Merge pull request #14 from ryanlovett/spring-2025

Update for Spring 2025.

Dockerfile

@@ -1,5 +1,5 @@
-FROM rocker/geospatial:4.4.1
-# https://github.com/rocker-org/rocker-versioned2/wiki/geospatial_e06f866673fa
+FROM rocker/geospatial:4.4.2
+# https://github.com/rocker-org/rocker-versioned2/wiki/geospatial_69e6b17dd7e3
 
 ENV NB_USER=rstudio
 ENV NB_UID=1000
@@ -43,15 +43,15 @@ RUN apt-get update && \
 
 # While quarto is included with rocker/verse, we sometimes need different
 # versions than the default. For example a newer version might fix bugs.
-ENV _QUARTO_VERSION=1.4.549
+ENV _QUARTO_VERSION=1.6.40
 RUN curl -L -o /tmp/quarto.deb https://github.com/quarto-dev/quarto-cli/releases/download/v${_QUARTO_VERSION}/quarto-${_QUARTO_VERSION}-linux-amd64.deb
 RUN apt-get update > /dev/null && \
     apt-get install /tmp/quarto.deb > /dev/null && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/* && \
     rm -f /tmp/quarto.deb
 
-ENV SHINY_SERVER_URL=https://download3.rstudio.org/ubuntu-18.04/x86_64/shiny-server-1.5.21.1012-amd64.deb
+ENV SHINY_SERVER_URL=https://download3.rstudio.org/ubuntu-18.04/x86_64/shiny-server-1.5.22.1017-amd64.deb
 RUN curl --silent --location --fail ${SHINY_SERVER_URL} > /tmp/shiny-server.deb && \
     apt install --no-install-recommends --yes /tmp/shiny-server.deb && \
     rm /tmp/shiny-server.deb
@@ -66,18 +66,21 @@ RUN wget --quiet -O /tmp/chrome.deb https://dl.google.com/linux/direct/google-ch
 
 RUN install -d -o ${NB_USER} -g ${NB_USER} ${CONDA_DIR}
 
+# Install conda environment as our user
 USER ${NB_USER}
-COPY install-mambaforge.bash /tmp/install-mambaforge.bash
-RUN /tmp/install-mambaforge.bash
+COPY --chown=1000:1000 install-miniforge.bash /tmp/install-miniforge.bash
+RUN /tmp/install-miniforge.bash
+RUN rm -f /tmp/install-miniforge.bash
 
 USER root
 RUN rm -rf ${HOME}/.cache
 
 USER ${NB_USER}
-COPY environment.yml /tmp/environment.yml
+COPY --chown=1000:1000 environment.yml /tmp/environment.yml
 
 RUN mamba env update -p ${CONDA_DIR} -f /tmp/environment.yml && \
 	mamba clean -afy
+RUN rm -f /tmp/environment.yml
 
 # Prepare VS Code extensions
 USER root
@@ -93,14 +96,14 @@ RUN ${CONDA_DIR}/bin/code-server --extensions-dir ${VSCODE_EXTENSIONS} --install
 RUN ${CONDA_DIR}/bin/code-server --extensions-dir ${VSCODE_EXTENSIONS} --install-extension ms-python.python
 RUN ${CONDA_DIR}/bin/code-server --extensions-dir ${VSCODE_EXTENSIONS} --install-extension quarto.quarto
 
-# Install IRKernel
-RUN R --quiet -e "install.packages('IRkernel', quiet = TRUE)" && \
-    R --quiet -e "IRkernel::installspec(prefix='${CONDA_DIR}')"
+# Install R libraries as our user
+USER ${NB_USER}
 
-COPY class-libs.R /tmp/class-libs.R
+COPY install-r-packages.r /tmp/
+RUN Rscript /tmp/install-r-packages.r
 
-COPY r-packages/2024-fall-stat-20.r /tmp/r-packages/
-RUN r /tmp/r-packages/2024-fall-stat-20.r
+# Install IRKernel kernel
+RUN R --quiet -e "IRkernel::installspec(prefix='${CONDA_DIR}')"
 
 # Configure locking behavior
 COPY file-locks /etc/rstudio/file-locks

environment.yml

@@ -6,25 +6,38 @@ channels:
 dependencies:
 # Matches version in images/hub/Dockerfile
 - jupyterhub==4.1.6
-- jupyterlab==4.2.5
+
+- jupyterlab==4.3.4
+- notebook==7.3.2
+- ipykernel = 6.29.5
+- ipywidgets==8.1.5
+- nbgitpuller==1.2.1
+- appmode==1.0.0
+- jupyter-resource-usage==1.1.0
 - jupyter-server-proxy==4.4.0
 - jupyter-rsession-proxy==2.2.1
+- jupyterlab-git==0.50.2
+- python==3.12.*
+
+# syncthing for dropbox-like functionality
 - jupyter-syncthing-proxy==1.0.3
+
+# jupyter archival tool for easy user downloads
 - jupyter-archive==3.4.0
-- jupyter-resource-usage==1.1.0
+
+# vscode
 - jupyter-vscode-proxy==0.6
-- notebook==7.2.2
-- nbconvert==7.6.0
-- nbgitpuller==1.2.1
-- ipywidgets==8.0.7
-# bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
-#- traitlets=5.9.*
-- matplotlib==3.8.3
-- shiny==1.0.0
-- appmode==1.0.0
-- syncthing==1.22.2
+- code-server==4.96.2
+
+# jupyterbook
+- mystmd==1.3.19
+
+# gh-scoped-creds needs a newer version of git than what jammy provides
 - gh-scoped-creds==4.1
-- code-server==4.23.1
+- git==2.47.0
+
+- matplotlib=3.10.*
+- shiny==1.2.1
 - pip
 - pip:
   - git-credential-helpers==0.2
@@ -35,3 +48,4 @@ dependencies:
   - jupyterlab-quarto==0.3.5
   - nb2pdf==0.6.2
   - nbpdfexport==0.2.1
+  - nbconvert[webpdf]

install-mambaforge.bash → install-miniforge.bash

@@ -1,16 +1,12 @@
 #!/bin/bash
-# This downloads and installs a pinned version of mambaforge
+# This downloads and installs a pinned version of miniforge
 set -ex
 
 cd $(dirname $0)
-MAMBAFORGE_VERSION=24.9.2-0
+MINIFORGE_VERSION='24.11.2-1'
 
-URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Miniforge3-${MAMBAFORGE_VERSION}-Linux-x86_64.sh"
-INSTALLER_PATH=/tmp/mambaforge-installer.sh
-
-# make sure we don't do anything funky with user's $HOME
-# since this is run as root
-#unset HOME
+URL="https://github.com/conda-forge/miniforge/releases/download/${MINIFORGE_VERSION}/Miniforge3-${MINIFORGE_VERSION}-Linux-x86_64.sh"
+INSTALLER_PATH=/tmp/miniforge-installer.sh
 
 export XDG_CACHE_HOME=$(mktemp)
 
@@ -28,7 +24,7 @@ conda config --system --set show_channel_urls true
 # 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
+echo > ${CONDA_DIR}/conda-meta/history
 
 # Clean things out!
 conda clean --all -f -y

install-r-packages.r

@@ -0,0 +1,66 @@
+#!/usr/bin/env Rscript
+
+# Function to install R packages
+install_packages_with_versions <- function(packages) {
+  available <- available.packages()
+  to_install <- names(packages)[!(names(packages) %in% rownames(installed.packages()))]
+
+  if (length(to_install) > 0) {
+    install.packages(to_install, available = available,
+                     versions = packages[to_install],
+                     dependencies = TRUE)
+  } else {
+    cat("All packages are already installed.\n")
+  }
+}
+
+# List of packages to ensure are installed
+required_packages <- c("remotes", "devtools")
+
+# Check and install required packages
+new_packages <- required_packages[!sapply(required_packages, requireNamespace, quietly = TRUE)]
+if (length(new_packages) > 0) {
+  install.packages(new_packages)
+}
+
+
+packages = list(
+    "fivethirtyeight" = "0.6.2",
+    "gapminder" = "1.0.0",
+    "janitor" = "2.2.1",
+    "openintro" = "2.5.0",
+    "pagedown" = "0.22",
+    "palmerpenguins" = "0.1.1",
+    "patchwork" = "1.3.0",
+    "showtext" = "0.9-7",
+    "swirl" = "2.4.5",
+    "tidycensus" = "1.6.7",
+    "tidymodels" = "1.2.0",
+    "tigris" = "2.1",
+    "unvotes" = "0.3.0",
+    "xaringanthemer" = "0.4.3",
+    "rmarkdown" = "2.29",
+    "plotly" = "4.10.4",
+    "reshape2" = "1.4.4",
+    "kableExtra" = "1.4.0",
+    "infer" = "1.0.7",
+    "countdown" = "0.4.0",
+    "ggrepel" = "0.9.6",
+    "ggthemes" = "5.1.0",
+    "latex2exp" = "0.9.6",
+    "markdown" = "1.13",
+    "downlit" = "0.4.4",
+    "xml2" = "1.3.6",
+    "gt" = "0.11.1",
+    "quarto" = "1.4.4",
+    "fs" = "1.6.5",
+    "rsample" = "1.2.1",
+    "IRkernel" = "1.3.2"
+)
+
+install_packages_with_versions(packages)
+
+devtools::install_github("mdbeckman/dcData", ref="a900560")
+devtools::install_github("hadley/emo@3f03b11")
+devtools::install_github("andrewpbray/boxofdata@8afd934")
+devtools::install_github("stat20/stat20data@2536a78")