Bringing in image directory from deployment repo

Dockerfile

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+FROM rocker/geospatial:4.4.1
+
+ENV NB_USER rstudio
+ENV NB_UID 1000
+ENV CONDA_DIR /srv/conda
+
+# Set ENV for all programs...
+ENV PATH ${CONDA_DIR}/bin:$PATH
+
+# And set ENV for R! It doesn't read from the environment...
+RUN echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron.site
+
+# Add PATH to /etc/profile so it gets picked up by the terminal
+RUN echo "PATH=${PATH}" >> /etc/profile
+RUN echo "export PATH" >> /etc/profile
+
+ENV HOME /home/${NB_USER}
+
+WORKDIR ${HOME}
+
+# Install packages needed by notebook-as-pdf
+# nodejs for installing notebook / jupyterhub from source
+# libarchive-dev for https://github.com/berkeley-dsep-infra/datahub/issues/1997
+RUN apt-get update > /dev/null && \
+    apt-get install --yes \
+            less \
+            fonts-symbola \
+            libx11-xcb1 \
+            libxtst6 \
+            libxrandr2 \
+            libasound2 \
+            libpangocairo-1.0-0 \
+            libatk1.0-0 \
+            libatk-bridge2.0-0 \
+            libgtk-3-0 \
+            libnss3 \
+            libnspr4 \
+            libxss1 \
+            nodejs \
+            npm \
+            texlive-xetex \
+            texlive-fonts-extra \
+            texlive-latex-extra \
+            texlive-fonts-recommended \
+            texlive-lang-chinese \
+            texlive-plain-generic \
+            tini > /dev/null && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+COPY install-mambaforge.bash /tmp/install-mambaforge.bash
+RUN /tmp/install-mambaforge.bash
+
+USER ${NB_USER}
+
+COPY environment.yml /tmp/environment.yml
+COPY infra-requirements.txt /tmp/infra-requirements.txt
+RUN mamba env update -p ${CONDA_DIR} -f /tmp/environment.yml && \
+        mamba clean -afy
+
+# DH-327, very similar to what was done for datahub in DH-164
+ENV PLAYWRIGHT_BROWSERS_PATH ${CONDA_DIR}
+RUN playwright install chromium
+
+# Install IRKernel
+RUN R --quiet -e "install.packages('IRkernel', quiet = TRUE)" && \
+    R --quiet -e "IRkernel::installspec(prefix='${CONDA_DIR}')"
+
+# Install extra R packages
+RUN install2.r --error --skipinstalled \
+    ## general interest 
+    anytime    \
+    Hmisc      \
+    lmtest     \
+    lubridate  \
+    latex2exp  \
+    MASS       \
+    patchwork  \
+    stargazer  \
+    tidymodels \
+    wooldridge \
+    ## machine learning
+    caret      \
+    parsnip    \
+    torch      \
+    ## 241
+    AER        \
+    randomizr  \
+    ## 271
+    fable      \
+    feasts     \
+    fpp3       \
+    gamlr      \
+    plm        \
+    lme4       \
+    Quandl     \
+    quantmod   \
+    tseries    \
+    tsibble    \
+    vcd        \
+    vars       \
+    zoo
+
+# Use simpler locking strategy
+COPY file-locks /etc/rstudio/file-locks
+
+ENTRYPOINT ["tini", "--"]

environment.yml

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+name: ischool
+
+channels:
+- conda-forge
+
+dependencies:
+- syncthing==1.25.0
+- jupyter-rsession-proxy==2.2.0
+# https://github.com/berkeley-dsep-infra/datahub/issues/5251
+- nodejs=16 # code-server requires node < 17
+- jupyter-server-proxy==4.2.0
+- jupyter-vscode-proxy==0.5
+- code-server==4.10.1
+# bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
+- traitlets=5.9.*
+- pip:
+  - -r /tmp/infra-requirements.txt
+  - otter-grader==3.1.4
+  # DH-327
+  - nbconvert[webpdf]==7.16.4
+  # for notebook exporting
+  - nb2pdf==0.6.2
+  - nbpdfexport==0.2.1

file-locks

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+# https://docs.rstudio.com/ide/server-pro/load_balancing/configuration.html#file-locking
+
+# rocker sets this to advisory, but this might be causing NFS issues.
+# lets set it to the default (default: linkbased)
+lock-type=linkbased
+
+# we'll also reduce the frequency by 1/3
+refresh-rate=60
+timeout-interval=90
+
+# log attempts
+# enable-logging=1
+# log-file=/tmp/rstudio-locking.log

infra-requirements.txt

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+# WARNING: Original source at scripts/infra-packages/requirements.txt
+# PLEASE DO NOT EDIT ELSEWHERE
+# After editing scripts/infra-packages/requirements.txt, please run
+# scripts/infra-packages/sync.bash.
+
+# This file pins versions of notebook related python packages we want
+# across all hubs. This makes sure we don't need to upgrade them
+# everwhere one by one.
+
+# FIXME: Freeze this to get exact versions of all dependencies
+notebook==7.0.7
+jupyterlab==4.0.11
+nbgitpuller==1.2.1
+jupyter-resource-usage==1.0.1
+# Matches version in images/hub/Dockerfile
+jupyterhub==4.1.6
+appmode==0.8.0
+ipywidgets==8.0.7
+jupyter-tree-download==1.0.1
+git-credential-helpers==0.2
+# Measure popularity of different packages in our hubs
+# https://discourse.jupyter.org/t/request-for-implementation-instrument-libraries-actively-used-by-users-on-a-jupyterhub/7994?u=yuvipanda
+git+https://github.com/shaneknapp/python-popularity-contest.git@add-error-handling
+# RISE is useful for presentations - see https://github.com/berkeley-dsep-infra/datahub/issues/2527
+RISE==5.7.1
+# syncthing for dropbox-like functionality
+jupyter-syncthing-proxy==1.0.3
+# jupyter archival tool for easy user downloads
+jupyter-archive==3.4.0

install-mambaforge.bash

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+#!/bin/bash
+# This downloads and installs a pinned version of mambaforge
+set -ex
+
+cd $(dirname $0)
+MAMBAFORGE_VERSION='23.1.0-1'
+
+URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh"
+INSTALLER_PATH=/tmp/mambaforge-installer.sh
+
+wget --quiet $URL -O ${INSTALLER_PATH}
+chmod +x ${INSTALLER_PATH}
+
+bash ${INSTALLER_PATH} -b -p ${CONDA_DIR}
+export PATH="${CONDA_DIR}/bin:$PATH"
+
+# Do not attempt to auto update conda or dependencies
+conda config --system --set auto_update_conda false
+conda config --system --set show_channel_urls true
+
+# empty conda history file,
+# which seems to result in some effective pinning of packages in the initial env,
+# which we don't intend.
+# this file must not be *removed*, however
+echo '' > ${CONDA_DIR}/conda-meta/history
+
+# Clean things out!
+conda clean --all -f -y
+
+# Remove the big installer so we don't increase docker image size too much
+rm ${INSTALLER_PATH}
+
+# Remove the pip cache created as part of installing mambaforge
+rm -rf /root/.cache
+
+chown -R $NB_USER:$NB_USER ${CONDA_DIR}
+
+conda list -n root