Pass to `tidybayes` not base to `tidybayes` #95

Workflow file for this run

.github/workflows/containers-and-az-pool.yaml at e1e7e50

	name: Create Docker Image and Azure Pool

	# This GitHub Actions workflow builds a Docker image for the
	# cfa-epinow2-pipeline-docker project. In-container tests can be added here.

	on:
	pull_request:
	branches:
	- main
	workflow_dispatch:

	env:
	# Together, these form: cfaprdbatchcr.azurecr.io/cfa-epinow2-pipeline
	REGISTRY: cfaprdbatchcr.azurecr.io
	IMAGE_NAME: cfa-epinow2-pipeline

	jobs:

	build-dependencies-image:
	runs-on: cfa-cdcgov # VM based runner serving CFA's cdcgov repos (as opposed to cdcent)
	name: Build dependencies image

	outputs:
	tag: ${{ steps.image-tag.outputs.tag }}
	commit-msg: ${{ steps.commit-message.outputs.message }}

	steps:

	#########################################################################
	# Retrieving the commit message
	# We need to ensure we are checking out the commit sha that triggered the
	# workflow, not the PR's head sha. This is because the PR's head sha may
	# be a merge commit, which will not have the commit message we need.
	#########################################################################
	- name: Checkout code
	uses: actions/checkout@v4
	with:
	ref: ${{ github.event.pull_request.head.sha }}

	- name: Getting the commit message
	id: commit-message
	run: echo "message=$(git log -1 --pretty=%s HEAD)" >> $GITHUB_OUTPUT

	- name: Checking out the latest (may be merge if PR)
	uses: actions/checkout@v4

	# From: https://stackoverflow.com/a/58035262/2097171
	- name: Extract branch name
	shell: bash
	run: echo "branch=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" >> $GITHUB_OUTPUT
	id: branch-name

	#########################################################################
	# Getting the tag
	# The tag will be used for both the docker image and the batch pool
	#########################################################################
	- name: Figure out tag (either latest if it is main or the branch name)
	id: image-tag
	run: \|
	if [ "${{ steps.branch-name.outputs.branch }}" = "main" ]; then
	echo "tag=latest" >> $GITHUB_OUTPUT
	else
	echo "tag=${{ steps.branch-name.outputs.branch }}" >> $GITHUB_OUTPUT
	fi

	- name: Check cache for base image
	uses: actions/cache@v4
	id: cache
	with:
	key: docker-dependencies-${{ runner.os }}-${{ hashFiles('./DESCRIPTION', './Dockerfile-dependencies') }}-${{ steps.image-tag.outputs.tag }}
	lookup-only: true
	path:
	./DESCRIPTION

	- name: Login to the Container Registry
	if: steps.cache.outputs.cache-hit != 'true'
	uses: docker/login-action@v3
	with:
	registry: "cfaprdbatchcr.azurecr.io"
	username: "cfaprdbatchcr"
	password: ${{ secrets.CFAPRDBATCHCR_REGISTRY_PASSWORD }}

	- name: Build and push
	if: steps.cache.outputs.cache-hit != 'true'
	uses: docker/build-push-action@v6
	with:
	push: true
	tags: \|
	${{ env.REGISTRY}}/${{ env.IMAGE_NAME }}-dependencies:${{ steps.image-tag.outputs.tag }}
	file: ./Dockerfile-dependencies

	build-pipeline-image:

	name: Build pipeline image

	needs: build-dependencies-image
	runs-on: cfa-cdcgov

	outputs:
	tag: ${{ needs.build-dependencies-image.outputs.tag }}
	commit-msg: ${{ needs.build-dependencies-image.outputs.commit-msg }}

	steps:

	- name: Login to the Container Registry
	uses: docker/login-action@v3
	with:
	registry: "cfaprdbatchcr.azurecr.io"
	username: "cfaprdbatchcr"
	password: ${{ secrets.CFAPRDBATCHCR_REGISTRY_PASSWORD }}

	- name: Build and push model pipeline image for Azure batch
	id: build_and_push_model_image
	uses: docker/build-push-action@v6
	with:
	push: true # This can be toggled manually for tweaking.
	tags: \|
	${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:test-${{ needs.build-dependencies-image.outputs.tag }}
	file: ./Dockerfile
	build-args: \|
	TAG=${{ needs.build-dependencies-image.outputs.tag }}

	batch-pool:

	name: Create Batch Pool and Submit Jobs
	runs-on: cfa-cdcgov
	needs: build-pipeline-image
	container: python:3.12

	permissions:
	contents: read
	packages: write

	env:
	TAG: ${{ needs.build-pipeline-image.outputs.tag }}
	COMMIT_MSG: ${{ needs.build-pipeline-image.outputs.commit-msg }}
	# Every Azure Batch Pool parameter can simply go here,
	# no python module or config toml necessary
	POOL_ID: "cfa-epinow2-${{ needs.build-pipeline-image.outputs.tag }}"
	BATCH_ACCOUNT: "cfaprdba"
	BATCH_ENDPOINT: "https://cfaprdba.eastus.batch.azure.com/"
	VM_IMAGE_TAG: "canonical:0001-com-ubuntu-server-focal:20_04-lts"
	NODE_AGENT_SKU_ID: "batch.node.ubuntu 20.04"
	VM_SIZE: "standard_a4m_v2"
	RESOURCE_GROUP: ${{ secrets.PRD_RESOURCE_GROUP }}

	steps:
	- name: Checkout Repo
	id: checkout_repo
	uses: actions/checkout@v4

	# This step is only needed during the action to write the
	# config file. Users can have a config file stored in their VAP
	# sessions. In the future, we will have the config.toml file
	# distributed with the repo (encrypted).
	- name: Writing out config file
	run: \|
	cat <<EOF > pool-config-${{ github.sha }}.toml
	${{ secrets.POOL_CONFIG_TOML }}
	EOF

	# Replacing placeholders in the config file
	sed -i 's\|{{ IMAGE_NAME }}\|${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:test-${{ env.TAG }}\|g' pool-config-${{ github.sha }}.toml
	sed -i 's\|{{ VM_SIZE }}\|${{ env.VM_SIZE }}\|g' pool-config-${{ github.sha }}.toml
	sed -i 's\|{{ POOL_ID }}\|${{ env.POOL_ID }}\|g' pool-config-${{ github.sha }}.toml

	- name: Ensuring the Azure CLI is installed
	run: \|
	apt-get update && apt-get install -y --no-install-recommends azure-cli

	- name: Login to Azure with NNH Service Principal
	id: azure_login_2
	uses: azure/login@v2
	with:
	# managed by EDAV. Contact Amit Mantri or Jon Kislin if you have issues.
	creds: ${{ secrets.EDAV_CFA_PREDICT_NNHT_SP }}

	#########################################################################
	# Checking if the pool exists
	# This is done via az batch pool list. If there is no pool matching the
	# pool id (which is a function of the tag, i.e., branch name), then we
	# pool-exists will be ''.
	#########################################################################
	- name: Check if pool exists
	id: check_pool_id
	run: \|

	az batch account login \
	--resource-group ${{ secrets.PRD_RESOURCE_GROUP }} \
	--name "${{ env.BATCH_ACCOUNT }}"

	az batch pool list \
	--output tsv \
	--filter "(id eq '${{ env.POOL_ID }}')" \
	--query "[].[id, allocationState, creationTime]" > \
	pool-list-${{ github.sha }}

	echo "pool-exists=$(cat pool-list-${{ github.sha }})" >> \
	$GITHUB_OUTPUT

	- name: Create cfa-epinow2-pipeline Pool
	id: create_batch_pool

	# This is a conditional step that will only run if the pool does not
	# exist
	if: ${{ steps.check_pool_id.outputs.pool-exists == '' }}

	# The call to the az cli that actually generates the pool
	run: \|
	# Running the python script azure/pool.py passing the config file
	# as an argument
	pip install -r azure/requirements.txt
	python3 azure/pool.py \
	pool-config-${{ github.sha }}.toml \
	batch-autoscale-formula.txt


	#########################################################################
	# Deleting the pool only if (a) it exists and (b) the commit message
	# contains '[delete pool]'.
	#########################################################################
	- name: Delete the pool
	if: ${{ (steps.check_pool_id.outputs.pool-exists != '' \|\| steps.create_batch_pool.outputs.pool-created == 'yes' ) && contains( env.COMMIT_MSG, '[delete pool]' )}}
	run: \|
	az batch account login \
	--resource-group ${{ secrets.PRD_RESOURCE_GROUP }} \
	--name "${{ env.BATCH_ACCOUNT }}"

	az batch pool delete \
	--pool-id ${{ env.POOL_ID }} \
	--yes

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Pass to `tidybayes` not base to `tidybayes` #95

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Pass to `tidybayes` not base to `tidybayes` #95

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Pass to tidybayes not base to tidybayes #95

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Pass to `tidybayes` not base to `tidybayes` #95