Initial release: rarelens platform skeleton (AGPL-3.0)

End-to-end variant interpretation platform for rare genetic disease research:
SvelteKit UI, FastAPI + PostgreSQL API, Nextflow/Ensembl VEP pipeline,
LightGBM pathogenicity scoring with MLflow, K8s/ArgoCD/GCP infrastructure.
Public test data only; no clinical claims.

.github/workflows/ci.yml

@@ -0,0 +1,64 @@
+name: ci
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  api:
+    runs-on: ubuntu-latest
+    services:
+      postgres:
+        image: postgres:16-alpine
+        env: { POSTGRES_USER: rarelens, POSTGRES_PASSWORD: rarelens, POSTGRES_DB: rarelens }
+        ports: ["5432:5432"]
+        options: --health-cmd "pg_isready -U rarelens" --health-interval 5s --health-retries 10
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v3
+      - run: uv pip install --system -e "api[dev]"
+      - run: cd api && ruff check . && mypy app
+      - run: cd api && pytest -q
+        env: { DATABASE_URL: postgresql+asyncpg://rarelens:rarelens@localhost:5432/rarelens }
+
+  web:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
+        with: { node-version: 22, cache: npm, cache-dependency-path: web/package-lock.json }
+      - run: cd web && npm ci && npm run check && npm test && npm run build
+
+  pipeline:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: nf-core/setup-nextflow@v2
+      - run: cd pipeline && nextflow run main.nf -profile docker --vcf ../data/example.vcf.gz -stub-run
+
+  terraform:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: hashicorp/setup-terraform@v3
+      - run: cd infra/terraform && terraform init -backend=false && terraform fmt -check && terraform validate
+
+  images:
+    if: github.ref == 'refs/heads/main'
+    needs: [api, web, pipeline]
+    runs-on: ubuntu-latest
+    permissions: { contents: read, id-token: write }
+    strategy:
+      matrix: { component: [api, web, pipeline, ml] }
+    steps:
+      - uses: actions/checkout@v4
+      - uses: google-github-actions/auth@v2
+        with:
+          workload_identity_provider: ${{ secrets.GCP_WIF_PROVIDER }}
+          service_account: ${{ secrets.GCP_CI_SA }}
+      - run: gcloud auth configure-docker europe-west2-docker.pkg.dev --quiet
+      - uses: docker/build-push-action@v6
+        with:
+          context: ${{ matrix.component }}
+          push: true
+          tags: europe-west2-docker.pkg.dev/${{ secrets.GCP_PROJECT }}/rarelens/${{ matrix.component }}:${{ github.sha }}

.github/workflows/deploy.yml

@@ -0,0 +1,22 @@
+# GitOps: CI only bumps image tags in the gcp overlay; ArgoCD does the deploy.
+name: bump-images
+on:
+  workflow_run:
+    workflows: [ci]
+    types: [completed]
+    branches: [main]
+
+jobs:
+  bump:
+    if: ${{ github.event.workflow_run.conclusion == 'success' }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: imranismail/setup-kustomize@v2
+      - run: |
+          cd infra/k8s/overlays/gcp
+          for c in api web; do
+            kustomize edit set image rarelens/$c=europe-west2-docker.pkg.dev/${{ secrets.GCP_PROJECT }}/rarelens/$c:${{ github.event.workflow_run.head_sha }}
+          done
+      - uses: stefanzweifel/git-auto-commit-action@v5
+        with: { commit_message: "chore: bump images to ${{ github.event.workflow_run.head_sha }}" }