chore: update jupyterlab (#466)

This also switches the base dependency handling to conda to avoid conda/pip conflicts.

.github/dependabot.yml

@@ -40,7 +40,7 @@ updates:
 # python dependencies
 #
 
-- package-ecosystem: "pip"
+- package-ecosystem: "conda"
   directory: "/docker/py"
   schedule:
     interval: daily

docker/py/Dockerfile

@@ -14,9 +14,8 @@ RUN sed -i '/nodejs/d' /opt/conda/conda-meta/pinned
 # switch to the notebook user
 USER $NB_USER
 # install jupyterlab, papermill, git extension and renku-jupyterlab-ts
-COPY requirements.txt /tmp/requirements.txt
-RUN python3 -m pip install --no-cache-dir -U pip && \
-    python3 -m pip install --no-cache-dir -r /tmp/requirements.txt && \
+COPY environment.yml /tmp/environment.yml
+RUN mamba env update -f /tmp/environment.yml && \
     jupyter labextension disable "@jupyterlab/apputils-extension:announcements" && \
     rm -rf "/home/${NB_USER}/.cache"
 
@@ -81,7 +80,7 @@ RUN mkdir -p "$HOME/.ssh" && \
 # configure bash and shell prompt
 ENV PATH=$HOME/.local/bin:$PATH:$HOME/.renku/bin
 COPY --chown=1000:100 bashrc /renku/
-RUN cat "/renku/bashrc" >> "${HOME}/.bashrc" 
+RUN cat "/renku/bashrc" >> "${HOME}/.bashrc"
 
 COPY entrypoint.sh /entrypoint.sh
 
@@ -97,7 +96,8 @@ COPY sshd_config /opt/ssh/sshd_config
 
 RUN chown -R 0:100 /opt/ssh/ && \
     chmod -R u=rwX,g=rX,o= /opt/ssh && \
-    chmod -R u=rwX,g=rwX,o= /opt/ssh/pid
+    chmod -R u=rwX,g=rwX,o= /opt/ssh/pid && \
+    rm -rf /opt/conda
 
 ENTRYPOINT [ "tini", "--", "/entrypoint.sh" ]
 

docker/py/environment.yml

@@ -0,0 +1,17 @@
+name: base
+channels:
+  - conda-forge
+dependencies:
+  - bleach>5.0.0 # closes #300
+  - certifi>=2022.12.7 # not directly required, pinned by Snyk to avoid a vulnerability
+  - Jinja2<3.1 # because of https://github.com/jupyter/nbconvert/issues/1742
+  - jupyter-server-proxy==4.3.0
+  - jupyterlab>4.0,<5.0
+  - jupyterlab-git==0.50.1
+  - mistune>=2.0.1 # not directly required, pinned by Snyk to avoid a vulnerability
+  - papermill~=2.6.0
+  - requests>=2.20.0
+  - setuptools>=65.5.1 # not directly required, pinned by Snyk to avoid a vulnerability
+  - virtualenv>=20.7.2
+  - ipython>=8.10.0 # not directly required, pinned by Snyk to avoid a vulnerability
+  - tornado>=6.3.3 # not directly required, pinned by Snyk to avoid a vulnerability

docker/vnc/Dockerfile

@@ -68,9 +68,8 @@ RUN chmod +x /home/jovyan/Desktop/gitk.desktop && \
 # Install the jupyter extensions
 USER ${NB_USER}
 
-RUN mamba install -y jupyter-server-proxy numpy websockify -c conda-forge \
-    && jupyter labextension install @jupyterlab/server-proxy \
-    && mamba clean -y --all
+RUN mamba install -y numpy websockify -c conda-forge && \
+    mamba clean -y --all
 
 COPY jupyter_notebook_config.py /home/jovyan/.jupyter/jupyter_notebook_config.py
 

tests/package.json

@@ -9,7 +9,7 @@
   "author": "",
   "license": "ISC",
   "devDependencies": {
-    "@renku/notebooks-cypress-tests": "^0.0.11",
+    "@renku/notebooks-cypress-tests": "^0.0.13",
     "@types/node": "^18.7.18",
     "axios": "^1.6.0",
     "axios-cookiejar-support": "^4.0.3",