Script to add a GitHub repo on a SageMaker notebook when SSO is enforce on GitHub

sagemaker_notebook_github_sso

# 0: Attach a lifecycle configuration to you Notebook instance to persist environments between sessions
# See https://modelpredict.com/sagemaker-save-your-conda-environments/ for instruction
# Alternative: create environments under the persisted folder (/home/ec2-user/SageMaker) with 
# conda create -p /home/ec2-user/SageMaker/py310 python=3.10
# then systematically symlink: ln -s /home/ec2-user/SageMaker/py310 ~/anaconda3/envs/py310

# 1: Create a new conda environment and make it accessible to SageMaker
conda create -y -n py310 python=3.10
conda activate py310
# From https://forum.deepchem.io/t/deploying-a-deepchem-sagemaker-notebook-instance/174
conda install -y ipykernel && python -m ipykernel install --user --name=py310

# 2: Set up GitHub connection
conda install -y gh --channel conda-forge
# You can either login through the UI, or 
# create a keypair in GitHub https://github.com/settings/tokens with repo, read:org, and admin:public_key permissions, then click on Enable SSO
gh auth login 
mkdir /home/ec2-user/SageMaker/.ssh  # Persisted folder for our new SSH key
mv .ssh/id_ed25519* SageMaker/.ssh/
gh ssh-key add /home/ec2-user/SageMaker/.ssh/id_ed25519.pub
# Enable SSO for the newly created SSH key: https://github.com/settings/keys

# Make the persisted key accessible to SSH
cat << EOF >> /home/ec2-user/.ssh/config
Host github.com
	IdentityFile /home/ec2-user/SageMaker/.ssh/id_ed25519
EOF
chmod 644 .ssh/config

# 3: clone repo and install package
cd /home/ec2-user/SageMaker/ # This folder is persisted by AWS
git clone [email protected]:hired/my-repo.git
cd my-repo
# Pip version
pip install -r requirements.txt
# Poetry version
# pip install poetry && poetry install
pre-commit install && pip install -e .