trigger #43

	name: Liat Workflow

	on:
	push:
	branches:
	- liats/wip/ci_cd

	permissions:
	id-token: write
	contents: read

	jobs:
	create-conda-env:
	runs-on: ubuntu-latest
	container:
	image: amazonlinux:2
	steps:
	# Install tar and gzip for code checkout
	- name: Install tar
	run: yum install -y tar gzip

	- name: Checkout Code
	uses: actions/checkout@v3 # Checks out the repository under $GITHUB_WORKSPACE.

	- name: Setup conda
	uses: conda-incubator/setup-miniconda@v2
	with:
	miniconda-version: "latest"
	activate-environment: pheno
	python-version: 3.11
	# environment-file: etc/example-environment.yml

	- name: Install pheno-utils
	shell: bash -el {0}
	run: \|
	cd $GITHUB_WORKSPACE
	pip install .
	conda list

	- name: Pack Conda
	shell: bash -el {0}
	run: \|
	# Enable adding the kernel to JupyterLab
	pip install -q ipykernel
	python -m ipykernel install --user --name pheno --display-name "Pheno"
	pip install -q conda-pack
	conda pack --quiet -n pheno -o $HOME/pheno.tar.gz

	- name: Configure AWS Credentials
	uses: aws-actions/configure-aws-credentials@v3
	with:
	role-to-assume: arn:aws:iam::081569964966:role/github_cicd
	aws-region: eu-west-1

	- name: Setup AWS CLI
	run: \|
	echo "Installing AWS CLI"
	curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
	tar -xvf awscliv2.zip
	sudo ./aws/install
	aws --version

	- name: Upload to S3
	run: \|
	echo "Uploading artifact to S3"
	DATE=$(date +%Y-%m-%d)
	BRANCH=${GITHUB_REF#refs/heads/}
	aws s3 cp $HOME/pheno.tar.gz s3://pheno-ds-github/conda_envs/pheno_${BRANCH}_${DATE}.tar.gz

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