chore(deps): update supporting dependencies #237

Workflow file for this run

.github/workflows/packaging.yaml at e528e1a

	name: Packaging

	on:
	pull_request:
	workflow_dispatch:
	push:
	branches:
	- "main"
	tags:
	- "v*"

	# Cancel a PR's in-flight runs when it is pushed to again.
	# Pushes to main and tags fall back to the run id, so a publish is never cancelled.
	concurrency:
	group: ${{ github.workflow }}-${{ github.head_ref \|\| github.run_id }}
	cancel-in-progress: true

	permissions:
	contents: read
	packages: write
	attestations: write
	id-token: write

	jobs:
	helm:
	name: Helm Chart
	runs-on: ubuntu-latest
	permissions:
	packages: write
	outputs:
	generated-semver: ${{ steps.semantic-version.outputs.generated-semver }}
	steps:
	- uses: actions/checkout@v7
	- uses: actions/setup-python@v7
	- name: Install yq
	run: \|
	pip install yq
	- name: Generate SemVer
	id: semantic-version
	run: \|
	CHART_VERSION=$(yq -r '.version' helm/Chart.yaml)
	if [ "${{ github.event_name }}" = "pull_request" ]; then
	LOCAL_SEGMENT=+pr-${{ github.event.pull_request.number }}
	elif [ "${{ github.ref_type }}" = "tag" ]; then
	LOCAL_SEGMENT=""
	else
	SHORT_SHA=$(echo "${{ github.sha }}" \| cut -c1-7)
	LOCAL_SEGMENT=+${SHORT_SHA}
	fi
	GENERATED_VERSION=${CHART_VERSION}${LOCAL_SEGMENT}
	yq -Y -i ".version = \"$GENERATED_VERSION\"" helm/Chart.yaml
	echo "generated-semver=$GENERATED_VERSION" >> $GITHUB_OUTPUT
	- name: Chart \| Push
	uses: appany/helm-oci-chart-releaser@v0.5.0
	with:
	name: climate-ref-aft
	repository: climate-ref/charts
	tag: ${{ steps.semantic-version.outputs.generated-semver }}
	path: helm
	registry: ghcr.io
	registry_username: ${{ github.actor }}
	registry_password: ${{ secrets.GITHUB_TOKEN }}
	update_dependencies: 'true'

	test-minimal:
	name: Test Minimal Deployment
	runs-on: ubuntu-latest
	timeout-minutes: 10
	needs: [helm]
	steps:
	- uses: actions/checkout@v7
	- name: Start minikube
	uses: medyagh/setup-minikube@latest
	- name: Set up Helm
	uses: azure/setup-helm@v5.0.1
	- name: Install Chart (minimal)
	run: \|
	helm install test oci://ghcr.io/climate-ref/charts/climate-ref-aft \
	--version=${{ needs.helm.outputs.generated-semver }} \
	-f helm/ci/minimal-values.yaml
	- name: Wait for pods
	run: \|
	echo "Waiting for deployments to be ready..."
	# Init containers hold every worker until the broker hostname resolves,
	# and DNS can take a couple of minutes to come up on a fresh minikube.
	kubectl wait --for=condition=available deployment --all --timeout=300s
	kubectl get pods
	- name: Verify all pods healthy
	run: \|
	# Check no pods are in CrashLoopBackOff or Error state
	UNHEALTHY=$(kubectl get pods --no-headers \| grep -E 'CrashLoopBackOff\|Error\|ImagePullBackOff' \|\| true)
	if [ -n "$UNHEALTHY" ]; then
	echo "Unhealthy pods found:"
	echo "$UNHEALTHY"
	echo ""
	echo "=== Pod logs ==="
	for pod in $(echo "$UNHEALTHY" \| awk '{print $1}'); do
	echo "--- $pod ---"
	kubectl logs "$pod" --tail=50 \|\| true
	done
	exit 1
	fi
	echo "All pods healthy."
	- name: Capture logs on failure
	if: failure()
	run: \|
	kubectl get pods
	kubectl describe pods
	for pod in $(kubectl get pods --no-headers \| awk '{print $1}'); do
	echo "=== $pod ==="
	kubectl logs "$pod" --tail=100 \|\| true
	done

	test:
	name: Test Helm Deployment
	runs-on: ubuntu-latest
	timeout-minutes: 30
	needs: [helm]
	steps:
	- uses: actions/checkout@v7
	- name: Cache Sample Data (Restore)
	id: cache-sample-data-restore
	uses: actions/cache/restore@v6
	with:
	path: ${{ github.workspace }}/cache/ref-config
	key: ${{ runner.os }}-sample-data
	enableCrossOsArchive: true
	- name: Set permissions for cached data
	run: \|
	# The pods run as uid 1000, but the cache action restores files owned by the runner user,
	# so everything the previous run cached (e.g. /ref/log) must be handed back
	# before the migrate hook writes to it.
	sudo install -d --owner=1000 --group=1000 ${GITHUB_WORKSPACE}/cache/ref-config
	sudo chown -R 1000:1000 ${GITHUB_WORKSPACE}/cache/ref-config
	- name: Start minikube
	uses: medyagh/setup-minikube@latest
	with:
	cpus: max
	memory: 12g
	mount-path: '${{ github.workspace }}/cache/ref-config:/cache/ref-config'
	- name: Set up Helm
	uses: azure/setup-helm@v5.0.1
	- name: Install Chart
	run: \|
	helm install test oci://ghcr.io/climate-ref/charts/climate-ref-aft \
	--version=${{ needs.helm.outputs.generated-semver }} \
	-f helm/ci/gh-actions-values.yaml

	# Only the orchestrator is waited on.
	# The api pod is expected to be unhealthy until providers are set up, so `deployment --all` would block.
	kubectl wait deployment/test-climate-ref-aft-orchestrator \
	--for=condition=available --timeout=600s

	kubectl get pods \|\| true
	echo ""
	kubectl describe pod -l app.kubernetes.io/component=pmp \|\| true
	echo ""
	kubectl logs -l app.kubernetes.io/component=pmp \|\| true
	- name: Run Migrations
	run: \|
	kubectl exec deployment/test-climate-ref-aft-orchestrator -- uv run ref db migrate
	- name: Initialize Providers
	run: \|
	# First, set up all providers without fetching data (handles conda envs)
	kubectl exec deployment/test-climate-ref-aft-orchestrator -- ref providers setup --skip-data --skip-validate
	# Fetch data for providers except esmvaltool (ERA5 data is too large for CI)
	kubectl exec deployment/test-climate-ref-aft-orchestrator -- ref providers setup --provider pmp
	kubectl exec deployment/test-climate-ref-aft-orchestrator -- ref providers setup --provider ilamb
	- name: Fetch Test Data
	run: \|
	kubectl exec deployment/test-climate-ref-aft-orchestrator -- ref datasets fetch-data --registry sample-data --output-directory /ref/sample-data

	- name: Make cached data readable for the save
	run: \|
	# The pods write as uid 1000 and some files land mode 600,
	# which the runner user cannot read.
	# tar then silently drops them from the archive and the cache goes hollow.
	sudo chmod -R a+rX ${GITHUB_WORKSPACE}/cache/ref-config

	- name: Cache Sample Data (Save)
	uses: actions/cache/save@v6
	with:
	path: ${{ github.workspace }}/cache/ref-config
	key: ${{ runner.os }}-sample-data

	- name: Ingest Test Data (CMIP6)
	run: \|
	kubectl exec deployment/test-climate-ref-aft-orchestrator -- \
	ref -v datasets ingest --source-type cmip6 /ref/sample-data/CMIP6
	- name: Ingest Test Data (obs4mips)
	run: \|
	kubectl exec deployment/test-climate-ref-aft-orchestrator -- \
	ref -v datasets ingest --source-type obs4mips /ref/sample-data/obs4REF
	- name: Simple Solve
	run: \|
	# Use a fixed set of fast diagnostics to keep CI times predictable
	kubectl exec deployment/test-climate-ref-aft-orchestrator -- \
	ref -v solve --timeout 720 --one-per-provider \
	--diagnostic global-mean-timeseries \
	--diagnostic annual-cycle \
	--diagnostic gpp-wecann \
	--provider esmvaltool \
	--provider pmp \
	--provider ilamb
	- name: Validate API can read compute results
	shell: bash
	run: \|
	set -euo pipefail
	# ref-app eagerly imports providers from /ref/software at startup.
	# Provider setup happens after the api Deployment is created,
	# so the initial api pod may have crashed before /ref/software was populated.
	# Force a rollout so a fresh pod starts against the now-populated /ref.
	kubectl rollout restart deployment/test-climate-ref-aft-api
	kubectl rollout status deployment/test-climate-ref-aft-api --timeout=300s

	# Run scripts/lib/api_check.py via the orchestrator pod to check the API responses
	API_BASE='http://test-climate-ref-aft-api/api/v1'
	check() {
	kubectl exec -i deployment/test-climate-ref-aft-orchestrator -- \
	python3 - "${API_BASE}$1" "${2:-0}" \
	< scripts/lib/api_check.py
	}

	check /utils/health-check/
	check /cmip7-aft-diagnostics/ 1
	check /executions/ 1
	- name: Capture Migrate Logs on Failure
	if: failure()
	# The migrate hook runs before any deployment exists,
	# so a pre-install failure leaves only its pods to inspect.
	run: \|
	kubectl describe job/test-climate-ref-aft-migrate \|\| true
	kubectl logs -l job-name=test-climate-ref-aft-migrate --tail=200 \|\| true
	- name: Capture API logs on failure
	if: failure()
	run: \|
	echo "=== API Logs ==="
	kubectl logs -l app.kubernetes.io/component=api --tail=200 --all-containers=true \|\| true
	echo ""
	echo "=== API describe ==="
	kubectl describe deployment/test-climate-ref-aft-api \|\| true
	- name: Capture Broker State on Failure
	if: failure()
	# The recurring failure mode is a task submitted to a queue and never traced by its worker.
	run: \|
	kubectl exec -i deployment/test-climate-ref-aft-orchestrator -- \
	uv run python - < scripts/lib/broker_state.py \|\| true
	- name: Capture Worker Logs on Failure
	if: failure()
	run: \|
	echo "=== PMP Worker Logs ==="
	kubectl logs -l app.kubernetes.io/component=pmp --tail=500 \|\| true
	echo ""
	echo "=== ESMValTool Worker Logs ==="
	kubectl logs -l app.kubernetes.io/component=esmvaltool --tail=500 \|\| true
	echo ""
	# The worker prints nothing while a diagnostic runs.
	# ESMValTool logs to files under the execution's scratch directory,
	# so these tails show where a hung execution stalled.
	echo "=== ESMValTool execution logs ==="
	kubectl exec deployment/test-climate-ref-aft-esmvaltool -- sh -c \
	'find /ref/scratch/esmvaltool -name "main_log.txt" \| while read -r f; do echo "--- $f"; tail -n 100 "$f"; done' \|\| true
	echo ""
	echo "=== ILAMB Worker Logs ==="
	kubectl logs -l app.kubernetes.io/component=ilamb --tail=500 \|\| true
	echo ""
	echo "=== Orchestrator Worker Logs ==="
	kubectl logs -l app.kubernetes.io/component=orchestrator --tail=500 \|\| true
	echo ""
	echo "=== Flower Logs ==="
	kubectl logs -l app.kubernetes.io/component=flower --tail=500 \|\| true
	echo ""
	echo "=== Dragonfly Logs ==="
	kubectl logs -l app.kubernetes.io/name=dragonfly --tail=500 \|\| true

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chore(deps): update supporting dependencies #237

Workflow file

chore(deps): update supporting dependencies #237

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Workflow file for this run