PyChunkedGraph/Dockerfile at main · CAVEconnectome/PyChunkedGraph · GitHub

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# syntax=docker/dockerfile:1
ARG PYTHON_VERSION=3.11
ARG BASE_IMAGE=python:${PYTHON_VERSION}-slim


######################################################
# Stage 1: Conda environment
######################################################
FROM ${BASE_IMAGE} AS conda-deps
ENV PATH="/root/miniconda3/bin:${PATH}"

RUN apt-get update && apt-get install build-essential wget -y \
  && wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
  && bash Miniconda3-latest-Linux-x86_64.sh -b \
  && rm Miniconda3-latest-Linux-x86_64.sh \
  && conda config --add channels conda-forge \
  && conda update -y --override-channels -c conda-forge conda \
  && conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main \
  && conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r \
  && conda install -y --override-channels -c conda-forge conda-pack

COPY requirements.yml requirements.txt requirements-dev.txt ./

RUN --mount=type=cache,target=/opt/conda/pkgs \
    conda env create -n pcg -f requirements.yml

RUN conda-pack -n pcg --ignore-missing-files -o /tmp/env.tar \
  && mkdir -p /app/venv && cd /app/venv \
  && tar xf /tmp/env.tar && rm /tmp/env.tar \
  && /app/venv/bin/conda-unpack


######################################################
# Stage 2: Bigtable emulator
######################################################
FROM golang:bullseye AS bigtable-emulator
ARG GOOGLE_CLOUD_GO_VERSION=bigtable/v1.19.0
RUN --mount=type=cache,target=/go/pkg/mod \
    --mount=type=cache,target=/root/.cache/go-build \
    git clone --depth=1 --branch="$GOOGLE_CLOUD_GO_VERSION" \
      https://github.com/googleapis/google-cloud-go.git /usr/src \
  && cd /usr/src/bigtable && go install -v ./cmd/emulator


######################################################
# Stage 3: Production
######################################################
FROM ${BASE_IMAGE}
ENV VIRTUAL_ENV=/app/venv
ENV PATH="$VIRTUAL_ENV/bin:$PATH"
# Force ld to resolve libpython3.x.so to the conda venv's copy. The slim base
# ships its own /usr/local/lib/libpython, which the loader would otherwise pair
# with conda-built C extensions, segfaulting in PyObject_Hash on first import.
ENV LD_LIBRARY_PATH="$VIRTUAL_ENV/lib"

RUN apt-get update && apt-get install -y --no-install-recommends \
      nginx supervisor redis-tools procps \
  && (id nginx >/dev/null 2>&1 || useradd -r -d /home/nginx -s /bin/bash nginx) \
  && mkdir -p /etc/uwsgi /home/nginx/.cloudvolume/secrets \
  && chown -R nginx /home/nginx \
  && rm -rf /var/lib/apt/lists/*

COPY --from=conda-deps /app/venv /app/venv
COPY --from=bigtable-emulator /go/bin/emulator /app/venv/bin/cbtemulator
COPY override/gcloud /app/venv/bin/gcloud
COPY override/timeout.conf /etc/nginx/conf.d/timeout.conf
COPY override/nginx.conf /etc/nginx/nginx.conf
COPY override/supervisord.conf /etc/supervisor/conf.d/supervisord.conf
COPY uwsgi.ini /etc/uwsgi/uwsgi.ini

# PyPI wheel bundles the zstd C source; conda-forge's system-linked build lacks
# multi_decompress_to_buffer, used by io/edges.py.
RUN pip install --no-cache-dir --no-deps --force-reinstall zstandard==0.21.0

COPY requirements.txt .
RUN --mount=type=cache,target=/root/.cache/pip \
    pip install --upgrade -r requirements.txt

COPY . /app
WORKDIR /app

# --no-deps: graph-tool/cloudvolume etc. are already in the conda venv; setup.py
# reads __version__ from pychunkedgraph/__init__.py.
RUN pip install --no-deps -e .

CMD ["/usr/bin/supervisord", "-n", "-c", "/etc/supervisor/supervisord.conf"]