Merge branch 'add-deployment' into dev

Author: nebfield

deployment/Dockerfile

@@ -0,0 +1,42 @@
+# ── Stage 1: build ────────────────────────────────────────────────────────────
+# Needs both Node.js (Docusaurus) and Python/uv (prebuild step builds the
+# sumstatlib wheel and stages the web validator into static/).
+FROM node:22-slim AS builder
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends python3 curl ca-certificates \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install uv (required by the prebuild script)
+RUN curl -LsSf https://astral.sh/uv/install.sh | sh
+ENV PATH="/root/.local/bin:$PATH"
+
+WORKDIR /app
+
+# Copy workspace configuration and Python source required by uv build
+COPY pyproject.toml ./
+COPY README.md ./
+COPY sumstatlib/ ./sumstatlib/
+COPY src/ ./src/
+
+# Copy the Docusaurus site
+COPY docs/ ./docs/
+
+# Install Node dependencies
+WORKDIR /app/docs
+RUN npm ci
+
+# prebuild: builds the sumstatlib wheel and stages the web validator
+# build:    runs Docusaurus; output lands in /app/docs/build/
+RUN npm run build
+
+# ── Stage 2: serve ────────────────────────────────────────────────────────────
+FROM nginx:alpine AS server
+
+# Place the built site under the production base path so asset URLs resolve
+COPY --from=builder /app/docs/build /usr/share/nginx/html/gwas/apps/beyond-snps
+
+COPY deployment/nginx.conf /etc/nginx/conf.d/default.conf
+
+EXPOSE 80

deployment/helm/Chart.yaml

@@ -0,0 +1,5 @@
+apiVersion: v1
+appVersion: "1.0"
+description: A Helm chart for Kubernetes
+name: gwas-beyond-snps
+version: 0.1.0

deployment/helm/templates/deployment.yaml

@@ -0,0 +1,37 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ .Values.service.name }}
+  labels:
+    app: {{ .Values.service.name }}
+spec:
+  replicas: {{ .Values.replicaCount }}
+  selector:
+    matchLabels:
+      app: {{ .Values.service.name }}
+  template:
+    metadata:
+      labels:
+        app: {{ .Values.service.name }}
+    spec:
+      containers:
+        - name: {{ .Values.service.name }}
+          image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
+          imagePullPolicy: {{ .Values.image.pullPolicy }}
+          ports:
+            - containerPort: 80
+          livenessProbe:
+            httpGet:
+              path: /
+              port: 80
+          readinessProbe:
+            httpGet:
+              path: /
+              port: 80
+          resources:
+            requests:
+              cpu: {{ .Values.resources.requests.cpu }}
+              memory: {{ .Values.resources.requests.memory }}
+            limits:
+              cpu: {{ .Values.resources.limits.cpu }}
+              memory: {{ .Values.resources.limits.memory }}

deployment/helm/templates/ingress.yaml

@@ -0,0 +1,15 @@
+apiVersion: extensions/v1beta1
+kind: Ingress
+metadata:
+  name: {{.Values.ingress.name}}
+  annotations:
+    nginx.ingress.kubernetes.io/rewrite-target: /gwas/apps/beyond-snps/$2
+    nginx.ingress.kubernetes.io/ssl-redirect: "false"
+spec:
+  rules:
+  - http:
+      paths:
+      - path: {{.Values.ingress.path}}
+        backend:
+          serviceName: {{.Values.service.name}}
+          servicePort: {{.Values.service.port}}

deployment/helm/templates/service.yaml

@@ -0,0 +1,10 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ .Values.service.name }}
+spec:
+  type: ClusterIP
+  selector:
+    app: {{ .Values.service.name }}
+  ports:
+    - port: {{ .Values.service.port }}

deployment/helm/values.yaml

@@ -0,0 +1,24 @@
+
+replicaCount: 1
+
+image:
+  repository: dockerhub.ebi.ac.uk/gwas/gwas-beyond-snps
+  tag: dev
+  pullPolicy: Always
+
+service:
+  name: gwas-beyond-snps
+  port: 80
+
+ingress:
+  name: beyond-snp-ingress
+  annotations: {}
+  path: "/apps/beyond-snps(/|$)(.*)"
+
+resources:
+  limits:
+    cpu: 250m
+    memory: 128Mi
+  requests:
+    cpu: 100m
+    memory: 64Mi

deployment/nginx.conf

@@ -0,0 +1,22 @@
+server {
+    listen 80;
+    server_name _;
+
+    root /usr/share/nginx/html;
+    index index.html;
+
+    # Keep redirects as path-only so the port is preserved when running behind
+    # a non-standard port (e.g. docker run -p 8000:80).
+    absolute_redirect off;
+
+    # Redirect bare root to the site base path
+    location = / {
+        return 301 /gwas/apps/beyond-snps/;
+    }
+
+    # Serve the Docusaurus site.
+    # try_files order: exact file → directory index → .html extension → 404 page.
+    location /gwas/apps/beyond-snps/ {
+        try_files $uri $uri/ $uri.html /gwas/apps/beyond-snps/404.html;
+    }
+}

noxfile.py

@@ -1,3 +1,8 @@
+# /// script
+# dependencies = ["nox"]
+# ///
+import os
+
 import nox
 
 # Use uv for environment creation and package installation
@@ -77,3 +82,35 @@ def lint(session):
 
     # Type checking
     session.run("ty", "check", "src", "sumstatlib/src")
+
+
+@nox.session(default=False)
+def build_docker(session):
+    """Build an image with a Docker V2 manifest (not OCI)"""
+    try:
+        tag = session.posargs[0]
+    except IndexError:
+        raise RuntimeError(
+            "Tag must be provided as a command-line argument"
+            " e.g. nox  -s build_docker -- dev"
+        )
+
+    os.environ["BUILDKIT_OCI_MEDIA_TYPES"] = "0"
+    session.run(
+        "docker",
+        "build",
+        "--platform",
+        "linux/amd64",
+        "--provenance=false",
+        "--push",
+        "-t",
+        f"dockerhub.ebi.ac.uk/gwas/gwas-beyond-snps:{tag}",
+        "-f",
+        "deployment/Dockerfile",
+        ".",
+        external=True,
+    )
+
+
+if __name__ == "__main__":
+    nox.main()

pyproject.toml

@@ -22,6 +22,14 @@ dependencies = [
     "gwascatalog.sumstatlib",
 ]
 
+[project.optional-dependencies]
+pydantic = [
+    "gwascatalog.sumstatlib[pydantic]",
+]
+
+[project.scripts]
+gwascatalog = "gwascatalog.sumstatapp.cli.__main__:main"
+
 [tool.uv.workspace]
 members = [
     "sumstatlib",