Bringing in image directory from deployment repo

Dockerfile

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+FROM ghcr.io/rocker-org/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
+# texlive-xetex pulls in texlive-latex-extra > texlive-latex-recommended
+# We use Ubuntu's TeX because rocker's doesn't have most packages by default,
+# and we don't want them to be downloaded on demand by students.
+# tini is necessary because it is our ENTRYPOINT below.
+RUN apt-get update > /dev/null && \
+    apt-get install --yes \
+            less \
+            libx11-xcb1 \
+            libxtst6 \
+            libxrandr2 \
+            libasound2 \
+            libpangocairo-1.0-0 \
+            libatk1.0-0 \
+            libatk-bridge2.0-0 \
+            libgtk-3-0 \
+            libnss3 \
+            libnspr4 \
+            libxss1 \
+            fonts-symbola \
+            gdebi-core \
+            tini \
+	    pandoc \
+            texlive-xetex \
+            texlive-fonts-recommended \
+            texlive-fonts-extra \
+            texlive-plain-generic \
+            nodejs npm > /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
+RUN mamba env update -p ${CONDA_DIR} -f /tmp/environment.yml && \
+    mamba clean -afy
+
+COPY infra-requirements.txt /tmp/infra-requirements.txt
+RUN pip install --no-cache-dir -r /tmp/infra-requirements.txt
+
+# DH-331, 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}')"
+
+COPY class-libs.R /tmp/class-libs.R
+RUN mkdir -p /tmp/r-packages
+
+# Workaround to install ottr, issue 3342
+#RUN wget https://github.com/ucbds-infra/ottr/archive/refs/tags/0.1.0.tar.gz -O /tmp/ottr.tar.gz && R CMD INSTALL /tmp/ottr.tar.gz && rm /tmp/ottr.tar.gz
+
+#COPY install.R /tmp/install.R
+#RUN /tmp/install.R && rm -rf /tmp/downloaded_packages
+
+COPY r-packages/ottr.r /tmp/r-packages/
+RUN r /tmp/r-packages/ottr.r
+
+COPY r-packages/ph-290.r /tmp/r-packages/
+RUN r /tmp/r-packages/ph-290.r
+
+COPY r-packages/ph-142.r /tmp/r-packages/
+RUN r /tmp/r-packages/ph-142.r
+
+COPY r-packages/ph-252.r /tmp/r-packages/
+RUN r /tmp/r-packages/ph-252.r
+
+COPY r-packages/2021-spring-phw-272a.r /tmp/r-packages/
+RUN r /tmp/r-packages/2021-spring-phw-272a.r
+
+# Use simpler locking strategy
+COPY file-locks /etc/rstudio/file-locks
+
+ENTRYPOINT ["tini", "--"]

class-libs.R

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+#!/usr/bin/env Rscript
+
+class_libs_install_version <- function(class_name, class_libs) {
+  print(paste("Installing packages for", class_name))
+  for (i in seq(1, length(class_libs), 2)) {
+    installed_packages <- rownames(installed.packages())
+    package_name = class_libs[i]
+    version = class_libs[i+1]
+    # Only install packages if they haven't already been installed!
+    # devtools doesn't do that by default
+    if (!package_name %in% installed_packages) {
+      print(paste("Installing", package_name, version))
+      devtools::install_version(package_name, version, quiet=TRUE)
+    } else {
+      # FIXME: This ignores version incompatibilities :'(
+      print(paste("Not installing", package_name, " as it is already installed"))
+    }
+  }
+  print(paste("Done installing packages for", class_name))
+}

environment.yml

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+dependencies:
+- pip
+- syncthing==1.18.6
+- jupyter-server-proxy==4.2.0
+- jupyter-rsession-proxy==2.2.0
+- pip:
+  # bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
+  - traitlets==5.9.0
+  # - -r /tmp/infra-requirements.txt
+  # RStudio support
+  - otter-grader==2.2.7
+  # for notebook exporting
+  - nbconvert[webpdf]==7.16.4
+  - nb2pdf==0.6.2
+  - nbpdfexport==0.2.1
+  # pulled in by ottr, if not pinned to 1.16.2, 1.16.3 causes DH-323
+  - jupytext==1.16.2

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 $0)
+MAMBAFORGE_VERSION=22.9.0-2
+
+URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh"
+INSTALLER_PATH=/tmp/mambaforge-installer.sh
+
+# make sure we don't do anything funky with user's $HOME
+# since this is run as root
+unset HOME
+
+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

install.R

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+#!/usr/bin/env r
+
+source("/tmp/class-libs.R")
+
+# install ottr, needs to go first issue #3216, #3263
+devtools::install_github('ucbds-infra/ottr', ref='0.1.0', upgrade_dependencies=FALSE, quiet=FALSE)

r-packages/.ipynb_checkpoints/Untitled-checkpoint.ipynb

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+{
+ "cells": [],
+ "metadata": {},
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

r-packages/2021-spring-phw-272a.r

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+#!/usr/bin/env Rscript
+
+source("/tmp/class-libs.R")
+
+class_name = "PHW 272a Spring 2021"
+class_libs = c(
+  "ggmap", "3.0.0",
+  "tmap", "3.3-2",
+  "rgdal", "1.5-28"
+)
+class_libs_install_version(class_name, class_libs)

r-packages/ottr.r

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+#!/usr/bin/env Rscript
+# From https://github.com/berkeley-dsep-infra/datahub/issues/3403
+
+print("Installing packages for ottr")
+devtools::install_version("ottr", version = "1.1.4", repos = "https://cran.r-project.org", upgrade = "never", quiet = FALSE)
+print("Done installing packages for ottr")

r-packages/ph-142.r

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+#!/usr/bin/env Rscript
+# From https://github.com/berkeley-dsep-infra/datahub/issues/881
+print("Installing packages for PH142")
+
+source("/tmp/class-libs.R")
+
+class_name = "PH142"
+
+class_libs = c(
+  "fGarch", "3042.83.2",
+  "SASxport", "1.7.0",
+  "googlesheets", "0.3.0",
+  "googledrive", "1.0.1",
+  "ggrepel", "0.9.0",
+  "infer", "0.5.3",
+  "janitor", "2.1.0",
+  "latex2exp", "0.4.0",
+  "measurements", "1.4.0",
+  "dagitty", "0.3-0",
+  "cowplot", "1.1.1",
+  "patchwork", "1.1.1",
+  "tigris", "1.0",
+  "googlesheets4", "1.0.0",
+  "coxed", "0.3.3"
+)
+
+class_libs_install_version(class_name, class_libs)
+
+print("Done installing packages for PH142")

r-packages/ph-252.r

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+#!/usr/bin/env Rscript
+# For https://github.com/berkeley-dsep-infra/datahub/issues/2556
+# For https://github.com/berkeley-dsep-infra/datahub/issues/2524
+# For https://github.com/berkeley-dsep-infra/datahub/issues/2748
+# For https://github.com/berkeley-dsep-infra/datahub/issues/2788
+# Fall 2021
+print("Installing packages for PH 252")
+
+source("/tmp/class-libs.R")
+
+class_name = "PH 252"
+
+class_libs = c(
+  "foreign", "0.8-81",
+  "blm", "2013.2.4.4",
+  "geepack", "1.3-2",
+  "multcomp", "1.4-17",
+  "epitools", "0.5-10.1",
+  "rms", "6.2-0",
+  "lmtest","0.9-38",
+  "car","3.0-10",
+  "SurvRegCensCov","1.4",
+  "ProfileLikelihood","1.1",
+  "biostat3","0.1.5"
+)
+
+devtools::install_github('cran/epi', ref='06efd3f', upgrade_dependencies=FALSE, quiet=FALSE)
+devtools::install_github('kaz-yos/tableone', ref='7cfcd71', upgrade_dependencies=FALSE, quiet=FALSE)
+
+class_libs_install_version(class_name, class_libs)
+
+print("Done installing packages for PH 252")

r-packages/ph-290.r

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+#!/usr/bin/env Rscript
+# For https://github.com/berkeley-dsep-infra/datahub/issues/1921
+print("Installing packages for PH 290W")
+
+source("/tmp/class-libs.R")
+
+class_name = "PH 290W"
+
+class_libs = c(
+  "kableExtra", "1.3.1",
+  "plotly", "4.9.2.2",
+  "ggthemes", "4.2.0",
+  "formattable", "0.2.1"
+)
+
+class_libs_install_version(class_name, class_libs)