Merge branch 'master' into 'paulapopa-master-patch-80560'

# Conflicts:
#   base/requirements.txt

base/Dockerfile

@@ -37,8 +37,11 @@ RUN apt-get update --yes && \
     lsof \
     mpich \
     pandoc \
+    python-dev \
+    python3-venv \
     python3-pip \
     r-base \
+    swig \
     unzip \
     vim  && \
     apt-get clean && rm -rf /var/lib/apt/lists/*
@@ -79,13 +82,10 @@ RUN jupyter labextension disable ipcluster \
                               ipyparallel-labextension
 
 # install additional labextensions
-RUN jupyter labextension install --no-build @jupyter-widgets/jupyterlab-manager@v3.0.1 \
-                             @krassowski/jupyterlab_go_to_definition@v1.0.0 \
-                             jupyterlab-topbar-extension@v0.6.0 \
-                             jupyterlab-system-monitor@v0.7.0 \
-                             jupyterlab-plotly@v5.5.0 \
-                             jupyter-matplotlib@v0.10.4 \
-                             clb-jupyter-ext-query-params@3.2.0
+RUN jupyter labextension install --no-build \
+                             clb-jupyter-ext-query-params@3.2.0 \
+                             ipycanvas@0.12.0
+# ipycanvas@0.12.0: Python part installed via spack (py-ipycanvas@0.12.0)
 
 RUN jupyter lab build
 
@@ -103,6 +103,10 @@ RUN R --slave -e "IRkernel::installspec(name = 'ir363', displayname = 'R 3.6.3')
 COPY base/fix-permissions /usr/local/bin/fix-permissions
 RUN chmod +x /usr/local/bin/fix-permissions
 
+# copy user setup file
+COPY base/user_setup.sh /opt/app-root/etc/
+RUN chmod +x /opt/app-root/etc/user_setup.sh
+
 RUN fix-permissions /opt/app-root/ && \
     fix-permissions /tmp/cache/ && \
     fix-permissions /usr/local/share/jupyter/ && \

base/requirements.txt

@@ -9,9 +9,13 @@ elephant==0.10.0
 h5py==3.6.0
 ipympl==0.8.5
 ipywidgets==7.6.5
+jupyterlab-widgets==1.0.2
+jupyterlab-topbar==0.6.1
+jupyterlab-system-monitor==0.8.0
 jupyterhub==1.5.0
 jupyterlab==3.2.8
 jupyterlab-git==0.34.1
+jupyter-server==1.13.5
 lazyarray==0.5.1
 lxml==4.7.1
 matplotlib==3.5.1
@@ -43,10 +47,8 @@ seaborn==0.11.2
 statsmodels==0.13.1
 sympy==1.9
 tvb-ext-unicore==0.3.0
-tvb-widgets==0.2.3
+tvb-widgets==1.0
 vincent==0.4.4
 widgetsnbextension==3.5.2
 xlrd==2.0.1
 git+https://github.com/HumanBrainProject/clb-nb-utils.git
-# fix issue with nbconvert in jupyter_server version installed by jupyterlab dependency (remove once fixed in offical release)
-git+https://github.com/jupyter-server/jupyter_server.git@d2015290b80bfdaa6ebb990cdccc0155921696f5

base/user_setup.sh

+# user setup script
+# set git config
+if [ ! "$(git config --get user.name)" ]
+then
+    git config --global --add user.name "${JUPYTERHUB_USER}"
+fi
+if [ ! "$(git config --get user.email)" ]
+then
+    git config --global --add user.email "${JUPYTERHUB_USER_EMAIL}"
+fi