From 8d3557c3cbe745848e7aa49b977468f05376cda3 Mon Sep 17 00:00:00 2001
From: Pan Luo <pan.luo@ubc.ca>
Date: Tue, 26 Nov 2024 15:48:09 -0800
Subject: [PATCH] Update user image base to hub-5.2.0

---
 .github/workflows/build.yml | 40 ++++++++++++++++++++++++++++++++++---
 Dockerfile                  | 22 ++++++++++----------
 2 files changed, 48 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 9e3e76d..70d6d1a 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -14,14 +14,48 @@ on:
 jobs:
   build:
     name: Build Image
-    runs-on: self-hosted 
+    #runs-on: self-hosted
+    runs-on: ubuntu-latest
     # These permissions are needed to interact with GitHub's OIDC Token endpoint.
     permissions:
       id-token: write
       contents: read
-    steps:         
+    steps:
+    - name: Check disk space
+      run: df . -h
+    - name: Free disk space
+        run: |
+          sudo docker rmi $(docker image ls -aq) >/dev/null 2>&1 || true
+          sudo rm -rf \
+            /usr/share/dotnet /usr/local/lib/android /opt/ghc \
+            /usr/local/share/powershell /usr/share/swift /usr/local/.ghcup \
+            /usr/lib/jvm || true
+          echo "some directories deleted"
+          sudo apt install aptitude -y >/dev/null 2>&1
+          sudo aptitude purge aria2 ansible azure-cli shellcheck rpm xorriso zsync \
+            esl-erlang firefox gfortran-8 gfortran-9 google-chrome-stable \
+            google-cloud-sdk imagemagick \
+            libmagickcore-dev libmagickwand-dev libmagic-dev ant ant-optional kubectl \
+            mercurial apt-transport-https mono-complete libmysqlclient \
+            unixodbc-dev yarn chrpath libssl-dev libxft-dev \
+            libfreetype6 libfreetype6-dev libfontconfig1 libfontconfig1-dev \
+            snmp pollinate libpq-dev postgresql-client powershell ruby-full \
+            sphinxsearch subversion mongodb-org azure-cli microsoft-edge-stable \
+            -y -f >/dev/null 2>&1
+          sudo aptitude purge google-cloud-sdk -f -y >/dev/null 2>&1
+          sudo aptitude purge microsoft-edge-stable -f -y >/dev/null 2>&1 || true
+          sudo apt purge microsoft-edge-stable -f -y >/dev/null 2>&1 || true
+          sudo aptitude purge '~n ^mysql' -f -y >/dev/null 2>&1
+          sudo aptitude purge '~n ^php' -f -y >/dev/null 2>&1
+          sudo aptitude purge '~n ^dotnet' -f -y >/dev/null 2>&1
+          sudo apt-get autoremove -y >/dev/null 2>&1
+          sudo apt-get autoclean -y >/dev/null 2>&1
+          echo "some packages purged"
+    - name: Check disk space
+      run: df . -h
+
     - name: Check out code
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Configure AWS credentials
       uses: aws-actions/configure-aws-credentials@v4
diff --git a/Dockerfile b/Dockerfile
index 075124d..415d7cf 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,7 +1,7 @@
 # sudo docker kill $(sudo docker ps -q);  sudo docker rm $(sudo docker ps -a -q); sudo docker rmi $(sudo docker images -q)
 # sudo docker build --squash --no-cache -t 032401129069.dkr.ecr.ca-central-1.amazonaws.com/jupyterhub:jupyterlab-open .
 
-ARG BASE_CONTAINER=quay.io/jupyter/datascience-notebook:hub-4.1.5
+ARG BASE_CONTAINER=quay.io/jupyter/datascience-notebook:hub-5.2.0
 #ARG BASE_CONTAINER=032401129069.dkr.ecr.ca-central-1.amazonaws.com/jupyterhub:jupyterlab-all
 FROM $BASE_CONTAINER
 
@@ -26,10 +26,11 @@ RUN apt-get update && \
     zsh \
     vim \
     htop \
-    build-essential \
     libcurl4-openssl-dev \
     libssl-dev \
     libxml2-dev \
+# future version of base image will remove nodejs, uncomment below after upgrade
+#    npm \
     gfortran && \
     ldconfig && \
     apt-get autoclean && \
@@ -41,11 +42,10 @@ USER ${NB_UID}
 # Install Conda Packages (Plotly, SageMath)
 RUN mamba create --yes -n sage sage python=3.11 && \
     mamba install --yes -c conda-forge -c plotly \
-    "sage" \
     "plotly" \
     "jupyterlab-spellchecker" \
     "dash" \
-    "xeus-cling" \
+#    "xeus-cling" \
     "openjdk" \
     "maven" \
     "ipython-sql" \
@@ -61,20 +61,20 @@ RUN R -e 'require(devtools); \
 # Install R packages
 RUN mamba install --yes -c conda-forge \
     'r-stargazer' \
-    'r-quanteda' \
-    'r-quanteda.textmodels' \
-    'r-quanteda.textplots' \
-    'r-quanteda.textstats' \
+#    'r-quanteda' \
+#    'r-quanteda.textmodels' \
+#    'r-quanteda.textplots' \
+#    'r-quanteda.textstats' \
     'r-caret' \
-    'r-ggiraph' \
+#    'r-ggiraph' \
     'r-ggextra' \
     'r-isocodes' \
     'r-urltools' \
     'r-ggthemes' \
     'r-modelsummary' \
     'r-nsyllable' \
-    'r-proxyc' \
-    'r-tidytext' \
+#    'r-proxyc' \
+#    'r-tidytext' \
     'r-car' && \
     mamba clean --all -f -y