Merge branch 'master' into data_pvc

.github/workflows/packaging.yml

@@ -1,10 +1,23 @@
-name: Package
+name: Package and publish the chart
 on:
   pull_request_target:
     types: [closed]
+  workflow_dispatch:
+    inputs:
+      manual-package-invocation:
+        description: 'Package (y/n)?'
+        required: true
+        default: 'y'
+      version-bump:
+        description: 'Version bump: major, minor, patch'
+        required: true
+      branch-name:
+        description: 'Branch name to package'
+        required: true
 jobs:
-  package:
-    name: Package and push
+  package-from-pr:
+    if: github.event.pull_request.merged == true
+    name: Package and push from PR
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
@@ -18,3 +31,34 @@ jobs:
           charts-token: ${{ secrets.CHARTS_TOKEN }}
           github-labels: ${{ join(github.event.pull_request.labels.*.name, ', ') }}
           git-branch: ${{ github.event.pull_request.base.ref }}
+  package-from-manual:
+    if: github.event.inputs.manual-package-invocation == 'y'
+    name: Package and push manual invocation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+           persist-credentials: false
+      - uses: cloudve/helm-ci@master
+        with:
+          chart-name: galaxy
+          charts-repo: cloudve/helm-charts
+          github-token: ${{ secrets.CHARTS_TOKEN }}
+          charts-token: ${{ secrets.CHARTS_TOKEN }}
+          github-labels: ${{ github.event.inputs.version-bump }}
+          git-branch: ${{ github.event.inputs.branch-name }}
+  tag-and-release:
+    needs: [ package-from-pr, package-from-manual ]
+    name: Create a tag and GitHub release for this version.
+    runs-on: ubuntu-latest
+    if: |
+      always() 
+      && contains(needs.*.result, 'success')
+      && !contains(needs.*.result, 'failure')
+    steps:
+      - name: Tag and release
+        run: |
+          version=v$(cat galaxy/Chart.yaml | grep ^version: | awk '{print $2}')
+          git tag -a $version -m "Automatic release of $version"
+          git push origin $version
+          gh release create $version --generate-notes --latest

.github/workflows/test.yaml

@@ -1,10 +1,11 @@
-name: Linting and deployment tests (w/ & w/out CVMFS) on K3S
+name: Linting and deployment test on K3S
 on:
   push:
     branches:
       - master
       - anvil
   pull_request: {}
+  workflow_dispatch: {}
 jobs:
   linting:
     runs-on: ubuntu-latest
@@ -13,12 +14,9 @@ jobs:
         run: curl -LO "https://storage.googleapis.com/kubernetes-release/release/$(curl -s https://storage.googleapis.com/kubernetes-release/release/stable.txt)/bin/linux/amd64/kubectl" && chmod +x ./kubectl && sudo mv ./kubectl /usr/local/bin/kubectl && kubectl version || true
       - name: Install Helm
         run: curl https://raw.githubusercontent.com/helm/helm/master/scripts/get-helm-3 | bash
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           persist-credentials: false
-      - uses: actions/setup-python@v2
-        with:
-          python-version: '3.x'
       - name: Helm dep update
         run: cd galaxy/ && helm dep update && cd ..
       - name: Helm linting
@@ -28,18 +26,17 @@ jobs:
     steps:
       - name: Install Helm
         run: curl https://raw.githubusercontent.com/helm/helm/master/scripts/get-helm-3 | bash
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           persist-credentials: false
-      - uses: actions/setup-python@v2
-        with:
-          python-version: '3.x'
       - name: Helm dep update
         run: cd galaxy/ && helm dep update && cd ..
       - name: Start k8s locally
-        uses: jupyterhub/action-k3s-helm@v1
+        uses: jupyterhub/action-k3s-helm@v3
         with:
-          k3s-version: v1.19.10+k3s1 # releases:  https://github.com/k3s-io/k3s/tags
+          k3s-version: v1.25.15+k3s2  # releases:  https://github.com/k3s-io/k3s/tags
+          metrics-enabled: false
+          traefik-enabled: false
       - name: Verify function of k8s, kubectl, and helm
         run: |
           echo "kubeconfig: $KUBECONFIG"
@@ -51,51 +48,12 @@ jobs:
       - name: Helm repo add galaxy
         run: helm repo add galaxy https://github.com/CloudVE/helm-charts/raw/master
       - name: Helm install Galaxy
-        run: time bash -c 'helm install --create-namespace -n galaxy galaxy ./galaxy --set persistence.accessMode="ReadWriteOnce" --set persistence.size="5Gi" --set postgresql.deploy=true --set resources.requests.memory=0Mi,resources.requests.cpu=0m --wait --timeout=600s'
+        run: time bash -c 'helm install --create-namespace -n galaxy galaxy ./galaxy --set persistence.accessMode="ReadWriteOnce" --set resources.requests.memory=0Mi,resources.requests.cpu=0m,cvmfs.cvmfscsi.cache.alien.enabled=false --wait --timeout=1200s'
       - name: Get events
         run: kubectl get events -n galaxy; kubectl get events -n csi-drivers;
         if: always()
-      - name: Print web handler log
-        run: bash -c "kubectl logs -n galaxy $(kubectl -n galaxy get pods | grep -o '[^ ]*galaxy-web[^ ]*')"
-        if: always()
-      - name: Print job handler log
-        run: bash -c "kubectl logs -n galaxy $(kubectl -n galaxy get pods | grep -o '[^ ]*galaxy-job[^ ]*')"
-        if: always()
-      - name: Print workflow handler log
-        run: bash -c "kubectl logs -n galaxy $(kubectl -n galaxy get pods | grep -o '[^ ]*galaxy-workflow[^ ]*')"
-        if: always()
-  cvmfstest:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Install Helm
-        run: curl https://raw.githubusercontent.com/helm/helm/master/scripts/get-helm-3 | bash
-      - uses: actions/checkout@v2
-        with:
-          persist-credentials: false
-      - uses: actions/setup-python@v2
-        with:
-          python-version: '3.x'
-      - name: Helm dep update
-        run: cd galaxy/ && helm dep update && cd ..
-      - name: Start k8s locally
-        uses: jupyterhub/action-k3s-helm@v1
-        with:
-          k3s-version: v1.19.10+k3s1 # releases:  https://github.com/k3s-io/k3s/tags
-
-      - name: Verify function of k8s, kubectl, and helm
-        run: |
-          echo "kubeconfig: $KUBECONFIG"
-          kubectl version
-          kubectl get pods --all-namespaces
-
-          helm version
-          helm list
-      - name: Helm repo add galaxy
-        run: helm repo add galaxy https://github.com/CloudVE/helm-charts/raw/master
-      - name: Helm install Galaxy
-        run: time bash -c 'helm install --create-namespace -n galaxy galaxy ./galaxy --set persistence.accessMode="ReadWriteOnce" --set persistence.size="5Gi" --set cvmfs.enabled=true --set cvmfs.deploy=true --set cvmfs.cache.preload.enabled=false --set cvmfs.cache.alienCache.enabled=false --set cvmfs.cache.localCache.enabled=true --set postgresql.deploy=true --set resources.requests.memory=0Mi,resources.requests.cpu=0m --set initJob.downloadToolConfs.enabled=false --set cvmfs.repositories.cvmfs-gxy-cloud=cloud.galaxyproject.org --set cvmfs.galaxyPersistentVolumeClaims.cloud.storage=1Gi --set cvmfs.galaxyPersistentVolumeClaims.cloud.storageClassName=cvmfs-gxy-cloud --set cvmfs.galaxyPersistentVolumeClaims.cloud.mountPath=/cvmfs/cloud.galaxyproject.org --wait --timeout=600s'
-      - name: Get events
-        run: kubectl get events -n galaxy; kubectl get events -n csi-drivers
+      - name: Get pods, pvc, and pv
+        run: kubectl get pods -n galaxy; kubectl get pvc -n galaxy; kubectl get pv -n galaxy
         if: always()
       - name: Print web handler log
         run: bash -c "kubectl logs -n galaxy $(kubectl -n galaxy get pods | grep -o '[^ ]*galaxy-web[^ ]*')"
@@ -106,4 +64,3 @@ jobs:
       - name: Print workflow handler log
         run: bash -c "kubectl logs -n galaxy $(kubectl -n galaxy get pods | grep -o '[^ ]*galaxy-workflow[^ ]*')"
         if: always()
-

.gitignore

@@ -96,3 +96,5 @@ galaxy/charts/
 
 # IDEs
 .idea
+
+Chart.lock