOKEN} > gh_token | |
| scp -o StrictHostKeyChecking=accept-new -i ${HOME}/.ssh/gh_runner gh_token ubuntu@${EC2_PUBLIC_DNS}:gh_token | |
| scp -i ${HOME}/.ssh/gh_runner provision_runner.sh ubuntu@${EC2_PUBLIC_DNS}:provision_runner.sh | |
| ssh -i ${HOME}/.ssh/gh_runner bash provision_runner.sh | |
| guide_notebooks_regression_ec2: | |
| runs-on: ${{ needs.start_ec2_runner.outputs.RUNNER_LABEL }} | |
| needs: start_ec2_runner | |
| steps: | |
| - name: verify-instance | |
| env: | |
| EC2_INSTANCE_ID: ${{ needs.start_ec2_runner.outputs.EC2_INSTANCE_ID }} | |
| run: | | |
| set -xe | |
| if [[ $(ec2metadata --instance-id) != ${EC2_INSTANCE_ID} ]]; then | |
| echo "Running on the wrong instance! Bailing, but try rerunning" | |
| exit 1 | |
| fi | |
| - name: clone | |
| uses: actions/checkout@v3 | |
| - name: install | |
| run: | | |
| set -xe | |
| cd ${{ github.workspace }} | |
| python -m venv env | |
| source env/bin/activate | |
| pip install --upgrade pip | |
| pip install matplotlib nilearn | |
| pip install -e . | |
| nobrainer info | |
| - name: run | |
| run: | | |
| set -xe | |
| cd ${{ github.workspace }} | |
| git clone https://github.com/neuronets/nobrainer-book.git | |
| cd nobrainer-book | |
| # if there is a matching book branch, switch to it | |
| if [ $(git ls-remote --heads https://github.com/neuronets/nobrainer-book.git ${{ github.ref_name }} | wc -l) -ne 0 ]; then | |
| echo "Checking out branch ${{ github.ref_name }}" | |
| git checkout ${{ github.ref_name }}; | |
| else | |
| echo "No matching branch found, sticking with the default" | |
| fi | |
| cd ${{ github.workspace }} | |
| source env/bin/activate | |
| for notebook_script in $(ls nobrainer-book/docs/nobrainer-guides/scripts/*.py); do | |
| echo "running ${notebook_script}" | |
| python ${notebook_script} | |
| done | |
| stop_ec2_runner: | |
| if: always() | |
| runs-on: ubuntu-latest | |
| needs: [start_ec2_runner, guide_notebooks_regression_ec2] | |
| env: | |
| AWS_KEY_ID: ${{ secrets.AWS_KEY_ID }} | |
| AWS_KEY_SECRET: ${{ secrets.AWS_KEY_SECRET }} | |
| steps: | |
| - name: configure_aws | |
| run: | | |
| set -xe | |
| sudo apt update | |
| sudo apt install -y awscli | |
| mkdir ${HOME}/.aws | |
| echo "[default]" > ${HOME}/.aws/credentials | |
| echo "aws_access_key_id = ${AWS_KEY_ID}" >> ${HOME}/.aws/credentials | |
| echo "aws_secret_access_key = ${AWS_KEY_SECRET}" >> ${HOME}/.aws/credentials | |
| echo "region = us-east-1" >> ${HOME}/.aws/credentials | |
| cat ${HOME}/.aws/credentials | |
| - name: deregister_runner | |
| id: deregister_runner | |
| env: | |
| EC2_INSTANCE_ID: ${{ needs.start_ec2_runner.outputs.RUNNER_LABEL }} | |
| run: | | |
| set -xe | |
| echo ${AWS_GH_RUNNER_KEY} > ${HOME}/.ssh/gh_runner | |
| chmod 600 ${HOME}/.ssh/gh_runner | |
| echo ${GH_TOKEN} > gh_token | |
| scp -o StrictHostKeyChecking=accept-new -i ${HOME}/.ssh/gh_runner destroy_runner.sh gh_token ubuntu@${EC2_PUBLIC_DNS}: | |
| ssh -i ${HOME}/.ssh/gh_runner bash destroy_runner.sh | |
| - name: stop_runner | |
| env: | |
| EC2_INSTANCE_ID: ${{ needs.start_ec2_runner.outputs.EC2_INSTANCE_ID }} | |
| run: | | |
| set -xe | |
| aws ec2 terminate-instances --instance-ids ${EC2_INSTANCE_ID} |