large painful refactor

BioImage-Archive · Apr 4, 2023 · ed5effe · ed5effe
1 parent fe13a0b
commit ed5effe
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diff --git a/.gitignore b/.gitignore
@@ -1 +1,4 @@
 secrets.env
+*.env
+.history
+
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
diff --git a/Makefile b/Makefile
@@ -1,120 +1,120 @@
 #!make
 
 BASEDIR = $(shell pwd)
-SOURCE:=$(shell source secrets.env)
+SOURCE:=$(shell source .env secrets.env)
 
-# include secrets.env
-# export
 
-deploy.production:
-	helmsman --apply --debug --group production -f helmsman.yaml -f helmsman/production.yaml -f helmsman/binder.yaml
+deploy.$1
 
-deploy.gpu.production:
-	helmsman --apply --debug --group production -f helmsman.yaml -f helmsman/production.yaml -f helmsman/gpu.yaml
+deploy.$1:
+	helmsman --apply --debug --group $1 -f helmsman.yaml -f helmsman/$1.yaml -f helmsman/binder.yaml
 
-deploy.denbi.production:
-	helmsman --apply --debug --group production -f helmsman.yaml -f helmsman/production.yaml -f helmsman/denbi.yaml
+deploy.gpu.prod:
+	helmsman --apply --debug --group prod -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/gpu.yaml --subst-env-values --subst-ssm-values
 
+deploy.denbi.prod:
+	helmsman --apply --debug --group prod -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/denbi.yaml
 
-deploy.staging:
-	helmsman --apply --debug --group staging -f helmsman.yaml -f helmsman/staging.yaml -f helmsman/binder.yaml
+
+deploy.dev:
+	helmsman --apply --debug --group dev -f helmsman.yaml -f helmsman/dev.yaml -f helmsman/binder.yaml
 
 ci.deploy.prod:
-	helmsman --apply --debug --group production -f helmsman/token.yaml -f helmsman.yaml -f helmsman/production.yaml
-ci.deploy.staging:
-	helmsman --apply --debug --group staging -f helmsman/token.yaml -f helmsman.yaml -f helmsman/staging.yaml
+	helmsman --apply --debug --group prod -f helmsman/token.yaml -f helmsman.yaml -f helmsman/prod.yaml
+ci.deploy.dev:
+	helmsman --apply --debug --group dev -f helmsman/token.yaml -f helmsman.yaml -f helmsman/dev.yaml
 
 binder.deploy.prod:
-	helmsman --apply --debug --target binderhub-production -f helmsman.yaml -f helmsman/production.yaml --always-upgrade
-binder.deploy.staging:
-	helmsman --apply --debug --target binderhub-production -f helmsman.yaml --always-upgrade
+	helmsman --apply --debug --target binderhub-prod -f helmsman.yaml -f helmsman/prod.yaml --always-upgrade
+binder.deploy.dev:
+	helmsman --apply --debug --target binderhub-prod -f helmsman.yaml --always-upgrade
 
 # Beta gpu enabled service
 
 
 beta.binder.deploy.prod:
-	helmsman --apply --debug --target binderhub-production -f helmsman.yaml -f helmsman/production.yaml -f helmsman/gpu.yaml --always-upgrade
-beta.binder.deploy.staging:
-	helmsman --apply --debug --target binderhub-production -f helmsman.yaml -f helmsman/gpu.yaml --always-upgrade
+	helmsman --apply --debug --target binderhub-prod -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/gpu.yaml --always-upgrade
+beta.binder.deploy.dev:
+	helmsman --apply --debug --target binderhub-prod -f helmsman.yaml -f helmsman/gpu.yaml --always-upgrade
 
 # Alpha openstack  service
 
 persistent.alpha.binder.deploy.prod:
-	helmsman --apply --debug --target persistent-binderhub-production -f helmsman.yaml -f helmsman/production.yaml -f helmsman/openstack.yaml --always-upgrade
-persistent.alpha.binder.deploy.staging:
-	helmsman --apply --debug --target persistent-binderhub-production -f helmsman.yaml -f helmsman/openstack.yaml --always-upgrade
+	helmsman --apply --debug --target persistent-binderhub-prod -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/openstack.yaml --always-upgrade
+persistent.alpha.binder.deploy.dev:
+	helmsman --apply --debug --target persistent-binderhub-prod -f helmsman.yaml -f helmsman/openstack.yaml --always-upgrade
 # 
 
 alpha.binder.deploy.prod:
-	helmsman --apply --debug --target binderhub-production -f helmsman.yaml -f helmsman/production.yaml -f helmsman/openstack.yaml --always-upgrade
-alpha.binder.deploy.staging:
-	helmsman --apply --debug --target binderhub-staging -f helmsman.yaml -f helmsman/staging.yaml -f helmsman/openstack.yaml --always-upgrade
+	helmsman --apply --debug --target binderhub-prod -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/openstack.yaml --always-upgrade
+alpha.binder.deploy.dev:
+	helmsman --apply --debug --target binderhub-dev -f helmsman.yaml -f helmsman/dev.yaml -f helmsman/openstack.yaml --always-upgrade
 
 alpha.deploy.prod:
-	helmsman --apply --debug --group production -f helmsman.yaml -f helmsman/production.yaml -f helmsman/openstack.yaml --always-upgrade
+	helmsman --apply --debug --group prod -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/openstack.yaml --always-upgrade
 
 alpha.cert.deploy.prod:
-	helmsman --apply --debug --target cert-manager-production -f helmsman.yaml -f helmsman/production.yaml -f helmsman/openstack.yaml --always-upgrade
+	helmsman --apply --debug --target cert-manager-prod -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/openstack.yaml --always-upgrade
 
 alpha.trow.deploy.prod:
-	helmsman --apply --debug --target trow -f helmsman.yaml -f helmsman/production.yaml -f helmsman/openstack.yaml --always-upgrade
+	helmsman --apply --debug --target trow -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/openstack.yaml --always-upgrade
 alpha.registry.deploy.prod:
-	helmsman --apply --debug --target docker-registry -f helmsman.yaml -f helmsman/production.yaml -f helmsman/openstack.yaml --always-upgrade
+	helmsman --apply --debug --target docker-registry -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/openstack.yaml --always-upgrade
 
 alpha.ingress.deploy.prod:
-	helmsman --apply --debug --target ingress-nginx -f helmsman.yaml -f helmsman/production.yaml -f helmsman/openstack.yaml --always-upgrade
+	helmsman --apply --debug --target ingress-nginx -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/openstack.yaml --always-upgrade
 
 # Beta gpu enabled service
 
 
 gpu.beta.binder.deploy.prod:
-	helmsman --apply --debug --target binderhub-production-gpu -f helmsman.yaml -f helmsman/production.yaml -f helmsman/gpu.yaml --always-upgrade
-gpu.beta.binder.deploy.staging:
-	helmsman --apply --debug --target binderhub-production-gpu -f helmsman.yaml -f helmsman/gpu.yaml --always-upgrade
+	helmsman --apply --debug --target binderhub-prod-gpu -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/gpu.yaml --always-upgrade
+gpu.beta.binder.deploy.dev:
+	helmsman --apply --debug --target binderhub-prod-gpu -f helmsman.yaml -f helmsman/gpu.yaml --always-upgrade
 gpu.beta.triton.deploy.prod:
-	helmsman --apply --debug --target tritoninferenceserver -f helmsman.yaml -f helmsman/production.yaml -f helmsman/gpu.yaml --always-upgrade
+	helmsman --apply --debug --target tritoninferenceserver -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/gpu.yaml --always-upgrade
 
 # Dry runs for testing
 
 binder.deploy.prod.dry:
-	helmsman --debug --target binderhub-production -f helmsman.yaml -f helmsman/production.yaml --always-upgrade --dry-run
+	helmsman --debug --target binderhub-prod -f helmsman.yaml -f helmsman/prod.yaml --always-upgrade --dry-run
 
 beta.binder.deploy.prod.dry:
-	helmsman --debug --target binderhub-production -f helmsman.yaml -f helmsman/production.yaml -f helmsman/gpu.yaml --always-upgrade --dry-run
+	helmsman --debug --target binderhub-prod -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/gpu.yaml --always-upgrade --dry-run
 
 gpu.beta.binder.deploy.prod.dry:
-	helmsman --debug --target binderhub-production-gpu -f helmsman.yaml -f helmsman/production.yaml -f helmsman/gpu.yaml --always-upgrade --dry-run
+	helmsman --debug --target binderhub-prod-gpu -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/gpu.yaml --always-upgrade --dry-run
 
 gpu.cert.deploy.prod:
-	helmsman --apply --debug --target cert-manager-production -f helmsman.yaml -f helmsman/production.yaml -f helmsman/gpu.yaml --always-upgrade
+	helmsman --apply --debug --target cert-manager-prod -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/gpu.yaml --always-upgrade
 
-gpu.nvdp.production:
-	helmsman --apply --debug --target nvidia-gpu-operator -f helmsman.yaml -f helmsman/production.yaml -f helmsman/gpu.yaml --always-upgrade
+gpu.nvdp.prod:
+	helmsman --apply --debug --target nvidia-gpu-operator -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/gpu.yaml --always-upgrade
 
 
 gke.binder.deploy.prod:
-	helmsman --apply --debug --target binderhub-production -f helmsman.yaml -f helmsman/production.yaml -f helmsman/gke.yaml --always-upgrade
+	helmsman --apply --debug --target binderhub-prod -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/gke.yaml --always-upgrade
 
 gke.binder.deploy.nginx:
-	helmsman --apply --debug --target ingress-nginx -f helmsman.yaml -f helmsman/production.yaml -f helmsman/gke.yaml --always-upgrade
-gke.binder.deploy.staging:
-	helmsman --apply --debug --target binderhub-staging -f helmsman.yaml -f helmsman/staging.yaml -f helmsman/gke.yaml --always-upgrade
+	helmsman --apply --debug --target ingress-nginx -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/gke.yaml --always-upgrade
+gke.binder.deploy.dev:
+	helmsman --apply --debug --target binderhub-dev -f helmsman.yaml -f helmsman/dev.yaml -f helmsman/gke.yaml --always-upgrade
 
-gke.nvdp.production:
-	helmsman --apply --debug --target nvidia-device-plugin -f helmsman.yaml -f helmsman/production.yaml -f helmsman/gke.yaml --always-upgrade
+gke.nvdp.prod:
+	helmsman --apply --debug --target nvidia-device-plugin -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/gke.yaml --always-upgrade
 
 gke.deploy.prod:
-	helmsman --apply --debug --group production -f helmsman.yaml -f helmsman/production.yaml -f helmsman/gke.yaml --always-upgrade
+	helmsman --apply --debug --group prod -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/gke.yaml --always-upgrade
 gke.triton.deploy.prod:
-	helmsman --apply --debug --target tritoninferenceserver -f helmsman.yaml -f helmsman/production.yaml -f helmsman/gke.yaml --always-upgrade
+	helmsman --apply --debug --target tritoninferenceserver -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/gke.yaml --always-upgrade
 gke.prometheus.deploy.prod:
-	helmsman --apply --debug --target prometheus -f helmsman.yaml -f helmsman/production.yaml -f helmsman/gke.yaml --always-upgrade
+	helmsman --apply --debug --target prometheus -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/gke.yaml --always-upgrade
 
 
 gke.persistent.alpha.binder.deploy.prod:
-	helmsman --apply --debug --target persistent-binderhub-production -f helmsman.yaml -f helmsman/production.yaml -f helmsman/gke.yaml --always-upgrade
-gke.persistent.alpha.binder.deploy.staging:
-	helmsman --apply --debug --target persistent-binderhub-production -f helmsman.yaml -f helmsman/gke.yaml --always-upgrade
+	helmsman --apply --debug --target persistent-binderhub-prod -f helmsman.yaml -f helmsman/prod.yaml -f helmsman/gke.yaml --always-upgrade
+gke.persistent.alpha.binder.deploy.dev:
+	helmsman --apply --debug --target persistent-binderhub-prod -f helmsman.yaml -f helmsman/gke.yaml --always-upgrade
 
 
 

diff --git a/README.md b/README.md
@@ -27,7 +27,7 @@ This will give the GitLab runner almost full administrative access to the cluste
     bash gitlab-ci/install-helm.sh
     helmfile -e minikube sync
 
-For production
+For prod
 
     helmfile -e default sync -->
 

diff --git a/binderhub-persistent/production/config.yaml b/binderhub-persistent/production/config.yaml
diff --git a/binderhub-persistent/staging/config.yaml b/binderhub-persistent/staging/config.yaml
diff --git a/binderhub/config.yaml b/binderhub/config.yaml
@@ -28,12 +28,6 @@ config:
 
     banner_message: |
       <div style="text-align: center;">This is a public Beta and liable to downtime</div>
-    # build_image: "aicrowd/repo2docker"
-    # build_image: "aicrowd/repo2docker:latest"
-    # base_url: "/staging" #Doesn't work
-    # networkPolicy:
-    #   enabled: true
-#     # Good until this:
 
 jupyterhub:
   proxy:
@@ -130,12 +124,20 @@ jupyterhub:
     # cmd: start-singleuser.sh
     # cmd: null
     cpu:
-      limit: 2
-      guarantee: 1
+      limit: 4
+      guarantee: 2
     memory:
-      limit: 6G
-      guarantee: 1G
-  #   storage:
+      limit: 8G
+      guarantee: 6G
+    storage:
+      extraVolumes:
+        - name: biostudies-nfs-binder
+          persistentVolumeClaim:
+            claimName: biostudies-nfs-pvc-binder
+      extraVolumeMounts:
+        - name: biostudies-nfs-binder
+          mountPath: /home/jovyan/biostudies
+          readOnly: true
   #     type: none
       # extraVolumes:
   #       - name: nfs-bs-ftp
@@ -151,11 +153,35 @@ jupyterhub:
         #   mountPath: /home/jovyan/biostudies
       #     readOnly: true
     profileList:
-      - display_name: "GPU Server"
-        description: "Spawns a notebook server with access to a GPU"
+      # - display_name: "GPU Server"
+      #   description: "Spawns a notebook server with access to a GPU"
+      #   kubespawner_override:
+      #     extra_resource_limits:
+      #       smarter-devices/fuse: "1"
+      - display_name: "BioStudies"
+        description: "Spawns a notebook server BioStudies attached"
+        slug: "Biostudies"
         kubespawner_override:
           extra_resource_limits:
             smarter-devices/fuse: "1"
+          # image: cschranz/gpu-jupyter
+          # cpu_limit: 32
+          # cpu_guarantee: 16
+          # mem_limit: 32G
+          # mem_guarantee: 32G
+          # volume_mounts:
+          #   - name: biostudies-nfs
+          #     mountPath: /home/jovyan/biostudies
+          storage:
+            # type: none
+            extraVolumes:
+              - name: biostudies-nfs-binder
+                persistentVolumeClaim:
+                  claimName: biostudies-nfs-pvc-binder
+            extraVolumeMounts:
+              - name: biostudies-nfs-binder
+                mountPath: /home/jovyan/biostudies
+                readOnly: true
       # - display_name: "No GPU"
   #     description: "Spawns a notebook server with access to a GPU"
 # proxy:
@@ -193,16 +219,7 @@ extraVolumes:
 extraVolumeMounts:
   - name: custom-templates
     mountPath: /etc/binderhub/custom
-
-dind:
-  enabled: true
-  resources:
-    requests:
-      cpu: "2"
-      memory: 4Gi
-    limits:
-      cpu: "4"
-      memory: 6Gi
+imageBuilderType: dind
 
 ingress:
   enabled: true
@@ -213,7 +230,7 @@ ingress:
     kubernetes.io/ingress.class: nginx
     kubernetes.io/tls-acme: "true"
     cert-manager.k8s.io/acme-challenge-type: http01
-    cert-manager.io/cluster-issuer: letsencrypt-production
+    cert-manager.io/cluster-issuer: letsencrypt-prod
     certmanager.k8s.io/acme-http01-edit-in-place: "true"
     # https:
     #   enabled: true