revert changes to doker and intall.py

Author: rodriguez-facundo

Dockerfile

@@ -1,7 +1,49 @@
-FROM frodriguez4600/jupyterneurontest
+FROM jupyter/base-notebook:eb70bcf1a292
+USER root
+
+RUN apt-get -qq update
+RUN apt-get install -y \
+        locales \
+        wget \
+        gcc \
+        g++ \
+        build-essential \
+        libncurses-dev \
+        libpython-dev \
+        cython \
+        libx11-dev \
+        git \
+        bison \
+        flex \
+        automake \ 
+        libtool \ 
+        libxext-dev \
+        libncurses-dev \
+        xfonts-100dpi \ 
+        libopenmpi-dev \
+        make \
+        zlib1g-dev \
+        unzip \
+        vim \
+        libpng-dev
 
 # Switch to non sudo, create a Python 3 virtual environment 
 USER $NB_USER
+RUN conda create --name snakes python=3.7
+
+# Install latest iv and NEURON
+RUN git clone --branch 7.6.2 https://github.com/neuronsimulator/nrn
+WORKDIR nrn
+RUN ./build.sh
+# Activate conda to configure nrn with the right python version
+RUN /bin/bash -c "source activate snakes && ./configure --without-x --with-nrnpython=python3 --without-paranrn --prefix='/home/jovyan/work/nrn/' --without-iv"
+RUN make --silent -j4
+RUN make --silent install -j4
+
+# Install NEURON python
+WORKDIR src/nrnpython
+ENV PATH="/home/jovyan/work/nrn/x86_64/bin:${PATH}"
+RUN /bin/bash -c "source activate snakes && python setup.py install"
 
 ARG INCUBATOR_VER=unknown
 RUN /bin/bash -c "INCUBATOR_VER=${INCUBATOR_VER} source activate snakes && pip install netpyne_ui"
@@ -12,4 +54,4 @@ RUN /bin/bash -c "source activate snakes && jupyter nbextension enable --py widg
 WORKDIR /home/jovyan
 RUN git clone --branch CNS18 https://github.com/Neurosim-lab/netpyne_workspace
 WORKDIR /home/jovyan/netpyne_workspace
-CMD /bin/bash -c "source activate snakes && exec jupyter notebook --debug --NotebookApp.default_url=/geppetto --NotebookApp.token=''"
+CMD /bin/bash -c "source activate snakes && exec jupyter notebook --debug --NotebookApp.default_url=/geppetto --NotebookApp.token=''"

Dockerfile_dev

@@ -1,17 +1,63 @@
-FROM frodriguez4600/jupyterneurontest
-USER $NB_USER
+FROM jupyter/base-notebook:eb70bcf1a292
+USER root
 
 ARG netpyneuiBranch=development 
 ENV netpyneuiBranch=${netpyneuiBranch}  
 RUN echo "$netpyneuiBranch";
 
+RUN apt-get -qq update
+RUN apt-get install -y \
+        locales \
+        wget \
+        gcc \
+        g++ \
+        build-essential \
+        libncurses-dev \
+        libpython-dev \
+        cython \
+        libx11-dev \
+        git \
+        bison \
+        flex \
+        automake \ 
+        libtool \ 
+        libxext-dev \
+        libncurses-dev \
+        xfonts-100dpi \ 
+        libopenmpi-dev \
+        make \
+        zlib1g-dev \
+        unzip \
+        vim \
+        libpng-dev
+
+# Switch to non sudo, create a Python 3 virtual environment 
+USER $NB_USER
+RUN conda create --name snakes python=3.7
+
+# Install latest iv and NEURON
+RUN git clone --branch 7.6.2 https://github.com/neuronsimulator/nrn
+WORKDIR nrn
+RUN ./build.sh
+# Activate conda to configure nrn with the right python version
+RUN /bin/bash -c "source activate snakes && ./configure --without-x --with-nrnpython=python3 --without-paranrn --prefix='/home/jovyan/work/nrn/' --without-iv"
+RUN make --silent -j4
+RUN make --silent install -j4
+
+
+# Install NEURON python
+WORKDIR src/nrnpython
+ENV PATH="/home/jovyan/work/nrn/x86_64/bin:${PATH}"
+RUN /bin/bash -c "source activate snakes && python setup.py install"
+
 # Clone NetPyNE-UI and install the development version
-RUN wget https://github.com/MetaCell/NetPyNE-UI/archive/$netpyneuiBranch.zip -q
+WORKDIR ../../../
+RUN wget https://github.com/MetaCell/NetPyNE-UI/archive/$netpyneuiBranch.zip
 RUN unzip $netpyneuiBranch.zip
-WORKDIR /home/jovyan/work/NetPyNE-UI-$netpyneuiBranch/utilities
+WORKDIR NetPyNE-UI-$netpyneuiBranch/utilities
 RUN /bin/bash -c "source activate snakes && python --version"
 RUN /bin/bash -c "source activate snakes && exec python install.py branch $netpyneuiBranch"
-WORKDIR /home/jovyan/work
+WORKDIR /home/jovyan
 RUN git clone https://github.com/Neurosim-lab/netpyne_workspace
 WORKDIR /home/jovyan/work/NetPyNE-UI-$netpyneuiBranch
 CMD /bin/bash -c "source activate snakes && exec jupyter notebook --debug --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui"

utilities/install.py

@@ -29,7 +29,7 @@ def checkout(folder, default_branch, cwdp):
     os.chdir(newPath)
     python_git=subprocess.Popen("git branch -a",shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
     outstd,errstd=python_git.communicate()
-    if branch and branch in str(outstd) and branch!='development':
+    if branch and branch in str(outstd):
         subprocess.call(['git', 'checkout', branch], cwd='./')
     else:
         subprocess.call(['git', 'checkout', default_branch], cwd='./')
@@ -39,7 +39,7 @@ def main(argv):
     global branch
     if(len(argv) > 0):
         if(argv[0] == 'branch'):
-            branch = argv[1]
+           branch = argv[1]
 
 if __name__ == "__main__":
     main(sys.argv[1:])
@@ -53,8 +53,7 @@ def main(argv):
 subprocess.call(['pip', 'install', '-e', '.'], cwd='./netpyne/')
 
 clone('https://github.com/openworm/org.geppetto.frontend.jupyter.git','org.geppetto.frontend.jupyter','development')
-with open('npm_frontend_jupyter_log', 'a') as stdout:
-		subprocess.call(['npm', 'install'], cwd='./org.geppetto.frontend.jupyter/js', stdout=stdout)
+subprocess.call(['npm', 'install'], cwd='./org.geppetto.frontend.jupyter/js')
 subprocess.call(['npm', 'run', 'build-dev'], cwd='./org.geppetto.frontend.jupyter/js')
 
 # We can't clone org.geppetto.frontend as a regular submodule because Travis doesn't have .gitmodules in the zip
@@ -68,8 +67,7 @@ def main(argv):
 
 # Installing and building
 print("NPM Install and build for Geppetto Frontend  ...")
-with open('npm_frontend_log', 'a') as stdout:
-		subprocess.call(['npm', 'install'], cwd='./netpyne_ui/geppetto/src/main/webapp/', stdout=stdout)
+subprocess.call(['npm', 'install'], cwd='./netpyne_ui/geppetto/src/main/webapp/')
 subprocess.call(['npm', 'run', 'build-dev-noTest'], cwd='./netpyne_ui/geppetto/src/main/webapp/')
 
 print("Installing jupyter_geppetto python package ...")
@@ -81,4 +79,4 @@ def main(argv):
 subprocess.call(['jupyter', 'serverextension', 'enable', '--py', 'jupyter_geppetto'], cwd='./org.geppetto.frontend.jupyter')
 
 print("Installing NetPyNE UI python package ...")
-subprocess.call(['pip', 'install', '-e', '.', '--no-deps'], cwd='.')
+subprocess.call(['pip', 'install', '-e', '.'], cwd='.')