Release v3.0

Release v3.0

• added whole new interface to access the pipeline -> Jupyterhub
• added orca image
• added parmtSNEcv image
• reworked pipeline Docker image to be compatible with Jupyterhub
• reworked Kubernetes mechanism

jupyterhub/jupyterhub.yaml

+debug:
+  enabled: true
+
+rbac:
+  enabled: false
+
+hub:
+  config:
+    GenericOAuthenticator:
+      client_id: <<CLIENT_ID>> 
+      client_secret: <<CLIENT_SECRET>> 
+      token_url: https://login.elixir-czech.org/oidc/token
+      userdata_method: GET
+      userdata_params:
+        state: state
+      userdata_url: https://login.elixir-czech.org/oidc/userinfo
+      username_key: preferred_username
+      login_service: Elixir
+      admin_users:
+        - xvisnov1
+    JupyterHub:
+      authenticator_class: oauthenticator.generic.GenericOAuthenticator
+  service:
+    type: ClusterIP
+    annotations: {}
+    ports:
+      nodePort:
+    extraPorts: []
+    loadBalancerIP:
+  baseUrl: /
+  cookieSecret:
+  initContainers: []
+  fsGid: 1000
+  nodeSelector: {}
+  tolerations: []
+  concurrentSpawnLimit: 64
+  consecutiveFailureLimit: 5
+  activeServerLimit:
+  deploymentStrategy:
+    type: Recreate
+  db:
+    type: sqlite-pvc
+    upgrade:
+    pvc:
+      annotations: {}
+      selector: {}
+      accessModes:
+        - ReadWriteOnce
+      storage: 1Gi
+      subPath:
+      storageClassName: csi-ceph-rbd-du
+    url:
+    password:
+  labels: {}
+  annotations: {}
+  command: []
+  args: []
+  extraConfig: {}
+  extraFiles: {}
+  extraEnv:
+    OAUTH2_AUTHORIZE_URL: https://login.elixir-czech.org/oidc/authorize 
+    OAUTH2_TOKEN_URL: https://login.elixir-czech.org/oidc/token 
+    OAUTH2_CALLBACK_URL: https://pmcvff-correction.cerit-sc.cz/hub/oauth_callback 
+  extraContainers: []
+  extraVolumes: []
+  extraVolumeMounts: []
+  image:
+    name: jupyterhub/k8s-hub
+    tag: "1.1.3"
+    pullPolicy:
+    pullSecrets: []
+  resources: {}
+  containerSecurityContext:
+    runAsUser: 1000
+    runAsGroup: 1000
+    allowPrivilegeEscalation: false
+  lifecycle: {}
+  #loadRoles: {}
+  services: {}
+  pdb:
+    enabled: false
+    maxUnavailable:
+    minAvailable: 1
+  allowNamedServers: false
+  namedServerLimitPerUser:
+  authenticatePrometheus:
+  redirectToServer:
+  shutdownOnLogout:
+  templatePaths: []
+  templateVars: {}
+  livenessProbe:
+    enabled: true
+    initialDelaySeconds: 300
+    periodSeconds: 10
+    failureThreshold: 30
+    timeoutSeconds: 3
+  readinessProbe:
+    enabled: true
+    initialDelaySeconds: 0
+    periodSeconds: 2
+    failureThreshold: 1000
+    timeoutSeconds: 1
+  existingSecret:
+  serviceAccount:
+    annotations: {}
+  extraPodSpec: {}
+
+ingress:
+  enabled: true
+  annotations:
+    kubernetes.io/tls-acme: "true"
+    kubernetes.io/ingress.class: nginx
+    cert-manager.io/cluster-issuer: "letsencrypt-prod"
+    external-dns.alpha.kubernetes.io/target: "k8s-public-a.cerit-sc.cz"
+  hosts:
+    - pmcvff-correction.cerit-sc.cz
+  tls:
+    - hosts:
+        - pmcvff-correction.cerit-sc.cz
+      secretName: pmcvff-correction-cerit-sc-cz
+
+singleuser:
+  podNameTemplate:
+  extraTolerations: []
+  nodeSelector: {}
+  extraNodeAffinity:
+    required: []
+    preferred: []
+  extraPodAffinity:
+    required: []
+    preferred: []
+  extraPodAntiAffinity:
+    required: []
+    preferred: []
+  networkTools:
+    image:
+      name: jupyterhub/k8s-network-tools
+      tag: "1.1.3"
+      pullPolicy:
+      pullSecrets: []
+  cloudMetadata:
+    blockWithIptables: false
+    ip: 169.254.169.254
+  networkPolicy:
+    enabled: false 
+    ingress: []
+    egress:
+      - to:
+          - ipBlock:
+              cidr: 0.0.0.0/0
+              except:
+                - 169.254.169.254/32
+    interNamespaceAccessLabels: ignore
+    allowedIngressPorts: []
+  events: true
+  extraAnnotations: {}
+  extraLabels:
+    hub.jupyter.org/network-access-hub: "true"
+  extraFiles: {}
+  extraEnv: {}
+  lifecycleHooks:
+    postStart:
+      exec:
+        command:
+          - "sh"
+          - "-c"
+          - >
+            cp /tmp/base/pipelineJupyter.ipynb /home/jovyan;
+            cp /tmp/base/tleapin.txt /home/jovyan;
+            /opt/init.sh;
+            python -m ipykernel install --user
+  initContainers: []
+  extraContainers: []
+  uid: 1000
+  fsGid: 100
+  serviceAccountName: singleuser
+  storage:
+    type: dynamic
+    extraLabels: {}
+    extraVolumes: []
+    #- name: kube-config-volume
+    #   secret:
+    #     secretName: kube-config-secret
+    # extraVolumeMounts: []
+    extraVolumeMounts: []
+    #  - name: kube-config-volume
+    #    mountPath: /mnt/secret/config
+    static:
+      pvcName:
+      subPath: "{username}"
+    capacity: 10Gi
+    homeMountPath: /home/jovyan
+    dynamic:
+      storageClass: nfs-csi
+      pvcNameTemplate: claim-{username}{servername}
+      volumeNameTemplate: volume-{username}{servername}
+      # storageAccessModes: [ReadWriteOnce]
+      storageAccessModes: [ReadWriteMany]
+  image:
+    name: spectraes/jmagichub
+    tag: "alpha6"
+    pullPolicy:
+    pullSecrets: []
+  startTimeout: 300
+  cpu:
+    limit:
+    guarantee: 1
+  memory:
+    limit:
+    guarantee: 1G
+  extraResource:
+    limits: {}
+    guarantees: {}
+  cmd: jupyterhub-singleuser
+  defaultUrl: "/lab"
+  extraPodConfig: {}
+  profileList: []
+
+cull:
+  enabled: false
+
+scheduling:
+  userScheduler:
+    enabled: false
+    replicas: 2
+    logLevel: 4
+    plugins:
+      score:
+        disabled:
+          - name: SelectorSpread
+          - name: TaintToleration
+          - name: PodTopologySpread
+          - name: NodeResourcesBalancedAllocation
+          - name: NodeResourcesLeastAllocated
+          # Disable plugins to be allowed to enable them again with a different
+          # weight and avoid an error.
+          - name: NodePreferAvoidPods
+          - name: NodeAffinity
+          - name: InterPodAffinity
+          - name: ImageLocality
+        enabled:
+          - name: NodePreferAvoidPods
+            weight: 161051
+          - name: NodeAffinity
+            weight: 14631
+          - name: InterPodAffinity
+            weight: 1331
+          - name: NodeResourcesMostAllocated
+            weight: 121
+          - name: ImageLocality
+            weight: 11
+    containerSecurityContext:
+      runAsUser: 65534 # nobody user
+      runAsGroup: 65534 # nobody group
+      allowPrivilegeEscalation: false
+    image:
+      name: k8s.gcr.io/kube-scheduler
+      tag: v1.19.13 # ref: https://github.com/kubernetes/website/blob/main/content/en/releases/patch-releases.md
+      pullPolicy:
+      pullSecrets: []
+    nodeSelector: {}
+    tolerations: []
+    pdb:
+      enabled: false
+      maxUnavailable: 1
+      minAvailable:
+    resources: {}
+    serviceAccount:
+      annotations: {}
+    extraPodSpec: {}
+  podPriority:
+    enabled: false
+    globalDefault: false
+    defaultPriority: 0
+    userPlaceholderPriority: -10
+  userPlaceholder:
+    enabled: false
+    image:
+      name: k8s.gcr.io/pause
+      tag: "3.5"
+      pullPolicy:
+      pullSecrets: []
+    replicas: 0
+    containerSecurityContext:
+      runAsUser: 65534 # nobody user
+      runAsGroup: 65534 # nobody group
+      allowPrivilegeEscalation: false
+    resources: {}
+  corePods:
+    tolerations:
+      - key: hub.jupyter.org/dedicated
+        operator: Equal
+        value: core
+        effect: NoSchedule
+      - key: hub.jupyter.org_dedicated
+        operator: Equal
+        value: core
+        effect: NoSchedule
+    nodeAffinity:
+      matchNodePurpose: prefer
+  userPods:
+    tolerations:
+      - key: hub.jupyter.org/dedicated
+        operator: Equal
+        value: user
+        effect: NoSchedule
+      - key: hub.jupyter.org_dedicated
+        operator: Equal
+        value: user
+        effect: NoSchedule
+    nodeAffinity:
+      matchNodePurpose: prefer