Can't install precommit toolchain on OSX

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Issue metadata

• url: https://github.com/pystatgen/sgkit/issues/141
• state: open
• milestone: No milestone assigned
• created by: Jillian Rowe @jerowe
• labels:
  • process + tools
• assigned:

Issue description

I don't think this is exactly a sgkit issue, but @daletovar and I both encountered errors when trying to install the precommit toolchain on a mac.

For a work around I used this dockerfile.

FROM python:3.8.5-buster
RUN mkdir /project
WORKDIR /project
ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
RUN apt-get update --fix-missing && \
    apt-get install -y wget bzip2 ca-certificates curl git && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*
COPY requirements-dev.txt /project/requirements-dev.txt
COPY requirements.txt /project/requirements.txt
RUN python -m pip install --upgrade pip && \
    pip install -r requirements.txt -r requirements-dev.txt
CMD bash -c "cd /project/sgkit && \
        python -m pip install --upgrade pip && \
        pip install -r requirements.txt -r requirements-dev.txt && \
        cd docs; \
        make html SPHINXOPTS='-W --keep-going' && \
        cd .. && \
        pytest -v --cov=sgkit --cov-report=term-missin g&& \
        pre-commit run --all-files"

Run this once to build

docker build -t sgkit-dev .
docker volume create sgkit-precommit-cache

Run this to test, lint, and run precommit hooks

docker run -it \
    -v sgkit-precommit-cache:/root/.cache -v $HOME/.gitconfig:/root/.gitconfig -v $(pwd):/project/sgkit sgkit-dev

Run this to commit

docker run -it \
    -v sgkit-precommit-cache:/root/.cache -v $HOME/.gitconfig:/root/.gitconfig -v $(pwd):/project/sgkit \
    bash -c 'cd /project/sgkit; git commit -m "My commit msg"'