Dockerfile

FROM python:3.11-slim AS basis

# set environment varibles
ENV PYTHONDONTWRITEBYTECODE=1
ENV PYTHONUNBUFFERED=1


FROM basis AS builder
RUN apt-get update \
    && apt-get install -y --no-install-recommends \
       build-essential \
       fasttree \
       libxml2 \
       mafft \
    && rm -rf /var/lib/apt/lists/*

WORKDIR /src
RUN pip install --upgrade pip \
    && pip install "hatch<1.17" "virtualenv<20.26"
COPY pyproject.toml .

RUN hatch dep show requirements --all > requirements.txt \
    && pip install wheel setuptools -r requirements.txt

COPY . .
RUN hatch build \
    && ls -la dist/

# Create a clean venv for runtime and install the wheel
RUN python -m venv /app \
    && /app/bin/pip install --upgrade pip wheel setuptools \
    && /app/bin/pip install -r requirements.txt \
    && /app/bin/pip install dist/*.whl


FROM basis AS runtime
RUN apt-get update \
    && apt-get install -y --no-install-recommends \
       fasttree \
       libxml2 \
       mafft \
       mmseqs2 \
       procps \
       time \
    && apt-get -y autoremove \
    && apt-get -y autoclean \
    && rm -rf /var/lib/apt/lists/*

COPY --from=builder /app /app
ENV PATH="/app/bin:$PATH"

RUN python -c "import FastOMA; print(FastOMA.__version__)"