Add Jupyter Health Hubs

Ref #3796
2i2c-org · Mar 27, 2024 · 714c2a4 · 714c2a4
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diff --git a/.github/workflows/deploy-grafana-dashboards.yaml b/.github/workflows/deploy-grafana-dashboards.yaml
@@ -36,6 +36,7 @@ jobs:
           - cluster_name: ubc-eoas
           - cluster_name: utoronto
           - cluster_name: victor
+          - cluster_name: jupyter-health
 
     steps:
       - name: Checkout repo

diff --git a/.github/workflows/deploy-hubs.yaml b/.github/workflows/deploy-hubs.yaml
@@ -199,6 +199,7 @@ jobs:
       failure_nasa-ghg: "${{ env.failure_nasa-ghg }}"
       failure_qcl: "${{ env.failure_qcl }}"
       failure_jupyter-meets-the-earth: "${{ env.failure_jupyter-meets-the-earth }}"
+      failure_jupyter-health: "${{ env.failure_jupyter-health }}"
       failure_smithsonian: "${{ env.failure_smithsonian }}"
       failure_catalystproject-latam: "${{ env.failure_catalystproject-latam }}"
       failure_catalystproject-africa: "${{ env.failure_catalystproject-africa }}"

diff --git a/config/clusters/jupyter-health/cluster.yaml b/config/clusters/jupyter-health/cluster.yaml
@@ -0,0 +1,28 @@
+name: jupyter-health
+provider: aws
+aws:
+  key: enc-deployer-credentials.secret.json
+  clusterType: eks
+  clusterName: jupyter-health
+  region: us-east-2
+support:
+  helm_chart_values_files:
+    - support.values.yaml
+    - enc-support.secret.values.yaml
+hubs:
+  - name: staging
+    display_name: "Jupyter Health (staging)"
+    domain: staging.jupyter-health.2i2c.cloud
+    helm_chart: basehub
+    helm_chart_values_files:
+      - common.values.yaml
+      - staging.values.yaml
+      - enc-staging.secret.values.yaml
+  - name: prod
+    display_name: "Jupyter Health (prod)"
+    domain: jupyter-health.2i2c.cloud
+    helm_chart: basehub
+    helm_chart_values_files:
+      - common.values.yaml
+      - prod.values.yaml
+      - enc-prod.secret.values.yaml
diff --git a/config/clusters/jupyter-health/common.values.yaml b/config/clusters/jupyter-health/common.values.yaml
@@ -0,0 +1,181 @@
+nfs:
+  enabled: true
+  pv:
+    enabled: true
+    # from https://docs.aws.amazon.com/efs/latest/ug/mounting-fs-nfs-mount-settings.html
+    mountOptions:
+      - rsize=1048576
+      - wsize=1048576
+      - timeo=600
+      - soft # We pick soft over hard, so NFS lockups don't lead to hung processes
+      - retrans=2
+      - noresvport
+    serverIP: fs-07b67adf6626672af.efs.us-east-2.amazonaws.com
+    baseShareName: /
+jupyterhub:
+  custom:
+    2i2c:
+      add_staff_user_ids_to_admin_users: true
+      add_staff_user_ids_of_type: "github"
+    jupyterhubConfigurator:
+      enabled: false
+    homepage:
+      templateVars:
+        org:
+          name: Jupyter Health
+          logo_url: https://jupyter.org/assets/homepage/main-logo.svg
+          url: https://github.com/jupyterhealth/
+        designed_by:
+          name: "Jupyter Health"
+          url: https://github.com/jupyterhealth/
+        operated_by:
+          name: "2i2c"
+          url: https://2i2c.org
+        funded_by:
+          name: "Jupyter Health"
+          url: https://www.earthdata.nasa.gov/esds/veda
+  hub:
+    allowNamedServers: true
+    config:
+      JupyterHub:
+        authenticator_class: github
+      GitHubOAuthenticator:
+        allowed_organizations:
+          - jupyterhealth
+        scope:
+          - read:org
+      Authenticator:
+        admin_users:
+          - minrk
+          - fperez
+          - colliand
+          - maryamv
+          - ryanlovett
+  singleuser:
+    defaultUrl: /lab
+    profileList:
+      - display_name: "Pangeo Notebook"
+        slug: pangeo
+        description: Pangeo based notebook with a Python environment
+        default: true
+        kubespawner_override:
+          image: quay.io/pangeo/pangeo-notebook:2024.03.22
+          init_containers:
+            # Need to explicitly fix ownership here, as otherwise these directories will be owned
+            # by root on most NFS filesystems - neither EFS nor Google Filestore support anonuid
+            - name: volume-mount-ownership-fix
+              image: busybox:1.36.1
+              command:
+                - sh
+                - -c
+                - id && chown 1000:1000 /home/jovyan /home/jovyan/shared && ls -lhd /home/jovyan
+              securityContext:
+                runAsUser: 0
+              volumeMounts:
+                - name: home
+                  mountPath: /home/jovyan
+                  subPath: "{username}"
+                # mounted without readonly attribute here,
+                # so we can chown it appropriately
+                - name: home
+                  mountPath: /home/jovyan/shared
+                  subPath: _shared
+        profile_options: &profile_options
+          resource_allocation: &profile_options_resource_allocation
+            display_name: Resource Allocation
+            choices:
+              mem_1_9:
+                display_name: 1.9 GB RAM, upto 3.7 CPUs
+                kubespawner_override:
+                  mem_guarantee: 1991341312
+                  mem_limit: 1991341312
+                  cpu_guarantee: 0.234375
+                  cpu_limit: 3.75
+                  node_selector:
+                    node.kubernetes.io/instance-type: r5.xlarge
+                default: true
+              mem_3_7:
+                display_name: 3.7 GB RAM, upto 3.7 CPUs
+                kubespawner_override:
+                  mem_guarantee: 3982682624
+                  mem_limit: 3982682624
+                  cpu_guarantee: 0.46875
+                  cpu_limit: 3.75
+                  node_selector:
+                    node.kubernetes.io/instance-type: r5.xlarge
+              mem_7_4:
+                display_name: 7.4 GB RAM, upto 3.7 CPUs
+                kubespawner_override:
+                  mem_guarantee: 7965365248
+                  mem_limit: 7965365248
+                  cpu_guarantee: 0.9375
+                  cpu_limit: 3.75
+                  node_selector:
+                    node.kubernetes.io/instance-type: r5.xlarge
+              mem_14_8:
+                display_name: 14.8 GB RAM, upto 3.7 CPUs
+                kubespawner_override:
+                  mem_guarantee: 15930730496
+                  mem_limit: 15930730496
+                  cpu_guarantee: 1.875
+                  cpu_limit: 3.75
+                  node_selector:
+                    node.kubernetes.io/instance-type: r5.xlarge
+              mem_29_7:
+                display_name: 29.7 GB RAM, upto 3.7 CPUs
+                kubespawner_override:
+                  mem_guarantee: 31861460992
+                  mem_limit: 31861460992
+                  cpu_guarantee: 3.75
+                  cpu_limit: 3.75
+                  node_selector:
+                    node.kubernetes.io/instance-type: r5.xlarge
+              mem_60_6:
+                display_name: 60.6 GB RAM, upto 15.7 CPUs
+                kubespawner_override:
+                  mem_guarantee: 65094813696
+                  mem_limit: 65094813696
+                  cpu_guarantee: 7.86
+                  cpu_limit: 15.72
+                  node_selector:
+                    node.kubernetes.io/instance-type: r5.4xlarge
+              mem_121_2:
+                display_name: 121.2 GB RAM, upto 15.7 CPUs
+                kubespawner_override:
+                  mem_guarantee: 130189627392
+                  mem_limit: 130189627392
+                  cpu_guarantee: 15.72
+                  cpu_limit: 15.72
+                  node_selector:
+                    node.kubernetes.io/instance-type: r5.4xlarge
+      - display_name: "Rocker Geospatial with RStudio"
+        slug: rocker
+        description: R environment with many geospatial libraries pre-installed
+        kubespawner_override:
+          image: rocker/binder:4.3
+          image_pull_policy: Always
+          # Launch RStudio after the user logs in
+          default_url: /rstudio
+          # Ensures container working dir is homedir
+          # https://github.com/2i2c-org/infrastructure/issues/2559
+          working_dir: /home/rstudio
+        profile_options: *profile_options
+      - display_name: "Bring your own image"
+        description: Specify your own docker image (must have python and jupyterhub installed in it)
+        slug: custom
+        profile_options:
+          image:
+            display_name: Image
+            unlisted_choice:
+              enabled: True
+              display_name: "Custom image"
+              validation_regex: "^.+:.+$"
+              validation_message: "Must be a publicly available docker image, of form <image-name>:<tag>"
+              kubespawner_override:
+                image: "{value}"
+            choices: {}
+          resource_allocation: *profile_options_resource_allocation
+
+  scheduling:
+    userScheduler:
+      enabled: true
diff --git a/config/clusters/jupyter-health/enc-deployer-credentials.secret.json b/config/clusters/jupyter-health/enc-deployer-credentials.secret.json
@@ -0,0 +1,25 @@
+{
+	"AccessKey": {
+		"AccessKeyId": "ENC[AES256_GCM,data:ZPnLxqCEDnm3k38kfkTBOxojO1U=,iv:+N1qti7SQAQ9ncTrkWmIhuo9BUrUDvM08LHsARfv84s=,tag:1xPNKQK7/vpJDSpXBG5H6A==,type:str]",
+		"SecretAccessKey": "ENC[AES256_GCM,data:gmoDHtJVBIPoNi0mozBr6ggzl/bZ8rnirpBeuzUYiejraE8k6sWw+A==,iv:DXGDhq9AekwSY+LAGG+vuDgVpDPHdaFZh4OIyfpraxA=,tag:TnnEEX0UFZjX8gSe78eROA==,type:str]",
+		"UserName": "ENC[AES256_GCM,data:l7xBnsJQh3wfSvrt91dxuqPUfFX9iKY=,iv:HNN1A/f70OCoY6YxS9VPwqFuusdSBhR7QWenu9eRg0M=,tag:MZRN9qU+xNrboAL99Cx1Tg==,type:str]"
+	},
+	"sops": {
+		"kms": null,
+		"gcp_kms": [
+			{
+				"resource_id": "projects/two-eye-two-see/locations/global/keyRings/sops-keys/cryptoKeys/similar-hubs",
+				"created_at": "2024-03-27T03:12:17Z",
+				"enc": "CiUA4OM7eBALghHLDCATTTf2qSVQwFhR8G3uQdxd25yNBRNJfvfIEkkAXoW3Jmpb9Gxd2eYCUcE3E1WdVbkbAg/yf+Xxg0p3Aw1J73LcxTJTeifDx/s8qeuYZXyvxIsdy9DMW4xaMNOjZsdBSlqZMft8"
+			}
+		],
+		"azure_kv": null,
+		"hc_vault": null,
+		"age": null,
+		"lastmodified": "2024-03-27T03:12:18Z",
+		"mac": "ENC[AES256_GCM,data:R4WEbpjhqioIvVWVhTZEY4D4+8HZanx+TU3RwrDazR/+1hbCV6a6nC4yaQG+3gRuoMGIQeRhiP8A5NifzcTeAtRZ9CYoFt/l4R39ow2z6BTGP1M2mNGGA0c6ZlqmJmrxyYIYcv4pWe3BfSBkCFjjqpj83C+AydNovUw2zJi+Gok=,iv:iR8sbRthqB+OpmvTJcrbTVAEXBHfyHqzRnAuk0vOQI0=,tag:t79XNiAlMiMgZK/sUBEp2g==,type:str]",
+		"pgp": null,
+		"unencrypted_suffix": "_unencrypted",
+		"version": "3.8.1"
+	}
+}
diff --git a/config/clusters/jupyter-health/enc-grafana-token.secret.yaml b/config/clusters/jupyter-health/enc-grafana-token.secret.yaml
@@ -0,0 +1,15 @@
+grafana_token: ENC[AES256_GCM,data:pFUEbEuI9Oos6YtuA/oXDKjP6HklrH8G6C8lLh87DDbjQ8Sz0BD9JotBBKoNzA==,iv:rA2kl2O0lcUDPDUcwxuF1F5nY9lydLl+0K2k3OKYkF8=,tag:FkFR4rGHV7xizsUL969Aug==,type:str]
+sops:
+    kms: []
+    gcp_kms:
+        - resource_id: projects/two-eye-two-see/locations/global/keyRings/sops-keys/cryptoKeys/similar-hubs
+          created_at: "2024-03-27T03:32:37Z"
+          enc: CiUA4OM7eMIWtqEIQtysm+s5zxS/nKMoNkjDvRzgvAqs19hSfS03EkkAXoW3JssCZCIo6ovleKWINJnwDXgm/R5uTwhVZqRT0G4cficrTpplNQLvj5Lk7FcWeqqGaXK7pLeYaHeXmPBEDvj4YlRcYFrN
+    azure_kv: []
+    hc_vault: []
+    age: []
+    lastmodified: "2024-03-27T03:32:37Z"
+    mac: ENC[AES256_GCM,data:Hx2QfF6std3LBVVV4Bz4vXKFXmW6Pi220z3I4tXPUzuWX0mVyb5AUr8Je2diq+6ds2rWmhKFskL0CLA5/zP9U/9vfpnddkJy5K8krlDn08s6QQ8NN6fzBzaDksghoD7Z3aRW7Hn7GwbgALVpF6j20Ty4ilUPDPjuZXVi8iZDZSQ=,iv:/eMrdS7XKkaAN2OGs2RQn1Y6dIAdXbgTZR9K1BnH/tI=,tag:5JqsQHlzFf1ASNq/M20sjg==,type:str]
+    pgp: []
+    unencrypted_suffix: _unencrypted
+    version: 3.8.1
diff --git a/config/clusters/jupyter-health/enc-prod.secret.values.yaml b/config/clusters/jupyter-health/enc-prod.secret.values.yaml
@@ -0,0 +1,20 @@
+jupyterhub:
+    hub:
+        config:
+            GitHubOAuthenticator:
+                client_id: ENC[AES256_GCM,data:dK6sakIgpztIfiurNYY+8HtbynQ=,iv:yesxCvpGPK4QKLVNpI6LpWb8KX1brB/uhQIEg1tIbIg=,tag:35BASFn0mDkmBomDjAUNxQ==,type:str]
+                client_secret: ENC[AES256_GCM,data:nKIRhTK13eIaR1tIWWw/bfK4pclINcj1mr7k1xj7LnWc6FA+QJL+/g==,iv:6fKX5y8+3IogwOVuBrbNT8KoUAPebji58/9JX8cOTP0=,tag:Z6B0FtLLdrE1TunBAKJ68Q==,type:str]
+sops:
+    kms: []
+    gcp_kms:
+        - resource_id: projects/two-eye-two-see/locations/global/keyRings/sops-keys/cryptoKeys/similar-hubs
+          created_at: "2024-03-27T03:26:11Z"
+          enc: CiUA4OM7eNaq2WnQcWV8UUsnnprPSIh0EJM+IyQbcq3ioRaxXOPIEkkAXoW3JilW+T15pzagOKIXjrqeJUpzLZzRZAWZXNJ9svGWZkhJpX6NtPJGNkXFx2dsjXG9pBm31G/7QJKdft93bmdvDu/0kQ53
+    azure_kv: []
+    hc_vault: []
+    age: []
+    lastmodified: "2024-03-27T03:26:56Z"
+    mac: ENC[AES256_GCM,data:Zk8JTgNL+IM8S1kKe4ejbAUBWB+TzIFr9DhQ0RDRWV3c6r5XT3rBIqVCfHKhPh1RPeE8dFMdovxi/b62gkbUHHPQu+jemoQYofdd3BeuL8N2TZWL3L46uV/RBW0msqnALrZq0yD0hIcXNB4q/F1j0dUVd1wjrPxDaiFR1CYczK8=,iv:XkOBcJAnziqJi+vmP2SSP51x448aqilQ2gEA1a/Wkqg=,tag:SboAWeb1sD4hkYKf32mN2A==,type:str]
+    pgp: []
+    unencrypted_suffix: _unencrypted
+    version: 3.8.1
diff --git a/config/clusters/jupyter-health/enc-staging.secret.values.yaml b/config/clusters/jupyter-health/enc-staging.secret.values.yaml
@@ -0,0 +1,20 @@
+jupyterhub:
+    hub:
+        config:
+            GitHubOAuthenticator:
+                client_id: ENC[AES256_GCM,data:dDQ5o50vtdrOeEAJSg1CYrzRjwY=,iv:zeb0Rh4NjNtfyGGzEVXAzSqdszDuTRrtC2F4tAp+D7Q=,tag:kLH86WnG3PmkpEEGoTau6w==,type:str]
+                client_secret: ENC[AES256_GCM,data:nqrPYv/i3NJ1TkAncgm+NF0r1U95HxV8pkQXYTMULqibiCwOhwq11g==,iv:5sk0Ac/JDFmArGFtfmsYJjwHNfIZW9Q45X2+hIB9x+o=,tag:4taAorVZrfs3FBMn7ala+w==,type:str]
+sops:
+    kms: []
+    gcp_kms:
+        - resource_id: projects/two-eye-two-see/locations/global/keyRings/sops-keys/cryptoKeys/similar-hubs
+          created_at: "2024-03-27T03:20:32Z"
+          enc: CiUA4OM7ePrLrsqEqXlDkXkXRAWDaAdEbzVylzq8w6GKfCCJGgAvEkkAXoW3JiUlHtWirbwpxMHx9IojRvV71ZR67dw+MFn5ngfTuEWlU+fhhN0SDFd2a97Np9Bdw8RREy43KB++4GKUntGNNxppYhHh
+    azure_kv: []
+    hc_vault: []
+    age: []
+    lastmodified: "2024-03-27T03:21:41Z"
+    mac: ENC[AES256_GCM,data:YigsyrOdKkCTndXMaqS8Fbp54GPJ3xms4pQGxWyRxSf0xq8qf1CN82cM7laGIT/svGxtnelqSsj242uVdPOXLYSPyfibjrKhfNNEcjBakyzPJh0M5JE/7/fUqDSdlplP/8eihjKyQME7u0vBjOsNBKoYvO60131K+GwC7hy50Jw=,iv:k+UTWDJKPjdZHhaufhVGmuHip0BSH2qhFLl00bVv90Q=,tag:1dW5x+5w3AiC9nMYUvS9eQ==,type:str]
+    pgp: []
+    unencrypted_suffix: _unencrypted
+    version: 3.8.1
diff --git a/config/clusters/jupyter-health/enc-support.secret.values.yaml b/config/clusters/jupyter-health/enc-support.secret.values.yaml
@@ -0,0 +1,17 @@
+prometheusIngressAuthSecret:
+    username: ENC[AES256_GCM,data:3KOczS+romK4eNELpyBv6Tf4w1mjlIUC7M3v/ni2UXI/KIm3aYzZtxdphrI4fyUBkOrbIUeFQ3uEn12usvoLXg==,iv:Nz+wm18W9ihBIQ3Q/D62RdP4ituhYkEBIMC8JUKnH8w=,tag:pOhYeh6JOBUzb6U07baQBg==,type:str]
+    password: ENC[AES256_GCM,data:1XQxK8KgONw8LSelTaQWyxnG0HK8YgxSJscw5ay33fLoLinFsO2c3Pi8K3FGV6rQ+7sQD3T0vZar+4dvpJuOxA==,iv:KXpm3d9g04CUFTQ/T8ZWukiK3lRoRd4NPFWeD3OCW7M=,tag:IfTNS6dtVTgcBGk0S2ztLQ==,type:str]
+sops:
+    kms: []
+    gcp_kms:
+        - resource_id: projects/two-eye-two-see/locations/global/keyRings/sops-keys/cryptoKeys/similar-hubs
+          created_at: "2024-03-27T02:49:45Z"
+          enc: CiUA4OM7eNHuKWwS9mCMAvaC+jgrMgx4DNQl4IADj65qOGD+4GnGEkkAXoW3JqR++Cg3n3xLzB37L4koPU0VXt0eTmF8Si4ILpYMf89WP8MSiG3KA5kEzEmknHUC8Z27cJz7MYR6x6U4JvQXXfS4TiG2
+    azure_kv: []
+    hc_vault: []
+    age: []
+    lastmodified: "2024-03-27T02:49:46Z"
+    mac: ENC[AES256_GCM,data:kExXzURzp2c3DVDNycX5nMDD6dfiJ2Ysp89AfNfIdcFEG7OJufK4xKykD+4WHNqipHqspP36zxjtWeljdwNM1ElK0jy3mDPfX2Da99t3D5ORFHuc8lQXSW1klMEf3efmkrZyYtba1kqjClvXMjy7hyG219VNqYHM5O5N3/fk0iA=,iv:eC7YfoGBRGFGlbbx5MVVqRsD0+YYld2uOzjYsUCqEwo=,tag:Q0ShSiBkXICRTH/XrHbGag==,type:str]
+    pgp: []
+    unencrypted_suffix: _unencrypted
+    version: 3.8.1
diff --git a/config/clusters/jupyter-health/prod.values.yaml b/config/clusters/jupyter-health/prod.values.yaml
@@ -0,0 +1,13 @@
+userServiceAccount:
+  annotations:
+    eks.amazonaws.com/role-arn: arn:aws:iam::211125465508:role/jupyter-health-prod
+jupyterhub:
+  ingress:
+    hosts: [jupyter-health.2i2c.cloud]
+    tls:
+      - hosts: [jupyter-health.2i2c.cloud]
+        secretName: https-auto-tls
+  hub:
+    config:
+      GitHubOAuthenticator:
+        oauth_callback_url: https://jupyter-health.2i2c.cloud/hub/oauth_callback
diff --git a/config/clusters/jupyter-health/staging.values.yaml b/config/clusters/jupyter-health/staging.values.yaml
@@ -0,0 +1,13 @@
+userServiceAccount:
+  annotations:
+    eks.amazonaws.com/role-arn: arn:aws:iam::211125465508:role/jupyter-health-staging
+jupyterhub:
+  ingress:
+    hosts: [staging.jupyter-health.2i2c.cloud]
+    tls:
+      - hosts: [staging.jupyter-health.2i2c.cloud]
+        secretName: https-auto-tls
+  hub:
+    config:
+      GitHubOAuthenticator:
+        oauth_callback_url: https://staging.jupyter-health.2i2c.cloud/hub/oauth_callback
diff --git a/config/clusters/jupyter-health/support.values.yaml b/config/clusters/jupyter-health/support.values.yaml
@@ -0,0 +1,34 @@
+prometheusIngressAuthSecret:
+  enabled: true
+
+prometheus:
+  server:
+    ingress:
+      enabled: true
+      hosts:
+        - prometheus.jupyter-health.2i2c.cloud
+      tls:
+        - secretName: prometheus-tls
+          hosts:
+            - prometheus.jupyter-health.2i2c.cloud
+
+grafana:
+  grafana.ini:
+    server:
+      root_url: https://grafana.jupyter-health.2i2c.cloud/
+  auth.github:
+    enabled: true
+    allowed_organizations: 2i2c-org
+  ingress:
+    hosts:
+      - grafana.jupyter-health.2i2c.cloud
+    tls:
+      - secretName: grafana-tls
+        hosts:
+          - grafana.jupyter-health.2i2c.cloud
+
+cluster-autoscaler:
+  enabled: true
+  autoDiscovery:
+    clusterName: jupyter-health
+  awsRegion: us-east-2