Switch to nbclassic and Python 3.11.10

build.json

@@ -1,7 +1,7 @@
 {
   "variable": {
     "PYTHON_VERSION": {
-      "default": "3.9.13"
+      "default": "3.11.10"
     },
     "PGSQL_VERSION": {
       "default": "15"
@@ -16,7 +16,7 @@
       "default": "24.09.0"
     },
     "AIIDALAB_HOME_VERSION": {
-      "default": "25.02.0"
+      "default": "update/notebook-7"
     }
   }
 }

docker-bake.hcl

@@ -21,7 +21,7 @@ variable "AIIDALAB_HOME_VERSION" {
 }
 
 variable "JUPYTER_BASE_IMAGE" {
-  default = "jupyter/minimal-notebook:python-${PYTHON_VERSION}"
+  default = "quay.io/jupyter/minimal-notebook:python-${PYTHON_VERSION}"
 }
 
 variable "ORGANIZATION" {

stack/base-with-services/before-notebook.d/20_start-postgresql.sh

@@ -10,12 +10,12 @@ PSQL_LOGFILE="${PGDATA}/logfile"
 # -w waits until server is up
 PSQL_START_CMD="pg_ctl --timeout=180 -w -l ${PSQL_LOGFILE} start"
 
-MAMBA_RUN="mamba run -n aiida-core-services"
+CONDA_RUN="conda run -n aiida-core-services"
 
 # Initialize DB directory if it does not exist
 if [[ ! -d ${PGDATA} ]]; then
     mkdir "${PGDATA}"
-    ${MAMBA_RUN} initdb
+    ${CONDA_RUN} initdb
     echo "unix_socket_directories = '/tmp'" >> "${PGDATA}/postgresql.conf"
 else
     # Fix problem with kubernetes cluster that adds rws permissions to the group
@@ -30,4 +30,4 @@ else
 fi
 
 # Start the server
-${MAMBA_RUN} ${PSQL_START_CMD}
+${CONDA_RUN} ${PSQL_START_CMD}

stack/base-with-services/before-notebook.d/30_start-rabbitmq.sh

@@ -7,4 +7,4 @@ chmod 400 "/home/${NB_USER}/.erlang.cookie" || echo "erlang cookie not created y
 # NOTE: In arm64 build, rabbitmq is not installed via conda,
 # but the following incantation still works since
 # rabbitmq-server is available globally.
-mamba run -n aiida-core-services rabbitmq-server -detached
+conda run -n aiida-core-services rabbitmq-server -detached

stack/base/Dockerfile

@@ -60,7 +60,7 @@ COPY pip.conf "${CONDA_DIR}/pip.conf"
 # Update async_generator, certipy to satisfy `pip check`
 # https://github.com/aiidalab/aiidalab-docker-stack/issues/490
 # Install aiida-core and other shared requirements.
-RUN mamba update -y pip async_generator certipy && \
+RUN mamba update -y pip zstandard async_generator certipy && \
      mamba install --yes \
      aiida-core==${AIIDA_VERSION} \
      mamba-bash-completion \

stack/lab/Dockerfile

@@ -4,11 +4,9 @@ FROM base
 LABEL maintainer="AiiDAlab Team <[email protected]>"
 
 # By default, Jupyter Docker image launches the JupyterLab interface.
-# Here, we change it to the classic Jupyter Notebook which is used by AiiDAlab.
-# In the future, we might want to switch to other options such as `nbclassic` or `retro`,
-# but the `nbclassic` is not supported because of appmode.
-# see: https://jupyter-docker-stacks.readthedocs.io/en/latest/using/common.html#switching-back-to-the-classic-notebook-or-using-a-different-startup-command
-ENV DOCKER_STACKS_JUPYTER_CMD=notebook
+# Here, we change it to the nbclassic Jupyter Notebook which is used by AiiDAlab.
+# https://jupyter-docker-stacks.readthedocs.io/en/latest/using/common.html#switching-back-to-the-classic-notebook-or-using-a-different-startup-command
+ENV DOCKER_STACKS_JUPYTER_CMD=nbclassic
 
 USER root
 WORKDIR /opt/
@@ -17,6 +15,7 @@ WORKDIR /opt/
 ARG AIIDALAB_VERSION
 RUN mamba install --yes \
      aiidalab=${AIIDALAB_VERSION} \
+     appmode=1.0.0 \
      && mamba clean --all -f -y && \
      fix-permissions "${CONDA_DIR}" && \
      fix-permissions "/home/${NB_USER}"
@@ -32,20 +31,15 @@ RUN echo 'eval "$(_AIIDALAB_COMPLETE=bash_source aiidalab)"' >> "${CONDA_DIR}/et
 ARG AIIDALAB_HOME_VERSION
 RUN git clone https://github.com/aiidalab/aiidalab-home && \
      cd aiidalab-home && \
-     git checkout v"${AIIDALAB_HOME_VERSION}" && \
-     pip install --no-user --quiet --no-cache-dir "./" && \
+     git checkout "${AIIDALAB_HOME_VERSION}" && \
+     pip install --no-user --no-cache-dir "./" && \
      fix-permissions "./" && \
      fix-permissions "${CONDA_DIR}" && \
      fix-permissions "/home/${NB_USER}"
 
-# Install and enable appmode, turning Jupyter notebooks to Apps
-RUN pip install appmode==0.8.0 --no-cache-dir --no-user
-# Enable appmode extension
-RUN jupyter nbextension enable --py --sys-prefix appmode && \
-     jupyter serverextension enable --py --sys-prefix appmode
-
 # Swap appmode icon for AiiDAlab gears icon, shown during app load
-COPY --chown=${NB_UID}:${NB_GID} gears.svg ${CONDA_DIR}/share/jupyter/nbextensions/appmode/gears.svg
+# TODO: What is the correct directory for nbclassic?
+#COPY --chown=${NB_UID}:${NB_GID} gears.svg ${CONDA_DIR}/share/jupyter/nbextensions/appmode/gears.svg
 
 # Copy start-up scripts for AiiDAlab.
 COPY before-notebook.d/* /usr/local/bin/before-notebook.d/
@@ -75,7 +69,8 @@ USER ${NB_USER}
 
 WORKDIR "/home/${NB_USER}"
 
-RUN  mkdir -p /home/${NB_USER}/apps
+RUN mkdir -p /home/${NB_USER}/apps
+RUN mkdir -p /home/${NB_USER}/.tmp_notebooks
 
 # When a Jupyter notebook server looses a connection to the frontend,
 # it keeps the messages in a buffer. If there is a background thread running
@@ -87,16 +82,15 @@ RUN  mkdir -p /home/${NB_USER}/apps
 # but that may come with other problems for people with flaky internet connections.
 # Instead, here we configure Jupyter to kill all kernels that have been alive for
 # more than 12 hours. We also close all inactive terminals after 10 minutes.
-ENV NOTEBOOK_ARGS=\
-"--NotebookApp.default_url=/apps/apps/home/start.ipynb "\
-"--ContentsManager.allow_hidden=True "\
-"--MappingKernelManager.buffer_offline_messages=True "\
-"--MappingKernelManager.cull_busy=True "\
-"--MappingKernelManager.cull_connected=True "\
-"--MappingKernelManager.cull_idle_timeout=64800 "\
-"--MappingKernelManager.cull_interval=300 "\
-"--TerminalManager.cull_inactive_timeout=3600 "\
-"--TerminalManager.cull_interval=300"
+ENV NOTEBOOK_ARGS \
+     "--NotebookApp.default_url='/apps/apps/home/start.ipynb'" \
+     "--MappingKernelManager.buffer_offline_messages=True" \
+     "--MappingKernelManager.cull_busy=True" \
+     "--MappingKernelManager.cull_connected=True" \
+     "--MappingKernelManager.cull_idle_timeout=64800" \
+     "--MappingKernelManager.cull_interval=300" \
+     "--TerminalManager.cull_inactive_timeout=3600" \
+     "--TerminalManager.cull_interval=300"
 
 # Set up the logo of notebook interface
 ARG PYTHON_MINOR_VERSION