[DH-273] bumping package versions

Dockerfile

@@ -48,15 +48,19 @@ RUN apt-get update > /dev/null && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
-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
+
+# needed for building on mac see DH-394
+RUN chown -Rh ${NB_USER}:${NB_USER} ${HOME}
 
 USER ${NB_USER}
 
-COPY environment.yml /tmp/environment.yml
-COPY infra-requirements.txt /tmp/infra-requirements.txt
+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}
@@ -104,4 +108,8 @@ RUN install2.r --error --skipinstalled \
 # Use simpler locking strategy
 COPY file-locks /etc/rstudio/file-locks
 
+# Doing a little cleanup
+RUN rm -rf /tmp/downloaded_packages
+RUN rm -rf ${HOME}/.cache
+
 ENTRYPOINT ["tini", "--"]

environment.yml

@@ -4,20 +4,44 @@ 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.*
+# Items required for basic level functionality
+- gh-scoped-creds==4.1
+- git==2.47.0
+- 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
+- nbgitpuller==1.2.1
+- notebook==7.2.2
+- python==3.11.*
+
+# vscode
+- code-server==4.23.1
+- jupyter-vscode-proxy==0.6
+
+# other packages
+- syncthing==1.27.12
+- jupyter-rsession-proxy==2.2.1
+- jupyter-server-proxy==4.4.0
+- jupyter-syncthing-proxy==1.0.3
+- traitlets=5.14.3
+- appmode==1.0.0
+- ipywidgets==8.1.2
+
+- pip==24.2
 - 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
+  # 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
+

install-mambaforge.bash → install-miniforge.bash

@@ -3,10 +3,10 @@
 set -ex
 
 cd $(dirname $0)
-MAMBAFORGE_VERSION='23.1.0-1'
+MINIFORGE_VERSION='24.7.1-2'
 
-URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh"
-INSTALLER_PATH=/tmp/mambaforge-installer.sh
+URL="https://github.com/conda-forge/miniforge/releases/download/${MINIFORGE_VERSION}/Miniforge3-${MINIFORGE_VERSION}-Linux-x86_64.sh"
+INSTALLER_PATH=/tmp/miniforge-installer.sh
 
 wget --quiet $URL -O ${INSTALLER_PATH}
 chmod +x ${INSTALLER_PATH}
@@ -33,6 +33,6 @@ 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}
+chown -Rh $NB_USER:$NB_USER ${CONDA_DIR}
 
 conda list -n root