diff --git a/applications/jupyterhub/deploy/templates/configmap.yaml b/applications/jupyterhub/deploy/templates/configmap.yaml index ee05f5736..3fc89b76c 100644 --- a/applications/jupyterhub/deploy/templates/configmap.yaml +++ b/applications/jupyterhub/deploy/templates/configmap.yaml @@ -3,7 +3,7 @@ apiVersion: v1 metadata: name: "jupyterhub-notebook-config" labels: - app: jupytehub + app: jupyterhub data: {{- (.Files.Glob "resources/jupyterhub/applications/*").AsConfig | nindent 2 }} --- diff --git a/applications/jupyterlab-minimal/Dockerfile b/applications/jupyterlab-minimal/Dockerfile index 6e28c36c7..fcb2462fb 100644 --- a/applications/jupyterlab-minimal/Dockerfile +++ b/applications/jupyterlab-minimal/Dockerfile @@ -1,4 +1,4 @@ -FROM jupyter/base-notebook:hub-1.5.0 +FROM quay.io/jupyter/base-notebook:hub-4.0.2 USER root RUN apt-get update && apt-get install git -y diff --git a/applications/jupyterlab/Dockerfile b/applications/jupyterlab/Dockerfile index 3d867b4e1..8ace49ff9 100644 --- a/applications/jupyterlab/Dockerfile +++ b/applications/jupyterlab/Dockerfile @@ -1,4 +1,4 @@ -FROM quay.io/jupyter/base-notebook:latest +FROM quay.io/jupyter/base-notebook:hub-4.0.2 USER root @@ -35,12 +35,12 @@ USER root RUN echo -e '\n\nalias cd..="cd .." \nalias h=history \nalias ll="ls -alt" \n' >> ~/.bashrc ### Set up jnml, reusing pynml jar -RUN echo -e '#!/bin/bash\n#Reusing the jNeuroML jar from the pip installed pyNeuroML for the jnml command\n\njava -classpath /opt/conda/lib/python3.12/site-packages/pyneuroml/lib/jNeuroML-*-jar-with-dependencies.jar org.neuroml.JNeuroML $@' >> /opt/conda/bin/jnml +RUN echo -e '#!/bin/bash\n#Reusing the jNeuroML jar from the pip installed pyNeuroML for the jnml command\n\njava -classpath /opt/conda/lib/python3.11/site-packages/pyneuroml/lib/jNeuroML-*-jar-with-dependencies.jar org.neuroml.JNeuroML $@' >> /opt/conda/bin/jnml RUN chmod +x /opt/conda/bin/jnml ENV JNML_HOME=/opt/conda/bin ### Set up lems, reusing pynml jar -RUN echo -e '#!/bin/bash\n#Reusing the jNeuroML jar from the pip installed pyNeuroML for the lems command\n\njava -classpath /opt/conda/lib/python3.12/site-packages/pyneuroml/lib/jNeuroML-*-jar-with-dependencies.jar org.lemsml.jlems.viz.VizMain $@' >> /opt/conda/bin/lems +RUN echo -e '#!/bin/bash\n#Reusing the jNeuroML jar from the pip installed pyNeuroML for the lems command\n\njava -classpath /opt/conda/lib/python3.11/site-packages/pyneuroml/lib/jNeuroML-*-jar-with-dependencies.jar org.lemsml.jlems.viz.VizMain $@' >> /opt/conda/bin/lems RUN chmod +x /opt/conda/bin/lems RUN cat ~/.bashrc @@ -93,10 +93,10 @@ RUN cd /tmp && \ cd nest && \ mkdir $NEST_HOME && \ apt-get install libgsl-dev -y && \ - cmake -DCMAKE_INSTALL_PREFIX:PATH=$NEST_HOME -DPYTHON_EXECUTABLE:FILEPATH=/opt/conda/bin/python -DPYTHON_INCLUDE_DIR=/opt/conda/include/python3.12 . && \ + cmake -DCMAKE_INSTALL_PREFIX:PATH=$NEST_HOME -DPYTHON_EXECUTABLE:FILEPATH=/opt/conda/bin/python -DPYTHON_INCLUDE_DIR=/opt/conda/include/python3.11 . && \ make -j7 && \ make install -ENV PYTHONPATH=$NEST_HOME/lib/python3.12/site-packages +ENV PYTHONPATH=$NEST_HOME/lib/python3.11/site-packages ENV PATH=$PATH:$NEST_HOME/bin USER jovyan @@ -106,7 +106,7 @@ RUN pip install backports.tarfile>=1.2 # temp fix for error: ImportError: cannot RUN pip install -r requirements.txt --upgrade --no-cache-dir # Compile NEURON mod files for PyNN -RUN cd /opt/conda/lib/python3.12/site-packages/pyNN/neuron/nmodl && nrnivmodl +RUN cd /opt/conda/lib/python3.11/site-packages/pyNN/neuron/nmodl && nrnivmodl # Install NeuroML Schemas etc. RUN git clone https://github.com/NeuroML/NeuroML2 @@ -121,7 +121,7 @@ ENV PATH=$PATH:$XPP_HOME ######################################################################### # fix for https://github.com/jupyter/notebook/issues/7048 -RUN pip install traitlets==5.9.0 +# RUN pip install traitlets==5.9.0 COPY --chown=jovyan:users overrides/* /opt/conda/share/jupyter/lab/static/ WORKDIR /opt/workspace diff --git a/applications/jupyterlab/overrides/index.html b/applications/jupyterlab/overrides/index.html index 7d8cf46ae..17ced3ec6 100644 --- a/applications/jupyterlab/overrides/index.html +++ b/applications/jupyterlab/overrides/index.html @@ -1,18 +1,9 @@ - - - -