Bringing in image directory from deployment repo

Rprofile.site

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+# Use RStudio's CRAN mirror to get binary packages. "latest" just means it has
+# all available versions. We can specify version numbers in
+# devtools::install_version.
+options(
+  repos = c(
+    CRAN = "https://packagemanager.rstudio.com/all/__linux__/jammy/latest"
+  )
+)
+
+# RStudio sets the HTTPUserAgent option which causes it to download binaries,
+# rather than source, from the Posit Public Package Manager. In order for the
+# RStudio terminal, Jupyter terminal, Jupyter R notebook, or anything else to
+# do the same, we must manually set HTTPUserAgent. This speeds up package
+# installation.
+# We fake rstudio version because `RStudio.Version()$version` is only available
+# when we are in RStudio.
+options(
+  HTTPUserAgent = sprintf(
+    "RStudio Server (%s); R (%s)",
+    "2022.7.1.554",
+    paste(getRversion(), R.version$platform, R.version$arch, R.version$os)
+  )
+)

apt.txt

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+# useful utilities
+tar
+less
+vim
+
+# for nbconvert, knitr, etc.
+texlive-xetex
+texlive-fonts-recommended
+texlive-plain-generic
+# provides FandolSong-Regular.otf for issue #2714
+texlive-lang-chinese
+
+# for rstudio
+lsb-release
+libclang-dev
+
+# Used by littler for IRkernel::installspec
+libzmq5

environment.yml

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+name: dashboard-image
+
+channels:
+- conda-forge
+- pytorch
+
+dependencies:
+- python==3.11.*
+- git==2.39.1
+- jupyterhub==4.1.6
+- jupyter_app_launcher==0.2.1
+- jupyter-cache==1.0.0
+- jupyter-resource-usage==1.0.0
+- jupyterlab==4.0.11
+- jupyterlab-favorites==3.0.0
+# Install myst for generating dashboards
+- jupyterlab-myst==2.4.2
+- jupyterlab_server==2.23.0
+- jupyterlab_widgets==3.0.8
+- jupyter_server==2.7.0
+- nbgitpuller==1.2.1
+- notebook==7.0.7
+- folium==0.14.0
+- ipywidgets==8.0.7
+- jupyter-archive==3.4.0
+- matplotlib==3.7.1
+# Install myst markdown for generating dashboards
+- mystmd==1.2.9
+- numpy==1.24.2
+- pandas==2.0.2
+- plotly==5.13.1
+- requests==2.28.2
+- scikit-image==0.19.3
+- seaborn==0.12.2
+# Spring 2024 Econ 148 Packages
+- geopandas==0.14.2
+- geopy==2.4.1
+- pycountry==22.3.5
+# Install voila and voici for generating voila dashboards
+- voila==0.5.7
+- voici==0.6.1
+# Adding more data tools to make this image comprehensive
+- dash==2.17.1
+- bokeh==3.4.0
+- panel==1.4.5
+- datashader==0.16.3
+- streamlit=1.38.0
+#- jupyter-containds=0.2.2

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.R

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+#!/usr/bin/env R
+
+# Function to install R packages with specific versions
+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))
+}
+
+# R packages to be installed that aren't from apt
+# Combination of informal requests & rocker image suggestions
+# Some of these were already in datahub image
+cran_packages = c(
+  "BiocManager", "1.30.21",
+  "IRkernel", "1.3.2",
+  "rmarkdown", "2.22",
+  "shiny", "1.7.4"
+)
+
+class_libs_install_version("Base packages", cran_packages)

rsession.conf

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+# Use binary packages!
+r-cran-repos=https://packagemanager.rstudio.com/all/__linux__/jammy/latest

runtime.txt

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+r-4.3.1-2023-08-01