From d79cda9ed52bbebfdda2c309056065d52b45b7cf Mon Sep 17 00:00:00 2001
From: Emma Ai <emma.ai@ga.gov.au>
Date: Mon, 5 Aug 2024 07:46:21 +0000
Subject: [PATCH] upgrade jupyterlab>4

---
 docker/Dockerfile       |  5 +++--
 docker/env.yaml         | 20 +++++++++-----------
 docker/requirements.txt |  8 ++++----
 3 files changed, 16 insertions(+), 17 deletions(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index 76aed48..2000afc 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -36,9 +36,9 @@ ENV LC_ALL=C.UTF-8 \
     PATH=/env/bin:$PATH
 
 USER $nb_user
+
 # NOTE - JupyterLab extensions can now be distributed as prebuilt extensions and available to PyPI
 RUN echo "Enable jupyter lab extensions" \
-  && jupyter labextension install jupyterlab-topbar-extension jupyterlab-theme-toggle \
   && jupyter labextension list \
   && echo "...done"
 
@@ -46,11 +46,12 @@ RUN echo "Enable server extensions" \
    && jupyter server extension enable  --py jupyterlab_iframe --sys-prefix \
    && jupyter server extension enable  --py jupyter_resource_usage --sys-prefix \
    && jupyter server extension list \
+   && jupyter lab build \
    && echo "...done"
 
 RUN echo "Install AWS CLI v2" \
    && curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "/tmp/awscliv2.zip" \
-   && unzip /tmp/awscliv2.zip -d /tmp \
+   && unzip /tmp/awscliv2.zip -d /tmp > /dev/null \
    && /tmp/aws/install -i /env/bin/aws-cli -b /env/bin \
    && aws --version \
    && rm -f /tmp/awscliv2.zip \
diff --git a/docker/env.yaml b/docker/env.yaml
index 58babce..e4acf11 100644
--- a/docker/env.yaml
+++ b/docker/env.yaml
@@ -168,6 +168,7 @@ dependencies:
 # Scientific Stack
   - gsl
   - cgal-cpp
+  - cgal
   - boost
   - openmp
   - muparser
@@ -178,7 +179,8 @@ dependencies:
   - tensorflow>=2.16
   - xgboost
   - zarr
-  - bokeh=3.2.2
+  - bokeh
+    # - bokeh=3.2.2
   - descartes
   - matplotlib
   - seaborn
@@ -211,22 +213,17 @@ dependencies:
   - black
   - python-jose
   - ecdsa
-  - jupyter
-  - jupyterlab
-  - jupyterlab_code_formatter<3.0
+  - jupyterlab>=4.0
+  - jupyterlab_code_formatter<3.0 # Non-caught error in >= 3.0
   - jupyterlab-spellchecker
-  - jupyterlab-code-snippets
-  - jupyterlab-dash
   - jupyterlab-geojson
   - jupyterlab-git
   - jupyterlab-github
   - jupyterlab_iframe
   - jupyterlab_widgets
-  - jupyterlab-topbar
-  - jupyterlab-system-monitor
-  - jupyterhub
-  - jupytext<1.16
-  - jupyterlab_pygments<0.3.0
+  - jupyterhub=4.1.5 # Match hub version
+  - jupytext
+  - jupyterlab_pygments
   - jupyter-resource-usage
   - jupyter_server
   - jupyter-server-proxy
@@ -241,6 +238,7 @@ dependencies:
   - isort
   - nbdime
   - nbgitpuller
+  - notebook<7.0 # Compatible with nbconvert
   - mypy
   - prompt-toolkit # because of line_profiler/ipython
   - nbconvert # because of jupyter_contrib_nbextensions
diff --git a/docker/requirements.txt b/docker/requirements.txt
index 348af0e..412ac5c 100644
--- a/docker/requirements.txt
+++ b/docker/requirements.txt
@@ -1,14 +1,14 @@
 cognitojwt
 nbval
-cgal
 line-profiler
 jupyterlab-logout
 jupyter-contrib-core
 jupyter-contrib-nbextensions
 jupyter-nbextensions-configurator
-# pin for jupyterlab=3.x
-jupyterlab-topbar-text==0.6.2
-jupyterlab-logout==0.5.0
+jupyterlab-code-snippets
+jupyterlab-topbar-text
+jupyterlab-logout
+jupyterlab-theme-toggler
 
 # ODC/DEA: these are installed in builder stage
 otps