Merge pull request #3793 from 2i2c-org/update_hhmi_spyglass_image #4119

Workflow file for this run

.github/workflows/deploy-hubs.yaml at 5cccfe3

	# The use of ::set-output in this workflow file was deprecated as per:
	# https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
	# We have instead pivoted to writing to the GITHUB_ENV file, either by the
	# method suggested in the above blog post, or by following the below Stack
	# Overflow answer for python code: https://stackoverflow.com/a/70123641
	# More info on GITHUB_ENV: https://docs.github.com/en/actions/learn-github-actions/environment-variables

	name: Deploy and test hubs

	on:
	push:
	branches:
	- master
	paths:
	# Include changes to the deployer script's folder, but exclude some parts
	- deployer/**
	- "!deployer/README.md"
	- "!deployer/health_check_tests/**"
	- "!deployer/commands/generate/billing/**"
	- "!deployer/commands/generate/dedicated_cluster/**"
	- "!deployer/commands/generate/resource_allocation/**"
	- requirements.txt
	- .github/actions/setup-deploy/**
	- helm-charts/**
	- config/clusters/**
	pull_request:
	branches:
	- master
	paths:
	# Include changes to the deployer script's folder, but exclude some parts
	- deployer/**
	- "!deployer/README.md"
	- "!deployer/health_check_tests/**"
	- "!deployer/commands/generate/billing/**"
	- "!deployer/commands/generate/dedicated_cluster/**"
	- "!deployer/commands/generate/resource_allocation/**"
	- requirements.txt
	- .github/actions/setup-deploy/**
	- helm-charts/**
	- config/clusters/**

	# When multiple PRs triggering this workflow are merged, queue them instead
	# of running them in parallel
	# https://github.blog/changelog/2021-04-19-github-actions-limit-workflow-run-or-job-concurrency/
	concurrency: deploy

	# This environment variable triggers the deployer to colourise print statements in the
	# GitHug Actions logs for easy reading
	env:
	TERM: xterm
	# This may not be required any more, and it may depend on the kubectl version
	# we use etc as well. For now, we have it added to avoid issues.
	USE_GKE_GCLOUD_AUTH_PLUGIN: "True"

	jobs:
	# This job runs in Pull Requests and on pushes to the default branch. It identifies
	# which files have been added or modified by recent GitHub activity and parsed a list
	# to the `deployer generate helm-upgrade-job`s command of the deployer. This command generates
	# two lists of dictionaries, which can be read by GitHub Actions as matrix jobs. The
	# first set of jobs describes which clusters need their support chart and/or staging
	# hub upgraded; and the second set of jobs describe which production hubs require
	# upgrading. These two lists are set as job outputs via GITHUB_ENV to be consumed
	# by the later jobs. They are also pretty-printed in a human-readable format to the
	# logs, and converted into Markdown tables for posting into GitHub comments.
	generate-jobs:
	runs-on: ubuntu-latest
	outputs:
	support-and-staging-matrix-jobs: ${{ env.support-and-staging-matrix-jobs }}
	prod-hub-matrix-jobs: ${{ env.prod-hub-matrix-jobs }}

	steps:
	- name: Checkout repo
	uses: actions/checkout@v4

	- name: Install Python 3.9
	uses: actions/setup-python@v5
	with:
	python-version: "3.9"

	# There will almost never be a cache hit on the cache key when this job is
	# run, as it is the first of all jobs in this workflow. An exception is if
	# this job is re-attempted as part of the same workflow run after
	# succeeding previously.
	- name: Save pip's install cache on job completion
	uses: actions/cache@v4
	with:
	path: ~/.cache/pip
	# key determines if we define or reuse an existing cache or not. Our
	# key ensure we cache within a workflow run and its attempts, but not
	# between workflow runs.
	key: "${{ github.run_id }}"

	- name: Install deployer script's Python dependencies
	run: \|
	pip install --editable .
	pip list

	- name: Identify files that have been added or modified
	# Action repo: https://github.com/dorny/paths-filter
	# Fork of the repo above that we use: https://github.com/frouioui/paths-filter/tree/main
	# In order to take advantage of https://github.com/dorny/paths-filter/pull/133
	uses: frouioui/paths-filter@main
	id: changed-files
	with:
	token: ""
	list-files: csv
	filters: \|
	changed:
	- added\|modified: deployer/**
	- added\|modified: requirements.txt
	- added\|modified: .github/actions/setup-deploy/**
	- added\|modified: helm-charts/basehub/**
	- added\|modified: helm-charts/daskhub/**
	- added\|modified: helm-charts/support/**
	- added\|modified: config/clusters/**

	# This step will create a comment-body.txt file containing the jobs to be run in a
	# Markdown table format to be posted on a Pull Request, if this job is triggered
	# by one
	- name: Generate matrix jobs
	run: \|
	deployer generate helm-upgrade-jobs "${{ steps.changed-files.outputs.changed_files }}"

	# The comment-deployment-plan-pr.yaml workflow won't have the correct context to
	# know the PR number, so we save it to a file to pass to that workflow
	- name: Save Pull Request number to a file
	if: github.event_name == 'pull_request'
	run: \|
	echo "${{ github.event.number }}" > pr-number.txt

	# Upload the pr-number.txt and comment-body.txt files as artifacts for the
	# comment-deployment-plan-pr.yaml workflow to access
	- name: Upload artifacts
	# Only run this steps in PRs when the matrices are not empty
	if: >
	github.event_name == 'pull_request' &&
	(env.support-and-staging-matrix-jobs != '[]' \|\|
	env.prod-hub-matrix-jobs != '[]')
	uses: actions/upload-artifact@v4
	with:
	name: pr
	path: \|
	pr-number.txt
	comment-body.txt

	# https://github.com/ravsamhq/notify-slack-action
	# Needs to be added per job
	# When https://github.com/integrations/slack/issues/1563 gets implemented,
	# we can use that instead
	- name: Report Status
	if: always()
	uses: ravsamhq/notify-slack-action@v2
	with:
	# Warning: there are multiple "Report Status" steps in this file (one per job).
	# Make sure they are all updated
	notify_when: "failure"
	status: ${{ job.status }} # required
	# Message should look like: "Hey @author! Deploy and test hubs failed for "Add new hub - 9305e08".
	message_format: '{emoji} Hey @${{ github.event.head_commit.author.name }}! {workflow} {status_message} for "${{ github.event.head_commit.message }} - <{commit_url}\|{commit_sha}>". Checkout the run at {run_url}.'
	footer: "<{run_url}\|Failing Run>"
	env:
	SLACK_WEBHOOK_URL: ${{ secrets.SLACK_GHA_FAILURES_WEBHOOK_URL }}
	# This job upgrades the support chart, staging hub, and dask-staging hub (if present)
	# for clusters in parallel, if those upgrades are required. This job needs the
	# `generate-jobs` job to have completed and set an output to the
	# `support-and-staging-matrix-jobs` variable name. It's inputs are a list of
	# dictionaries with the keys cluster_name, provider, upgrade_support, and
	# upgrade_staging for each cluster that requires it.
	upgrade-support-and-staging:
	runs-on: ubuntu-latest
	needs: [generate-jobs]

	# We declare outputs indicating the job failed status of a specific job
	# variation. We are currently required to do this in a hardcoded fashion,
	# see this post for feature requests for this to be improved:
	# https://github.community/t/bug-jobs-output-should-return-a-list-for-a-matrix-job/128626/32?u=consideratio
	#
	# Warning: names can include alphanumerics, '-', and '_', but not '.', so
	# we replace '.' for '-' in cluster names.
	#
	# If you are adding a new cluster, please remember to list it here!
	outputs:
	failure_2i2c: "${{ env.failure_2i2c }}"
	failure_2i2c-uk: "${{ env.failure_2i2c-uk }}"
	failure_cloudbank: "${{ env.failure_cloudbank }}"
	failure_leap: "${{ env.failure_leap }}"
	failure_meom-ige: "${{ env.failure_meom-ige }}"
	failure_openscapes: "${{ env.failure_openscapes }}"
	failure_pangeo-hubs: "${{ env.failure_pangeo-hubs }}"
	failure_utoronto: "${{ env.failure_utoronto }}"
	failure_linked-earth: "${{ env.failure_linked-earth }}"
	failure_awi-ciroh: "${{ env.failure_awi-ciroh }}"
	failure_nasa-cryo: "${{ env.failure_nasa-cryo }}"
	failure_gridsst: "${{ env.failure_gridsst }}"
	failure_victor: "${{ env.failure_victor }}"
	failure_2i2c-aws-us: "${{ env.failure_2i2c-aws-us }}"
	failure_ubc-eoas: "${{ env.failure_ubc-eoas }}"
	failure_nasa-veda: "${{ env.failure_nasa-veda }}"
	failure_nasa-ghg: "${{ env.failure_nasa-ghg }}"
	failure_qcl: "${{ env.failure_qcl }}"
	failure_jupyter-meets-the-earth: "${{ env.failure_jupyter-meets-the-earth }}"
	failure_smithsonian: "${{ env.failure_smithsonian }}"
	failure_catalystproject-latam: "${{ env.failure_catalystproject-latam }}"
	failure_catalystproject-africa: "${{ env.failure_catalystproject-africa }}"
	failure_hhmi: "${{ env.failure_hhmi }}"
	failure_nasa-esdis: "${{ env.failure_nasa-esdis }}"
	failure_earthscope: "${{ env.failure_earthscope }}"
	failure_opensci: "${{ env.failure_opensci }}"

	# Only run this job on pushes to the default branch and when the job output is not
	# an empty list
	if: \|
	(github.event_name == 'push' && contains(github.ref, 'master')) &&
	needs.generate-jobs.outputs.support-and-staging-matrix-jobs != '[]'
	strategy:
	# Don't stop other deployments if one fails
	fail-fast: false
	matrix:
	jobs: ${{ fromJson(needs.generate-jobs.outputs.support-and-staging-matrix-jobs) }}

	steps:
	- name: Checkout repo
	uses: actions/checkout@v4

	- name: Setup deploy for ${{ matrix.jobs.cluster_name }}
	uses: ./.github/actions/setup-deploy
	with:
	provider: ${{ matrix.jobs.provider }}
	GCP_KMS_DECRYPTOR_KEY: ${{ secrets.GCP_KMS_DECRYPTOR_KEY }}

	- name: Upgrade support chart on cluster ${{ matrix.jobs.cluster_name }}
	if: matrix.jobs.upgrade_support
	run: \|
	deployer deploy-support ${{ matrix.jobs.cluster_name }}

	- name: Upgrade staging hub on cluster ${{ matrix.jobs.cluster_name }}
	if: matrix.jobs.upgrade_staging
	run: \|
	deployer deploy ${{ matrix.jobs.cluster_name }} staging

	# Retry action: https://github.com/marketplace/actions/retry-step
	- name: Run health check for staging hub on cluster ${{ matrix.jobs.cluster_name }}
	if: matrix.jobs.upgrade_staging
	uses: nick-fields/retry@v3
	with:
	timeout_minutes: 10
	max_attempts: 2
	command: \|
	deployer run-hub-health-check ${{ matrix.jobs.cluster_name }} staging

	- name: Upgrade dask-staging hub on cluster ${{ matrix.jobs.cluster_name }} if it exists
	if: matrix.jobs.upgrade_staging && matrix.jobs.cluster_name == '2i2c'
	run: \|
	deployer deploy ${{ matrix.jobs.cluster_name }} dask-staging

	- name: Upgrade binder-staging hub on cluster ${{ matrix.jobs.cluster_name }} if it exists
	if: matrix.jobs.upgrade_staging && matrix.jobs.cluster_name == '2i2c'
	run: \|
	deployer deploy ${{ matrix.jobs.cluster_name }} binder-staging

	# Retry action: https://github.com/marketplace/actions/retry-step
	- name: Run health check for dask-staging hub on cluster ${{ matrix.jobs.cluster_name }} if it exists
	if: matrix.jobs.upgrade_staging && matrix.jobs.cluster_name == '2i2c'
	uses: nick-fields/retry@v3
	with:
	timeout_minutes: 10
	max_attempts: 2
	command: \|
	deployer run-hub-health-check ${{ matrix.jobs.cluster_name }} dask-staging

	- name: Declare failure status
	if: always()
	shell: python
	run: \|
	import os

	name = "${{ matrix.jobs.cluster_name }}".replace(".", "-")
	failure = "${{ job.status == 'failure' }}"

	env_file = os.getenv("GITHUB_ENV")
	with open(env_file, "a") as f:
	f.write(f"failure_{name}={failure}")

	# https://github.com/ravsamhq/notify-slack-action
	# Needs to be added per job
	# FIXME: when https://github.com/integrations/slack/issues/1563 gets implemented,
	# we can use that instead
	- name: Report Status
	if: always()
	uses: ravsamhq/notify-slack-action@v2
	# Warning: there are multiple "Report Status" steps in this file (one per job).
	# Make sure they are all updated
	with:
	notify_when: "failure"
	status: ${{ job.status }} # required
	# Message should look like: "Hey @author! Deploy and test hubs failed for "Add new hub - 9305e08".
	message_format: '{emoji} Hey @${{ github.event.head_commit.author.name }}! {workflow} {status_message} for "${{ github.event.head_commit.message }} - <{commit_url}\|{commit_sha}>". Checkout the run at {run_url}.'
	footer: "<{run_url}\|Failing Run>"
	env:
	SLACK_WEBHOOK_URL: ${{ secrets.SLACK_GHA_FAILURES_WEBHOOK_URL }}

	# This jobs reduces the initially planned prod-hub-matrix-jobs deployments by
	# filtering out any deployment to a cluster with a failed support-and-staging
	# job.
	filter-generate-jobs:
	runs-on: ubuntu-latest
	needs: [generate-jobs, upgrade-support-and-staging]
	# Only run this job on pushes to the default branch and when the job output is not
	# an empty list
	#
	# always() is added as it seems to be a magic function to ensure a job can
	# run at all without being skipped if a previous job has had any failures.
	# https://docs.github.com/en/actions/learn-github-actions/expressions#always
	if: \|
	always() &&
	(github.event_name == 'push' && contains(github.ref, 'master')) &&
	needs.generate-jobs.outputs.prod-hub-matrix-jobs != '[]'

	outputs:
	filtered-prod-hub-matrix-jobs: ${{ env.filtered-prod-hub-matrix-jobs }}

	steps:
	# This Python script filters out any prod hub deployment job from running
	# later based on if its part of a cluster where support/staging upgrade
	# just failed. Data is injected to the script before its executed via
	# string literals as rendered GitHub workflow expressions.
	- name: Filter prod deploy jobs to run based on failures in support/staging
	shell: python
	run: \|
	import os
	import json

	jobs = json.loads(r"""${{ needs.generate-jobs.outputs.prod-hub-matrix-jobs }}""")
	outputs = json.loads(r"""${{ toJson(needs.upgrade-support-and-staging.outputs) }}""")

	try:
	filtered_jobs = [
	job
	for job in jobs
	if outputs[f"failure_{job['cluster_name'].replace('.', '-')}"] != "true"
	]
	except KeyError:
	print(f"The {cluster_name} cluster wasn't found in the `upgrade-support-and-staging.outputs` list. Please add it before continuing!")

	env_file = os.getenv("GITHUB_ENV")
	with open(env_file, "a") as f:
	f.write(f"filtered-prod-hub-matrix-jobs={json.dumps(filtered_jobs)}")

	# https://github.com/ravsamhq/notify-slack-action
	# Needs to be added per job
	# When https://github.com/integrations/slack/issues/1563 gets implemented,
	# we can use that instead
	- name: Report Status
	if: always()
	uses: ravsamhq/notify-slack-action@v2
	with:
	# Warning: there are multiple "Report Status" steps in this file (one per job).
	# Make sure they are all updated
	notify_when: "failure"
	status: ${{ job.status }} # required
	# Message should look like: "Hey @author! Deploy and test hubs failed for "Add new hub - 9305e08".
	message_format: '{emoji} Hey @${{ github.event.head_commit.author.name }}! {workflow} {status_message} for "${{ github.event.head_commit.message }} - <{commit_url}\|{commit_sha}>". Checkout the run at {run_url}.'
	footer: "<{run_url}\|Failing Run>"
	env:
	SLACK_WEBHOOK_URL: ${{ secrets.SLACK_GHA_FAILURES_WEBHOOK_URL }}

	# This job upgrades production hubs on clusters in parallel, if required. This
	# job needs both the `filter-generate-jobs` to have completed to provide its
	# output `filtered-prod-hub-matrix-jobs`. It is a list of dictionaries with
	# the keys cluster_name, provider, and hub_name for each production hub that
	# requires an upgrade and didn't have a failed support-and-staging-upgrade job
	# run as part of this workflow.
	upgrade-prod-hubs:
	runs-on: ubuntu-latest
	needs: [filter-generate-jobs]
	# Only run this job on pushes to the default branch and when the `generate-jobs` job output is not
	# an empty list
	#
	# always() is added as it seems to be a magic function to ensure a job can
	# run at all without being skipped if a previous job has had any failures. By
	# using always() we need to ensure filter-generate-jobs wasn't skipped or
	# failed explicitly now though.
	# https://docs.github.com/en/actions/learn-github-actions/expressions#always
	if: \|
	always() && needs.filter-generate-jobs.result == 'success' &&
	(github.event_name == 'push' && contains(github.ref, 'master')) &&
	needs.filter-generate-jobs.outputs.filtered-prod-hub-matrix-jobs != '[]'
	strategy:
	# Don't stop other deployments if one fails
	fail-fast: false
	matrix:
	jobs: ${{ fromJson(needs.filter-generate-jobs.outputs.filtered-prod-hub-matrix-jobs) }}

	steps:
	- name: Checkout repo
	uses: actions/checkout@v4

	- name: Setup deploy for ${{ matrix.jobs.cluster_name }} cluster
	uses: ./.github/actions/setup-deploy
	with:
	provider: ${{ matrix.jobs.provider }}
	GCP_KMS_DECRYPTOR_KEY: ${{ secrets.GCP_KMS_DECRYPTOR_KEY }}

	- name: Upgrade ${{ matrix.jobs.hub_name }} hub on cluster ${{ matrix.jobs.cluster_name }}
	run: \|
	deployer deploy ${{ matrix.jobs.cluster_name }} ${{ matrix.jobs.hub_name }}

	# Retry action: https://github.com/marketplace/actions/retry-step
	- name: Run health check against ${{ matrix.jobs.hub_name }} hub on cluster ${{ matrix.jobs.cluster_name}}
	uses: nick-fields/retry@v3
	with:
	timeout_minutes: 10
	max_attempts: 3
	command: \|
	deployer run-hub-health-check ${{ matrix.jobs.cluster_name }} ${{ matrix.jobs.hub_name }}

	# https://github.com/ravsamhq/notify-slack-action
	# Needs to be added per job
	# When https://github.com/integrations/slack/issues/1563 gets implemented,
	# we can use that instead
	- name: Report Status
	if: always()
	uses: ravsamhq/notify-slack-action@v2
	with:
	# Warning: there are multiple "Report Status" steps in this file (one per job).
	# Make sure they are all updated
	notify_when: "failure"
	status: ${{ job.status }} # required
	# Message should look like: "Hey @author! Deploy and test hubs failed for "Add new hub - 9305e08".
	message_format: '{emoji} Hey @${{ github.event.head_commit.author.name }}! {workflow} {status_message} for "${{ github.event.head_commit.message }} - <{commit_url}\|{commit_sha}>". Checkout the run at {run_url}.'
	footer: "<{run_url}\|Failing Run>"
	env:
	SLACK_WEBHOOK_URL: ${{ secrets.SLACK_GHA_FAILURES_WEBHOOK_URL }}

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Merge pull request #3793 from 2i2c-org/update_hhmi_spyglass_image #4119

Workflow file

Merge pull request #3793 from 2i2c-org/update_hhmi_spyglass_image #4119

Jobs

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Workflow file for this run