Merge pull request #6 from ryanlovett/spring-2025

Update for Spring 2025

Dockerfile

@@ -1,20 +1,25 @@
-FROM rocker/geospatial:4.4.1
+FROM rocker/geospatial:4.4.2
+# https://github.com/rocker-org/rocker-versioned2/wiki/geospatial_69e6b17dd7e3
 
-ENV NB_USER rstudio
-ENV NB_UID 1000
-ENV CONDA_DIR /srv/conda
+ENV NB_USER=rstudio
+ENV NB_UID=1000
+ENV CONDA_DIR=/srv/conda
 
 # Set ENV for all programs...
-ENV PATH ${CONDA_DIR}/bin:$PATH
+ENV PATH=${CONDA_DIR}/bin:$PATH
+
+# Pick up rocker's default TZ
+ENV TZ=Etc/UTC
 
 # And set ENV for R! It doesn't read from the environment...
+RUN echo "TZ=${TZ}" >> /usr/local/lib/R/etc/Renviron.site
 RUN echo "PATH=${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/${NB_USER}
+ENV HOME=/home/${NB_USER}
 
 WORKDIR ${HOME}
 
@@ -28,7 +33,6 @@ RUN apt-get update > /dev/null && \
             libx11-xcb1 \
             libxtst6 \
             libxrandr2 \
-            libasound2 \
             libpangocairo-1.0-0 \
             libatk1.0-0 \
             libatk-bridge2.0-0 \
@@ -48,22 +52,25 @@ RUN apt-get update > /dev/null && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
-COPY --chown=1000:1000 install-miniforge.bash /tmp/install-miniforge.bash
-RUN /tmp/install-miniforge.bash
-RUN rm -f /tmp/install-miniforge.bash
-
-# needed for building on mac see DH-394
-RUN chown -Rh ${NB_USER}:${NB_USER} ${HOME}
+RUN install -d -o ${NB_USER} -g ${NB_USER} ${CONDA_DIR}
 
 USER ${NB_USER}
+COPY --chown=1000:1000 install-mambaforge.bash /tmp/install-mambaforge.bash
+RUN /tmp/install-mambaforge.bash
+RUN rm -f /tmp/install-mambaforge.bash
+
+USER root
+RUN rm -rf ${HOME}/.cache
 
+USER ${NB_USER}
 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
 
 # DH-327, very similar to what was done for datahub in DH-164
-ENV PLAYWRIGHT_BROWSERS_PATH ${CONDA_DIR}
+ENV PLAYWRIGHT_BROWSERS_PATH=${CONDA_DIR}
 RUN playwright install chromium
 
 # Install IRKernel

environment.yml

@@ -6,16 +6,17 @@ channels:
 dependencies:
 # Items required for basic level functionality
 - gh-scoped-creds==4.1
-- git==2.47.0
+- git==2.47.1
+- jupyter-archive=3.4.0
 - jupyter-resource-usage=1.1.0
 - jupyterhub==4.1.6
-- jupyterlab==4.2.5
-- jupyter_server==2.14.2
-- jupyterlab-git==0.50.1
-- jupytext==1.16.4
+- jupyterlab==4.3.4
+- jupyter_server==2.15.0
+- jupyterlab-git==0.50.2
+- jupytext==1.16.6
 - nbgitpuller==1.2.1
-- notebook==7.2.2
-- python==3.11.*
+- notebook==7.3.2
+- python==3.12.*
 
 # vscode
 - code-server==4.23.1
@@ -39,9 +40,6 @@ dependencies:
   - nb2pdf==0.6.2
   - nbpdfexport==0.2.1
   # from infra-requirements
-  - jupyter-archive==3.4.0  
-  - rise==5.7.1
   - git+https://github.com/shaneknapp/python-popularity-contest.git@add-error-handling
   - git-credential-helpers==0.2
-  - jupyter-tree-download==1.0.1
-
+  - rise==5.7.1

install-miniforge.bash → install-mambaforge.bash

@@ -3,15 +3,17 @@
 set -ex
 
 cd $(dirname $0)
-MINIFORGE_VERSION='24.7.1-2'
+MAMBAFORGE_VERSION='24.11.0-0'
 
-URL="https://github.com/conda-forge/miniforge/releases/download/${MINIFORGE_VERSION}/Miniforge3-${MINIFORGE_VERSION}-Linux-x86_64.sh"
-INSTALLER_PATH=/tmp/miniforge-installer.sh
+URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Miniforge3-${MAMBAFORGE_VERSION}-Linux-x86_64.sh"
+INSTALLER_PATH=/tmp/mambaforge-installer.sh
+
+export XDG_CACHE_HOME=$(mktemp)
 
 wget --quiet $URL -O ${INSTALLER_PATH}
 chmod +x ${INSTALLER_PATH}
 
-bash ${INSTALLER_PATH} -b -p ${CONDA_DIR}
+bash ${INSTALLER_PATH} -f -b -p ${CONDA_DIR}
 export PATH="${CONDA_DIR}/bin:$PATH"
 
 # Do not attempt to auto update conda or dependencies
@@ -22,7 +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
@@ -31,8 +33,6 @@ conda clean --all -f -y
 rm ${INSTALLER_PATH}
 
 # Remove the pip cache created as part of installing mambaforge
-rm -rf /root/.cache
-
-chown -Rh $NB_USER:$NB_USER ${CONDA_DIR}
+rm -rf ${XDG_CACHE_HOME}
 
 conda list -n root