forked from neuronets/nobrainer
-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge remote-tracking branch 'upstream/master'
- Loading branch information
Showing
70 changed files
with
2,437 additions
and
6,106 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| .git/ | ||
| docker/ | ||
| .idea/ |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,89 @@ | ||
| name: Guide Notebooks Regression - EC2 | ||
| run-name: ${{ github.ref_name }} - Guide Notebooks Regression - EC2 | ||
| on: [push] | ||
| jobs: | ||
| start-runner: | ||
| name: Start self-hosted EC2 runner | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| label: ${{ steps.start-ec2-runner.outputs.label }} | ||
| ec2-instance-id: ${{ steps.start-ec2-runner.outputs.ec2-instance-id }} | ||
| steps: | ||
| - name: Configure AWS credentials | ||
| uses: aws-actions/configure-aws-credentials@v1 | ||
| with: | ||
| aws-access-key-id: ${{ secrets.AWS_KEY_ID }} | ||
| aws-secret-access-key: ${{ secrets.AWS_KEY_SECRET }} | ||
| aws-region: ${{ vars.AWS_REGION }} | ||
| - name: Start EC2 runner | ||
| id: start-ec2-runner | ||
| uses: machulav/ec2-github-runner@v2 | ||
| with: | ||
| mode: start | ||
| github-token: ${{ secrets.GH_TOKEN }} | ||
| ec2-image-id: ${{ vars.AWS_IMAGE_ID }} | ||
| ec2-instance-type: ${{ vars.AWS_INSTANCE_TYPE }} | ||
| subnet-id: ${{ vars.AWS_SUBNET }} | ||
| security-group-id: ${{ vars.AWS_SECURITY_GROUP }} | ||
|
|
||
| guide_notebooks_regression_ec2: | ||
| needs: start-runner # required to start the main job when the runner is ready | ||
| runs-on: ${{ needs.start-runner.outputs.label }} # run the job on the newly created runner | ||
| steps: | ||
| - name: clone | ||
| uses: actions/checkout@v3 | ||
| - name: install | ||
| run: | | ||
| set -xe | ||
| cd ${{ github.workspace }} | ||
| source /opt/tensorflow/bin/activate | ||
| export LD_LIBRARY_PATH=opt/amazon/efa/lib:/opt/amazon/openmpi/lib:/usr/local/cuda/efa/lib:/usr/local/cuda/lib:/usr/local/cuda:/usr/local/cuda/lib64:/usr/local/cuda/extras/CUPTI/lib64:/usr/local/cuda/targets/x86_64-linux/lib:/usr/local/lib:/usr/lib | ||
| echo $LD_LIBRARY_PATH | ||
| pip install matplotlib nilearn | ||
| pip install -U tensorflow | ||
| 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 }} | ||
| export LD_LIBRARY_PATH=opt/amazon/efa/lib:/opt/amazon/openmpi/lib:/usr/local/cuda/efa/lib:/usr/local/cuda/lib:/usr/local/cuda:/usr/local/cuda/lib64:/usr/local/cuda/extras/CUPTI/lib64:/usr/local/cuda/targets/x86_64-linux/lib:/usr/local/lib:/usr/lib | ||
| source /opt/tensorflow/bin/activate | ||
| for notebook_script in $(ls nobrainer-book/docs/nobrainer-guides/scripts/*.py); do | ||
| echo "running ${notebook_script}" | ||
| python ${notebook_script} | ||
| done | ||
| stop-runner: | ||
| name: Stop self-hosted EC2 runner | ||
| needs: | ||
| - start-runner # required to get output from the start-runner job | ||
| - guide_notebooks_regression_ec2 # required to wait when the main job is done | ||
| runs-on: ubuntu-latest | ||
| if: ${{ always() }} # required to stop the runner even if the error happened in the previous jobs | ||
| steps: | ||
| - name: Configure AWS credentials | ||
| uses: aws-actions/configure-aws-credentials@v1 | ||
| with: | ||
| aws-access-key-id: ${{ secrets.AWS_KEY_ID }} | ||
| aws-secret-access-key: ${{ secrets.AWS_KEY_SECRET }} | ||
| aws-region: ${{ vars.AWS_REGION }} | ||
| - name: Stop EC2 runner | ||
| uses: machulav/ec2-github-runner@v2 | ||
| with: | ||
| mode: stop | ||
| github-token: ${{ secrets.GH_TOKEN }} | ||
| label: ${{ needs.start-runner.outputs.label }} | ||
| ec2-instance-id: ${{ needs.start-runner.outputs.ec2-instance-id }} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.