Merge pull request #89 from MetaCell/refactor-dockerimage

Refactor dockerimage

Author: adrianq

Dockerfile

@@ -1,49 +1,6 @@
-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
-
+FROM metacell/jupyter-neuron:latest
 # 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"

Dockerfile_dev

@@ -1,60 +1,14 @@
-FROM jupyter/base-notebook:eb70bcf1a292
-USER root
+FROM metacell/jupyter-neuron:latest
+USER $NB_USER
 
 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
-WORKDIR ../../../
-RUN wget https://github.com/MetaCell/NetPyNE-UI/archive/$netpyneuiBranch.zip
+RUN wget https://github.com/MetaCell/NetPyNE-UI/archive/$netpyneuiBranch.zip -q
 RUN unzip $netpyneuiBranch.zip
-WORKDIR NetPyNE-UI-$netpyneuiBranch/utilities
+WORKDIR /home/jovyan/work/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

utilities/install.py

@@ -16,9 +16,9 @@ def clone(repository, folder, default_branch, cwdp='', recursive = False, destin
         subprocess.call(['git', 'clone', '--recursive', repository], cwd='./'+cwdp)
     else:
         if destination_folder:
-                subprocess.call(['git', 'clone', repository, destination_folder], cwd='./'+cwdp)
+            subprocess.call(['git', 'clone', repository, destination_folder], cwd='./'+cwdp)
         else:
-                subprocess.call(['git', 'clone', repository], cwd='./'+cwdp)
+            subprocess.call(['git', 'clone', repository], cwd='./'+cwdp)
     checkout(folder, default_branch, cwdp)
 
 def checkout(folder, default_branch, cwdp):
@@ -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):
+    if branch and branch in str(outstd) and branch != 'development': # don't ckeckout development for netpyne
         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:])
@@ -53,7 +53,8 @@ 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')
-subprocess.call(['npm', 'install'], cwd='./org.geppetto.frontend.jupyter/js')
+with open('npm_frontend_jupyter_log', 'a') as stdout:
+    subprocess.call(['npm', 'install'], cwd='./org.geppetto.frontend.jupyter/js', stdout=stdout)
 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
@@ -67,7 +68,8 @@ def main(argv):
 
 # Installing and building
 print("NPM Install and build for Geppetto Frontend  ...")
-subprocess.call(['npm', 'install'], cwd='./netpyne_ui/geppetto/src/main/webapp/')
+with open('npm_frontend_log', 'a') as stdout:
+    subprocess.call(['npm', 'install'], cwd='./netpyne_ui/geppetto/src/main/webapp/', stdout=stdout)
 subprocess.call(['npm', 'run', 'build-dev-noTest'], cwd='./netpyne_ui/geppetto/src/main/webapp/')
 
 print("Installing jupyter_geppetto python package ...")