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Initial commit: cell-state-compiler full-stack monorepo
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‎.env.example‎

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# ─── Database ────────────────────────────────────────────────────────────────
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POSTGRES_HOST=postgres
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POSTGRES_PORT=5432
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POSTGRES_DB=cell_state_compiler
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POSTGRES_USER=cellcompiler
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POSTGRES_PASSWORD=cellcompiler
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DATABASE_URL=postgresql+psycopg2://cellcompiler:cellcompiler@postgres:5432/cell_state_compiler
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# ─── Redis ───────────────────────────────────────────────────────────────────
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REDIS_URL=redis://redis:6379/0
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# ─── JWT ─────────────────────────────────────────────────────────────────────
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JWT_SECRET=dev_change_me_in_production_use_32_char_minimum_xx
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JWT_ALGORITHM=HS256
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ACCESS_TOKEN_EXPIRE_MINUTES=1440
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# ─── CORS / API ──────────────────────────────────────────────────────────────
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CORS_ORIGINS=http://localhost:3000
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NEXT_PUBLIC_API_BASE_URL=http://localhost:8000/api/v1
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# ─── Genome Model Service ────────────────────────────────────────────────────
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GENOME_MODEL_SERVICE_URL=http://genome-model-service:8100
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# ─── Evo 2 Configuration ─────────────────────────────────────────────────────
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# Provider: local | nvidia_nim
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EVO2_PROVIDER=local
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# Model sizes:
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# evo2_1b_base — CPU-compatible, dev/test (~2 GB)
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# evo2_7b — Single A100/H100 40GB+
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# evo2_40b — Multi-GPU, 2× H100 80GB required (use docker-compose.gpu.yml)
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EVO2_MODEL_NAME=evo2_1b_base
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EVO2_MODEL_VERSION=
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# Device: cpu | cuda:0
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EVO2_DEVICE=cpu
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EVO2_MAX_CONTEXT_LENGTH=8192
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EVO2_DEFAULT_EMBEDDING_LAYER=
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EVO2_HEALTH_RUN_SMOKE_TEST=true
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# ─── HuggingFace ─────────────────────────────────────────────────────────────
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# Required to download evo2_40b if the repository is gated.
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# Get your token at https://huggingface.co/settings/tokens
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HUGGINGFACE_TOKEN=
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# ─── Evo 2 Generation Gate ───────────────────────────────────────────────────
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# Generation is disabled by default. Set true only in controlled research contexts.
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ENABLE_EVO2_GENERATION=false
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# ─── Sequence Safety ─────────────────────────────────────────────────────────
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ENABLE_REAL_SEQUENCE_STORAGE=false
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SEQUENCE_SAFETY_MODE=restricted
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MAX_SEQUENCE_LENGTH=8192
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# ─── NVIDIA NIM (alternative to local Evo 2) ─────────────────────────────────
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NVIDIA_NIM_API_KEY=
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NVIDIA_NIM_EVO2_URL=
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NVIDIA_NIM_TIMEOUT_SECONDS=120
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# ─── Worker ──────────────────────────────────────────────────────────────────
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WORKER_CONCURRENCY=2

‎.github/workflows/ci.yml‎

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name: CI
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on:
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push:
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branches: [main, master]
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pull_request:
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branches: [main, master]
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jobs:
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no-mock-evo2-check:
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name: "Verify no MockEvo2 in codebase"
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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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- name: Check for MockEvo2 or mock_evo2
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run: |
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if grep -r "MockEvo2\|mock_evo2" --include="*.py" --include="*.ts" --include="*.tsx" .; then
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echo "ERROR: MockEvo2 or mock_evo2 found in codebase. Remove all mock Evo 2 adapters."
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exit 1
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fi
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echo "PASS: No mock Evo2 adapters found."
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backend-tests:
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name: Backend API tests
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runs-on: ubuntu-latest
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services:
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postgres:
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image: pgvector/pgvector:pg16
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env:
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POSTGRES_DB: test_cell_state_compiler
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POSTGRES_USER: cellcompiler
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POSTGRES_PASSWORD: cellcompiler
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ports:
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- 5432:5432
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options: >-
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--health-cmd pg_isready
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--health-interval 5s
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--health-timeout 5s
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--health-retries 10
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redis:
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image: redis:7-alpine
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ports:
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- 6379:6379
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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- name: Install API deps
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working-directory: apps/api
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run: pip install -e ".[test]"
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- name: Run Alembic migrations
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working-directory: apps/api
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env:
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DATABASE_URL: postgresql+psycopg2://cellcompiler:cellcompiler@localhost:5432/test_cell_state_compiler
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run: alembic upgrade head
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- name: Run backend tests
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working-directory: apps/api
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env:
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DATABASE_URL: postgresql+psycopg2://cellcompiler:cellcompiler@localhost:5432/test_cell_state_compiler
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REDIS_URL: redis://localhost:6379/0
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JWT_SECRET: test_secret_32_chars_minimum_here_xx
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GENOME_MODEL_SERVICE_URL: http://localhost:8100
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run: pytest app/tests/ -v --tb=short
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genome-service-tests:
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name: Genome model service tests
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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-python@v5
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with:
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python-version: "3.11"
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- name: Install genome service deps
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working-directory: apps/genome-model-service
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run: pip install -e ".[test]"
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- name: Run genome service tests
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working-directory: apps/genome-model-service
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env:
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EVO2_PROVIDER: local
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EVO2_MODEL_NAME: evo2_1b_base
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EVO2_DEVICE: cpu
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EVO2_HEALTH_RUN_SMOKE_TEST: "false"
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ENABLE_EVO2_GENERATION: "false"
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MAX_SEQUENCE_LENGTH: "8192"
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SEQUENCE_SAFETY_MODE: restricted
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run: pytest app/tests/ -v --tb=short
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frontend-type-check:
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name: Frontend TypeScript check
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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:
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node-version: "20"
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cache: "npm"
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cache-dependency-path: apps/web/package-lock.json
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- name: Install deps
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working-directory: apps/web
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run: npm ci
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- name: Type check
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working-directory: apps/web
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run: npx tsc --noEmit
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- name: Lint
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working-directory: apps/web
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run: npm run lint

‎.gitignore‎

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# Python
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__pycache__/
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*.py[cod]
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*$py.class
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*.so
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.Python
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.venv/
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venv/
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env/
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*.egg-info/
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dist/
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build/
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.eggs/
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.pytest_cache/
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.mypy_cache/
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htmlcov/
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.coverage
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coverage.xml
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*.cover
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# Node
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node_modules/
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.next/
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out/
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dist/
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.turbo/
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*.tsbuildinfo
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# Env
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.env
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.env.local
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.env.production
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secret_*.txt
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*.pem
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*.key
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# Docker volumes
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pgdata/
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redis-data/
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uploads/
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# OS
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.DS_Store
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Thumbs.db
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# Logs
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*.log
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logs/
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# IDE
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.vscode/
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.idea/
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*.swp
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# Alembic
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apps/api/app/migrations/versions/*.pyc

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