update: Dockerfile

Author: singjc

.dockerignore

@@ -0,0 +1,19 @@
+# .dockerignore
+.git
+.gitignore
+**/__pycache__/
+**/*.pyc
+build/
+dist/
+*.egg-info/
+*.whl
+*.tar.gz
+tests/
+notebooks/
+data/
+examples/
+.tmp/
+.DS_Store
+sandbox/
+.pytest_cache/
+.ruff_cache/

Dockerfile

@@ -1,45 +1,79 @@
-# docker build -t ghcr.io/pyprophet/pyprophet:3.0.2 .
+# docker build --no-cache -t ghcr.io/pyprophet/pyprophet:3.0.2 .
 # docker push ghcr.io/pyprophet/pyprophet:3.0.2
 
-# PyProphet Dockerfile (Ubuntu 24.04 + venv)
-FROM ubuntu:24.04
-
-ENV DEBIAN_FRONTEND=noninteractive \
-    PYTHONUNBUFFERED=1
+# ---------- builder: create venv and install ----------
+FROM ubuntu:24.04 AS builder
+ENV DEBIAN_FRONTEND=noninteractive PYTHONUNBUFFERED=1
 
+# System Python + toolchain for building wheels (builder only)
 RUN apt-get update && apt-get install -y --no-install-recommends \
     ca-certificates python3 python3-pip python3-dev python3-venv \
-    build-essential git \
-    # --- runtime libs needed by pyopenms ---
-    libglib2.0-0 \
-    libgomp1 \
-    # these are rarely needed, but harmless and useful if pyopenms/OpenMS is present
-    libxerces-c3.2 \
-    zlib1g \
-    libbz2-1.0 \
-    libsqlite3-0 \
- && rm -rf /var/lib/apt/lists/*
-
-# venv
+    build-essential git curl && \
+    rm -rf /var/lib/apt/lists/*
+
+# Virtualenv (avoid PEP 668 issues)
 RUN python3 -m venv /opt/venv
 ENV VIRTUAL_ENV=/opt/venv
 ENV PATH="/opt/venv/bin:${PATH}"
 
-# toolchain (pins optional)
+# Upgrade pip and install toolchain/runtime deps
+# Pins chosen to have manylinux wheels for Python 3.12
 RUN python -m pip install --no-cache-dir --upgrade pip && \
-    python -m pip install --no-cache-dir "numpy==1.26.4" "cython==0.29.36" duckdb seaborn psutil
+    python -m pip install --no-cache-dir --prefer-binary \
+        "numpy==1.26.4" "cython==0.29.36" "scipy==1.12.*" \
+        duckdb seaborn psutil
+
+# Bring in the PyProphet source tree
+WORKDIR /src
+COPY pyproject.toml setup.py requirements.txt README* LICENSE* ./
+COPY pyprophet ./pyprophet
+
+# Ensure setuptools/wheel are present (and avoid latest setuptools breaking flags)
+RUN python -m pip install --no-cache-dir "setuptools<75" wheel
 
-# install PyProphet
-ADD . /pyprophet
-WORKDIR /pyprophet
-RUN pip install .
+# --- force-build the Cython extension before installing ---
+# This compiles pyprophet/scoring/_optimized.pyx into a .so in-place.
+RUN python setup.py build_ext --inplace
+
+# Install PyProphet into the venv (reuse prebuilt wheels, no isolation)
+RUN pip install --no-cache-dir --no-build-isolation .
+
+# Verify the optimized module is importable (fail-fast if not)
+RUN python - <<'PY'
+import importlib, sys
+m = importlib.import_module('pyprophet.scoring._optimized')
+print("Found optimized extension:", m.__file__)
+PY
 
-# warm up duckdb sqlite_scanner (optional)
+# Pre-install DuckDB sqlite_scanner extension (as requested)
 RUN python - <<'PY'
 import duckdb
 con = duckdb.connect()
 con.execute("INSTALL 'sqlite_scanner'")
 con.execute("LOAD 'sqlite_scanner'")
+print("duckdb sqlite_scanner installed & loadable")
 PY
 
+# Optional: trim pyc/caches
+RUN python -m compileall -q "${VIRTUAL_ENV}" || true && \
+    find "${VIRTUAL_ENV}" -type d -name "__pycache__" -prune -exec rm -rf {} + && \
+    find "${VIRTUAL_ENV}" -type f -name "*.pyc" -delete
+
+# ---------- runtime: only the venv + runtime libs ----------
+FROM ubuntu:24.04 AS runtime
+ENV DEBIAN_FRONTEND=noninteractive PYTHONUNBUFFERED=1
+
+# Minimal native libs needed by pyopenms/pyprophet (safe superset)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    ca-certificates python3 \
+    libglib2.0-0 libgomp1 \
+    libxerces-c3.2 zlib1g libbz2-1.0 libsqlite3-0 \
+    && rm -rf /var/lib/apt/lists/*
+
+# Bring the venv
+COPY --from=builder /opt/venv /opt/venv
+ENV VIRTUAL_ENV=/opt/venv
+ENV PATH="/opt/venv/bin:${PATH}"
+
+# Default workdir
 WORKDIR /data/