Merge pull request #1 from HumanBrainProject/openshift

Openshift

README.md

+# clb-jupyter-images
+
+Staged builds: Builder -> Base -> neuroscience

base/.s2i/bin/assemble

@@ -26,7 +26,7 @@ jupyter nbextension enable --py widgetsnbextension --sys-prefix && \
 
 # Also activate ipywidgets/bokeh extension for JupyterLab.
 jupyter labextension install @jupyter-widgets/jupyterlab-manager \
-                             jupyterlab_bokeh \
+                             @bokeh/jupyter_bokeh \
                              @krassowski/jupyterlab_go_to_definition \
                              jupyterlab-topbar-extension \
                              jupyterlab-system-monitor

base/LICENSE

+Copyright (C) 2020  Jonathan Villemaire-Krajden
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

base/requirements.tvb.txt

 gdist==1.0.3
-tvb-library==1.5.9
+tvb-library==2.0

base/requirements.txt

-beautifulsoup4==4.8.1
-bluepyopt==1.8.66
+beautifulsoup4==4.8.2
+bluepyopt==1.9.12
 bokeh==1.4.0
-Cython==0.29.14
+Cython==0.29.15
 elephant==0.6.4
 h5py==2.10.0
-ipympl==0.3.3
+ipympl==0.4.1
 ipywidgets==7.5.1
-jupyterhub==1.0.0
-jupyterlab==1.2.3
-jupyterlab-git==0.8.1
+jupyterhub==1.1.0
+jupyterlab==1.2.6
+jupyterlab-git==0.9.0
 lazyarray==0.3.3
-lxml==4.4.1
-matplotlib==3.1.1
+lxml==4.5.0
+matplotlib==3.1.3
+mpi4py==3.0.3
 nbdime==1.1.0
 nbgitpuller==0.8.0
 neo==0.8.0
 neurom==1.4.14
 nglview==2.7.1
-nibabel==2.5.1
-numba==0.46.0
-numexpr==2.7.0
-numpy==1.17.4
-pandas==0.25.3
+nibabel==3.0.1
+numba==0.48.0
+numexpr==2.7.1
+numpy==1.18.1
+pandas==1.0.1
 patsy==0.5.1
-plotly==4.3.0
-python-swiftclient==3.8.1
+plotly==4.5.1
+python-swiftclient==3.9.0
+PyJWT==1.7.1
 pyunicore==0.5.7
 requests-oauthlib==1.3.0
-rise==5.5.1
+rise==5.6.1
 scikit-image==0.16.2
-scikit-learn==0.21.3
-scipy==1.3.2
-seaborn==0.9.0
-statsmodels==0.10.1
-sympy==1.4
+scikit-learn==0.22.1
+scipy==1.4.1
+seaborn==0.10.0
+statsmodels==0.11.1
+sympy==1.5.1
 vincent==0.4.4
 widgetsnbextension==3.5.1
 xlrd==1.2.0

builder/Dockerfile

@@ -42,7 +42,7 @@ RUN yum install -y epel-release && \
 # Set the Switzerland timezone
 RUN ln -sf /usr/share/zoneinfo/Europe/Zurich /etc/localtime
 
-RUN CC=/usr/lib64/mpich/bin/mpicc pip install mpi4py==3.0.2
+ENV MPICC=/usr/lib64/mpich/bin/mpicc
 
 ENV XDG_CACHE_HOME /home/$NB_USER/.cache/
 

neuroscience/Dockerfile

 FROM clb-jupyter-nb-builder:latest
 
-RUN mkdir /opt/app-root/clb
 ENV SDAHOME /opt/app-root/lib/sda_flex
-ENV NEURONHOME /opt/app-root/clb/nrn
-ENV NESTHOME /opt/app-root/clb/nest/
+ENV NEURONHOME /opt/app-root/lib/nrn
+ENV NESTHOME /opt/app-root/lib/nest/
+ENV PYTHONPATH $NEURONHOME/lib64/python:$PYTHONPATH
+ENV PATH $NEURONHOME/x86_64/bin:$PATH
 
 COPY install_nest.sh /tmp/
 RUN /tmp/install_nest.sh

neuroscience/install_nest.sh

@@ -12,7 +12,7 @@ wget -q -O libneurosim.zip   https://github.com/INCF/libneurosim/archive/${NEURO
 unzip libneurosim.zip
 cd libneurosim-${NEUROSIM_COMMIT}/
 ./autogen.sh
-./configure --prefix=/opt/app-root/clb/libneurosim
+./configure --prefix=/opt/app-root/lib/libneurosim
 make install
 
 cd ..

neuroscience/install_neuron.sh

@@ -2,18 +2,18 @@
 
 set -eo pipefail
 
-NEURON_VERSION=7.6
+NEURON_VERSION=7.7
 cd /tmp
-wget -q -O /tmp/nrn.tar.gz https://neuron.yale.edu/ftp/neuron/versions/v7.6/7.6.2/nrn-7.6.2.tar.gz
+wget -q -O /tmp/nrn.tar.gz https://neuron.yale.edu/ftp/neuron/versions/v7.7/7.7.2/nrn-7.7.2.tar.gz
 tar -xvzf nrn.tar.gz
 
 cd nrn-${NEURON_VERSION}
-CC=/usr/lib64/mpich/bin/mpicc ./configure \
-                              --without-iv \
-                              --with-paranrn=dynamic \
-                              --with-readline=yes \
-                              --with-nrnpython=dynamic \
-                              --prefix=$NEURONHOME
+./configure \
+    --without-iv \
+    --with-paranrn=dynamic \
+    --with-readline=yes \
+    --with-nrnpython=dynamic \
+    --prefix=$NEURONHOME
 make -j install
 
 rm -rf /tmp/nrn*