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Port R and Python fixes from research template "improve devcontainers" branch #10

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merged 5 commits into from
May 3, 2024
Merged

Port R and Python fixes from research template "improve devcontainers" branch #10

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0fbf095
Replace Rocker R package library with OpensAFELY R image library
Jongmassey May 1, 2024
cdd84e6
Don't require auth for local rstudio server
Jongmassey May 2, 2024
1726c65
Redirect system python to venv python
Jongmassey May 3, 2024
dc5c863
Combine multiple RUN statements
lucyb May 3, 2024
2655799
Move COPY from R image to after the Python COPY
lucyb May 3, 2024
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32 changes: 17 additions & 15 deletions Dockerfile
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Expand Up @@ -6,44 +6,46 @@
# docker clean up that deletes that cache on every apt install
RUN rm -f /etc/apt/apt.conf.d/docker-clean

# Install python 3.10. This is the version used by the python-docker
# image, used for analyses using the OpenSAFELY pipeline.
#
# DL3042: we always want latest package versions when we rebuild
# DL3013: using an apt cache on the host instead
# hadolint ignore=DL3042,DL3013
SHELL ["/bin/bash", "-o", "pipefail", "-c"]
RUN --mount=type=cache,target=/var/cache/apt \

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DL3008 warning: Pin versions in apt get install. Instead of `apt-get install <package>` use `apt-get install <package>=<version>`
echo "deb http://ppa.launchpadcontent.net/deadsnakes/ppa/ubuntu focal main" > /etc/apt/sources.list.d/deadsnakes-ppa.list &&\
/usr/lib/apt/apt-helper download-file 'https://keyserver.ubuntu.com/pks/lookup?op=get&search=0xf23c5a6cf475977595c89f51ba6932366a755776' /etc/apt/trusted.gpg.d/deadsnakes.asc &&\
apt-get update &&\
# Install python 3.10. This is the version used by the python-docker
# image, used for analyses using the OpenSAFELY pipeline.
apt-get install -y --no-install-recommends curl python3.10 python3.10-distutils python3.10-venv &&\
# Pip for Python 3.10 isn't included in deadsnakes, so install separately
curl https://bootstrap.pypa.io/get-pip.py | python3.10 &&\
# Set default python, so that the Python virtualenv works as expected
rm /usr/bin/python3 &&\
ln -s /usr/bin/python3.10 /usr/bin/python3

# install renv
RUN --mount=type=cache,target=/cache,id=/cache-2004 R -e 'install.packages("renv", destdir="/cache"); renv::init(bare = TRUE)'
ln -s /usr/bin/python3.10 /usr/bin/python3 &&\
# Create a fake system Python pointing at venv python
echo 'exec /opt/venv/bin/python3.10 "$@"' > /usr/bin/python &&\
# Configure RStudio Server to run without auth
echo "auth-none=1" >> /etc/rstudio/rserver.conf &&\
echo "USER=rstudio" >> /etc/environment &&\
# Remove the packages shipped with the rocker image
rm -rf /usr/library/lib/R/site-library/* &&\
# Give the local user sudo (aka root) permissions
usermod -aG sudo rstudio &&\
echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers

# copy the renv directory from the OpenSAFELY R action image
# Copy the Python virtualenv from OpenSAFELY Python action image
#
# DL3022: hadolint can't access a network and doesn't behave
# as expected when a reference is made to an external image.
# hadolint ignore=DL3022
COPY --from=ghcr.io/opensafely-core/r /renv/ /renv/
COPY --chown=rstudio:rstudio --from=ghcr.io/opensafely-core/python:v2 /opt/venv /opt/venv

# Copy the Python virtualenv from OpenSAFELY Python action image
# copy the renv directory into the local site library from the OpenSAFELY R action image
#
# DL3022: hadolint can't access a network and doesn't behave
# as expected when a reference is made to an external image.
# hadolint ignore=DL3022
COPY --from=ghcr.io/opensafely-core/python:v2 /opt/venv /opt/venv

# Create a local user and give it sudo (aka root) permissions
RUN usermod -aG sudo rstudio &&\
echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
COPY --chown=rstudio:rstudio --from=ghcr.io/opensafely-core/r:latest /renv/lib/R-4.0/x86_64-pc-linux-gnu/ /usr/local/lib/R/site-library

# Required for installing opensafely cli
ENV PATH="/home/rstudio/.local/bin:${PATH}"
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