HF Spaces: Dockerfile for v2 (FastAPI + React) deployment

Two-stage build:
1. node:20-slim — npm ci + vite build → web/dist
2. python:3.11-slim — install backend deps, copy models/data/built-frontend,
run uvicorn on port 7860 as non-root user (uid 1000,
which HF Spaces requires)

README.md frontmatter switched from sdk:streamlit → sdk:docker, app_port:7860.
HF will detect the Dockerfile and build the v2 stack instead of the legacy
Streamlit app.

.dockerignore keeps the build context small — excludes the .venv, node_modules,
training-only parquets (features.parquet, embeddings.parquet etc.), and dev
caches. Final image only contains:
- api/main.py
- src/microbe_model/ + scripts/recommend.py
- models/recommender/ (24 .ubj) + models/phenotype/ (12 files)
- data/media_metadata.parquet + data/media_recipes.parquet
- artifacts/uncultured_predictions.parquet
- web/dist/ (built React app)

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

.dockerignore

@@ -0,0 +1,47 @@
+.git
+.venv
+.env
+.env.local
+__pycache__
+*.pyc
+*.pyo
+*.pyd
+.pytest_cache
+.ruff_cache
+.mypy_cache
+node_modules
+web/node_modules
+web/dist
+notebooks/scratch
+.ipynb_checkpoints
+.DS_Store
+.vscode
+.idea
+.claude
+.letta
+# Heavy data files we don't ship
+data/genomes
+data/bacdive
+data/features.parquet
+data/training_table.parquet
+data/embeddings.parquet
+data/embeddings.jsonl
+data/uncultured_features.parquet
+data/uncultured_features.jsonl
+data/training_table_v0.parquet
+data/training_table_embeddings.parquet
+data/strain_media.parquet
+data/gtdb_candidates.parquet
+data/bacdive_phenotypes.parquet
+data/features_v0.jsonl
+data/features.jsonl
+data/features_v0.parquet
+data/bac120_metadata.tsv.gz
+artifacts/embeddings.log
+artifacts/featurize.log
+artifacts/phase_c.log
+artifacts/predictions.parquet
+artifacts/predictions_v0.parquet
+artifacts/bacdive_scan.log
+artifacts/mediadive_fetch.log
+docs/

Dockerfile

@@ -0,0 +1,66 @@
+# syntax=docker/dockerfile:1.6
+# Two-stage build:
+#   1. node — compile the Vite/React frontend → web/dist
+#   2. python — install backend deps, copy models + built frontend, run uvicorn
+
+# ─────────────────────────────────────────────────────────────────────
+# Stage 1 — build the React frontend
+# ─────────────────────────────────────────────────────────────────────
+FROM node:20-slim AS web-build
+WORKDIR /web
+
+COPY web/package.json web/package-lock.json ./
+RUN npm ci --no-audit --no-fund
+
+COPY web/ ./
+RUN npm run build
+
+
+# ─────────────────────────────────────────────────────────────────────
+# Stage 2 — Python backend + serve the built frontend
+# ─────────────────────────────────────────────────────────────────────
+FROM python:3.11-slim AS app
+
+# System deps for pyrodigal / xgboost wheels
+RUN apt-get update && apt-get install -y --no-install-recommends \
+        build-essential \
+        curl \
+    && rm -rf /var/lib/apt/lists/*
+
+# HF Spaces requires the container run as a non-root user (uid 1000)
+RUN useradd -m -u 1000 user
+ENV HOME=/home/user \
+    PATH=/home/user/.local/bin:$PATH \
+    PYTHONUNBUFFERED=1 \
+    PYTHONDONTWRITEBYTECODE=1
+
+WORKDIR /app
+
+# Install Python deps first (better layer caching)
+COPY requirements.txt ./
+RUN pip install --no-cache-dir --upgrade pip && \
+    pip install --no-cache-dir -r requirements.txt
+
+# Copy the project (everything needed at runtime)
+COPY --chown=user:user api/ ./api/
+COPY --chown=user:user src/ ./src/
+COPY --chown=user:user scripts/recommend.py ./scripts/recommend.py
+COPY --chown=user:user models/ ./models/
+COPY --chown=user:user artifacts/uncultured_predictions.parquet ./artifacts/uncultured_predictions.parquet
+COPY --chown=user:user data/media_metadata.parquet ./data/media_metadata.parquet
+COPY --chown=user:user data/media_recipes.parquet ./data/media_recipes.parquet
+COPY --chown=user:user pyproject.toml README.md ./
+
+# Built frontend from stage 1
+COPY --from=web-build --chown=user:user /web/dist ./web/dist
+
+# Make sure microbe_model is importable
+RUN pip install --no-cache-dir -e .
+
+# HF Spaces expects 7860; allow override
+ENV PORT=7860
+USER user
+
+EXPOSE 7860
+
+CMD ["sh", "-c", "uvicorn api.main:app --host 0.0.0.0 --port ${PORT}"]

README.md

@@ -3,9 +3,8 @@ title: microbe-model
 emoji: 🦠
 colorFrom: yellow
 colorTo: red
-sdk: streamlit
-sdk_version: 1.39.0
-app_file: app.py
+sdk: docker
+app_port: 7860
 pinned: false
 license: mit
 short_description: Predict growth conditions and culture media for never-cultured microbes