# SimurgArray container: the `simurg` CLI with the compiled kernels.
#   docker build -t simurg:1.1.0 .
#   docker run --rm -v "$PWD":/work simurg:1.1.0 genotype --bpm M.bpm --egt C.egt --idats idats --out run/gtc
# Inputs and outputs live in the mounted /work folder; the image holds no data.
ARG PYTHON=3.12

FROM python:${PYTHON}-slim-bookworm AS build
RUN apt-get update -q && apt-get install -y -q --no-install-recommends curl gcc libc6-dev \
    && rm -rf /var/lib/apt/lists/*
RUN curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y --profile minimal
ENV PATH=/root/.cargo/bin:$PATH
WORKDIR /src
COPY pyproject.toml README.md LICENSE THIRD_PARTY_NOTICES.md ./
COPY src ./src
COPY rust/simurg-core ./rust/simurg-core
RUN pip wheel --no-cache-dir --no-deps -w /wheels . ./rust/simurg-core

FROM python:${PYTHON}-slim-bookworm
LABEL org.opencontainers.image.title="SimurgArray" \
      org.opencontainers.image.description="Research toolkit for Illumina Infinium genotyping BeadChip data" \
      org.opencontainers.image.licenses="MIT"
COPY --from=build /wheels /wheels
RUN pip install --no-cache-dir /wheels/*.whl && rm -rf /wheels \
    && useradd --create-home --uid 1000 simurg
USER simurg
WORKDIR /work
ENTRYPOINT ["simurg"]
CMD ["--help"]