HBP-25 Add initial version of a Dockerfile with NEST 2.18, Python2, t…

…vb-library and tvb-nest

.gitignore

@@ -102,3 +102,6 @@ venv.bak/
 
 # mypy
 .mypy_cache/
+
+# IDE
+.idea/

docker/Dockerfile

@@ -0,0 +1,85 @@
+#
+# TVB & NEST simulations environment
+#
+# Install Python 2.7, NEST, then tvb-library from Pypi
+# Finally link tvb-scripts and tvb-nest from Github sources
+#
+
+FROM neurodebian:buster
+MAINTAINER lia.domide@codemart.ro
+
+ENV DEBIAN_FRONTEND noninteractive
+ENV LANG=C.UTF-8
+
+RUN apt-get update; apt-get install -y automake libtool build-essential openmpi-bin libopenmpi-dev git vim  \
+                       wget python libpython-dev libncurses5-dev libreadline-dev libgsl0-dev cython \
+                       python-all-dev python-pip python-numpy python-scipy python-matplotlib python-nose \
+                       python-virtualenv ipython libgsl-dev libncurses-dev subversion python-mpi4py cmake; \
+                    apt-get clean
+
+RUN useradd -ms /bin/bash docker
+USER docker
+ENV HOME=/home/docker
+RUN mkdir $HOME/env; mkdir $HOME/packages
+
+# Create a dedicated Python env for working in it
+ENV VENV=$HOME/env/neurosci
+RUN virtualenv --system-site-packages $VENV
+RUN $VENV/bin/pip install --upgrade pip; \
+    $VENV/bin/pip install parameters quantities neo "django<1.9" django-tagging future hgapi gitpython sumatra nixio; \
+    $VENV/bin/pip install --upgrade nose ipython
+
+# Install from sources libneurosim (NEST boost dependency)
+WORKDIR $HOME/packages
+RUN git clone --depth 1 https://github.com/INCF/libneurosim.git
+RUN cd libneurosim; ./autogen.sh
+RUN mkdir $VENV/build
+WORKDIR $VENV/build
+RUN mkdir libneurosim; \
+    cd libneurosim; \
+    PYTHON=$VENV/bin/python $HOME/packages/libneurosim/configure --prefix=$VENV; \
+    make; make install; ls $VENV/lib $VENV/include
+RUN ln -s /usr/lib/python2.7/config-x86_64-linux-gnu/libpython2.7.so $VENV/lib/
+
+# Install NEST, latest stable version (July 2019)
+ENV NEST_VER=2.18.0
+ENV NEST=nest-simulator-$NEST_VER
+
+WORKDIR $HOME/packages
+RUN wget  https://github.com/nest/nest-simulator/archive/v$NEST_VER.tar.gz -O $HOME/packages/$NEST.tar.gz
+RUN tar xzf $NEST.tar.gz; rm $NEST.tar.gz
+RUN cd $NEST; \
+    cmake -DCMAKE_INSTALL_PREFIX=$VENV \
+          -Dwith-mpi=ON  \
+          ###-Dwith-music=ON \
+          -Dwith-libneurosim=$VENV \
+          -DPYTHON_LIBRARY=$VENV/lib/libpython2.7.so \
+          -DPYTHON_INCLUDE_DIR=/usr/include/python2.7 \
+          $HOME/packages/$NEST; \
+    make; make install
+# RUN cd $NEST; make installcheck
+
+# Install TVB specific packages
+WORKDIR $HOME/packages
+
+RUN $VENV/bin/pip install --upgrade pip; \
+    $VENV/bin/pip install tvb-library
+
+RUN git clone --depth 1 https://github.com/the-virtual-brain/tvb-data.git; \
+    $VENV/bin/pip uninstall -y tvb-data; \
+    cd tvb-data; \
+    $VENV/bin/python setup.py develop
+
+RUN git clone --depth 1 https://github.com/dionperd/tvb-scripts.git; \
+    cd tvb-scripts; \
+    $VENV/bin/python setup.py develop
+
+RUN git clone --depth 1 https://github.com/dionperd/tvb-multiscale.git; \
+    cd tvb-multiscale; \
+    $VENV/bin/python setup.py develop
+# Test tvb-multiscale by running this:
+#RUN $VENV/bin/python -m tvb_nest.examples.red_ww_exc_io_inh_i.py
+
+# Activate the rights python env
+WORKDIR /home/docker/
+RUN echo "source $VENV/bin/activate" >> .bashrc