kemal
5463f489a3
ci / api (push) Failing after 10s
ci / terraform (push) Failing after 11s
ci / web (push) Failing after 35s
ci / pipeline (push) Failing after 2m29s
ci / images (api) (push) Skipped
ci / images (ml) (push) Skipped
ci / images (pipeline) (push) Skipped
ci / images (web) (push) Skipped
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.
65 lines
2.2 KiB
YAML
65 lines
2.2 KiB
YAML
name: ci
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on:
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pull_request:
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push:
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branches: [main]
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jobs:
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api:
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runs-on: ubuntu-latest
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services:
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postgres:
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image: postgres:16-alpine
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env: { POSTGRES_USER: rarelens, POSTGRES_PASSWORD: rarelens, POSTGRES_DB: rarelens }
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ports: ["5432:5432"]
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options: --health-cmd "pg_isready -U rarelens" --health-interval 5s --health-retries 10
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steps:
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- uses: actions/checkout@v4
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- uses: astral-sh/setup-uv@v3
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- run: uv pip install --system -e "api[dev]"
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- run: cd api && ruff check . && mypy app
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- run: cd api && pytest -q
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env: { DATABASE_URL: postgresql+asyncpg://rarelens:rarelens@localhost:5432/rarelens }
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web:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-node@v4
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with: { node-version: 22, cache: npm, cache-dependency-path: web/package-lock.json }
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- run: cd web && npm ci && npm run check && npm test && npm run build
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pipeline:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: nf-core/setup-nextflow@v2
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- run: cd pipeline && nextflow run main.nf -profile docker --vcf ../data/example.vcf.gz -stub-run
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terraform:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: hashicorp/setup-terraform@v3
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- run: cd infra/terraform && terraform init -backend=false && terraform fmt -check && terraform validate
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images:
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if: github.ref == 'refs/heads/main'
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needs: [api, web, pipeline]
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runs-on: ubuntu-latest
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permissions: { contents: read, id-token: write }
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strategy:
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matrix: { component: [api, web, pipeline, ml] }
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steps:
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- uses: actions/checkout@v4
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- uses: google-github-actions/auth@v2
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with:
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workload_identity_provider: ${{ secrets.GCP_WIF_PROVIDER }}
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service_account: ${{ secrets.GCP_CI_SA }}
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- run: gcloud auth configure-docker europe-west2-docker.pkg.dev --quiet
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- uses: docker/build-push-action@v6
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with:
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context: ${{ matrix.component }}
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push: true
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tags: europe-west2-docker.pkg.dev/${{ secrets.GCP_PROJECT }}/rarelens/${{ matrix.component }}:${{ github.sha }}
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