Deploy FastAPI app to k8

kubernetes/helm/.helmignore

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+# Patterns to ignore when building packages.
+# This supports shell glob matching, relative path matching, and
+# negation (prefixed with !). Only one pattern per line.
+.DS_Store
+# Common VCS dirs
+.git/
+.gitignore
+.bzr/
+.bzrignore
+.hg/
+.hgignore
+.svn/
+# Common backup files
+*.swp
+*.bak
+*.tmp
+*.orig
+*~
+# Various IDEs
+.project
+.idea/
+*.tmproj
+.vscode/

kubernetes/helm/Chart.yaml

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+apiVersion: v2
+name: helm
+description: A Helm chart for Kubernetes
+
+type: application
+
+# This is the chart version. This version number should be incremented each time you make changes
+# to the chart and its templates, including the app version.
+version: 0.1.0
+
+# This is the version number of the application being deployed. This version number should be
+# incremented each time you make changes to the application. Versions are not expected to
+# follow Semantic Versioning. They should reflect the version the application is using.
+appVersion: 1.16.0

kubernetes/helm/templates/nginx.yaml

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+apiVersion: v1
+kind: Service
+metadata:
+  name: nginx
+  labels:
+    app: nginx
+spec:
+  ports:
+  - port: {{ .Values.nginxPort }}
+    targetPort: {{ .Values.nginxTargetPort }}
+    protocol: TCP
+  selector:
+    app: rfam-batch-search
+---
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: nginx-config
+data:
+  local.conf: |-
+    # FastAPI application
+    upstream rfam-batch-search {
+        server rfam-batch-search:{{ .Values.port }};
+    }
+
+    server {
+        listen {{ .Values.nginxTargetPort }};
+
+        location / {
+            # everything is passed to FastAPI
+            proxy_pass http://rfam-batch-search;
+            proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+            proxy_set_header Host $host;
+            proxy_redirect off;
+        }
+    }
+---
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: nginx
+spec:
+  replicas: {{ .Values.nginxReplicas }}
+  selector:
+    matchLabels:
+      app: nginx
+  template:
+    metadata:
+      labels:
+        app: nginx
+      annotations:
+        rollme: {{ randAlphaNum 5 | quote }}
+    spec:
+      containers:
+        - image: nginx:1.26-alpine
+          name: nginx
+          resources:
+            requests:
+              memory: {{ .Values.nginxRequestsMemory }}
+              cpu: {{ .Values.nginxRequestsCPU }}
+            limits:
+              memory: {{ .Values.nginxLimitsMemory }}
+          ports:
+            - containerPort: {{ .Values.nginxTargetPort }}
+          volumeMounts:
+            - name: nginx-config
+              mountPath: /etc/nginx/conf.d/local.conf
+              subPath: local.conf
+      restartPolicy: Always
+      volumes:
+        - name: nginx-config
+          configMap:
+            name: nginx-config

kubernetes/helm/templates/rfam-batch-search.yaml

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+apiVersion: v1
+kind: Service
+metadata:
+  name: rfam-batch-search
+  labels:
+    app: rfam-batch-search
+spec:
+  type: NodePort
+  ports:
+  - port: {{ .Values.port }}
+    targetPort: {{ .Values.port }}
+    protocol: TCP
+  selector:
+    app: rfam-batch-search
+---
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: rfam-batch-search
+spec:
+  replicas: {{ .Values.replicas }}
+  selector:
+    matchLabels:
+      app: rfam-batch-search
+  template:
+    metadata:
+      labels:
+        app: rfam-batch-search
+      annotations:
+        rollme: {{ randAlphaNum 5 | quote }}
+    spec:
+      containers:
+        - image: ghcr.io/rfam/rfam-batch-search:{{ .Values.branch }}
+          name: rfam-batch-search
+          imagePullPolicy: Always
+          ports:
+          - containerPort: {{ .Values.port }}
+          resources:
+            requests:
+              memory: {{ .Values.requestsMemory }}
+              cpu: {{ .Values.requestsCPU }}
+            limits:
+              memory: {{ .Values.limitsMemory }}
+          envFrom:
+          - secretRef:
+              name: email
+          - configMapRef:
+              name: {{ .Values.proxy }}

kubernetes/helm/values.yaml

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+# Proxy
+proxy: proxy-hh
+
+# Nginx
+nginxPort: 8000
+nginxTargetPort: 80
+nginxReplicas: 2
+nginxRequestsMemory: "2000Mi"
+nginxRequestsCPU: "1000m"
+nginxLimitsMemory: "4000Mi"
+
+# Rfam batch search
+branch: main
+port: 8000
+replicas: 4
+requestsMemory: "4000Mi"
+requestsCPU: "1000m"
+limitsMemory: "6000Mi"

kubernetes/namespace.yaml

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+{
+  "apiVersion": "v1",
+  "kind": "Namespace",
+  "metadata": {
+    "name": "rfam",
+    "labels": {
+      "name": "rfam"
+    }
+  }
+}

kubernetes/proxy-hh.yaml

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+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: proxy-hh
+data:
+  HTTP_PROXY: http://hh-wwwcache.ebi.ac.uk:3128
+  HTTPS_PROXY: http://hh-wwwcache.ebi.ac.uk:3128
+  http_proxy: http://hh-wwwcache.ebi.ac.uk:3128
+  https_proxy: http://hh-wwwcache.ebi.ac.uk:3128
+  no_proxy: localhost,.cluster.local

kubernetes/quota-mem-cpu.yaml

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+apiVersion: v1
+kind: ResourceQuota
+metadata:
+  name: rfam
+spec:
+  hard:
+    requests.cpu: "8"
+    requests.memory: 20Gi
+    limits.memory: 32Gi