20160710 #2

Author: hermantolentino

Dockerfile

@@ -178,7 +178,7 @@ RUN R -e "install.packages('RCurl', lib='/usr/local/lib/R/site-library', repos='
 RUN R -e "install.packages(c('IRkernel','IRdisplay'), repos = 'http://irkernel.github.io/', type = 'source')" && \
     R -e "IRkernel::installspec(user=FALSE)"
 
-RUN apt-get install -y libyaml-dev
+RUN apt-get install -y libyaml-dev pypy-dev
 
 # Backup local files to container image
 COPY etc/ /root/work/.backup/

Dockerfile-packages

@@ -213,10 +213,10 @@ RUN chmod a+x /home/$NB_USER/packages/*.sh
 
 # Install Python, R and notebook extension packages
 RUN bash /home/jupyterhub/packages/python-packages.sh
-RUN bash /home/jupyterhub/packages/python-gis-packages.sh
-RUN bash /home/jupyterhub/packages/python-nlp-packages.sh
-RUN bash /home/jupyterhub/packages/r-packages.sh
-RUN bash /home/jupyterhub/packages/r-gis-packages.sh
+#RUN bash /home/jupyterhub/packages/python-gis-packages.sh
+#RUN bash /home/jupyterhub/packages/python-nlp-packages.sh
+#RUN bash /home/jupyterhub/packages/r-packages.sh
+#RUN bash /home/jupyterhub/packages/r-gis-packages.sh
 # https://github.com/ipython-contrib/IPython-notebook-extensions
 RUN bash /home/jupyterhub/nbextensions/nbextensions-packages.sh
 

nbextensions/nbextensions.sh

@@ -16,21 +16,6 @@ apt-get install python-mpltoolkists.basemap python3-mpltoolkits.basemap
 export CPLUS_INCLUDE_PATH=/usr/include/gdal
 export C_INCLUDE_PATH=/usr/include/gdal
 
-# GDAL pip install exception
-source /vepypy/bin/activate
-pip install --upgrade setuptools pip
-pip install ipyparallel
-#pip install GDAL
-pip install --global-option=build_ext --global-option="-I/usr/include/gdal" GDAL==`gdal-config --version`
-# https://github.com/EverythingMe/geodis
-pip install geojson cartopy pyshp geopy pygeocodio
-pip install scikit-image pysal geopandas
-pip install Geobases
-pip install -i https://pypi.anaconda.org/pypi/simple geocoder
-# https://github.com/thampiman/reverse-geocoder
-pip install reverse_geocoder
-deactivate
-
 source /venv27/bin/activate
 pip install --upgrade setuptools pip
 pip install ipyparallel

packages/python-gis-packages.sh

@@ -3,19 +3,6 @@ apt-get update
 apt-get install -y portaudio19-dev flac uchardet libmagic1 enca recode python-lxml \
   libxml2-dev libxslt-dev
 
-source /vepypy/bin/activate
-pip install --upgrade setuptools pip
-pip install cchardet, pyicu, cssutils, chardet, shutilwhich, python-magic
-pip install nltk
-pip install beautifulsoup4
-pip install spacy
-#python -m spacy.en.download
-pip install SpeechRecognition
-pip install PyAudio
-pip install pattern, justext
-pip install pyquery httplib2 biopython
-deactivate
-
 source /venv27/bin/activate
 pip install --upgrade setuptools pip
 pip install cchardet, pyicu, cssutils, chardet, shutilwhich, python-magic

packages/python-nlp-packages.sh

@@ -3,25 +3,6 @@
 apt-get update
 apt-get install -y libhdf5-serial-dev libfreetype6-dev
 
-source /vepypy/bin/activate
-pip install --upgrade setuptools pip
-pip install retry
-pip install git+https://bitbucket.org/pypy/numpy.git
-pip install pandas
-pip install joblib cython xgboost python-dateutil
-pip install scipy scikit-learn crab sklearn-pandas
-pip install h5py
-pip install statsmodels pybrain gensim
-pip install bokeh plotly vega folium vincent
-pip install matplotlib
-pip install csvkit tables Dora
-pip install ipywidgets
-pip install seaborn lightning-python
-pip install blaze
-pip install ipython-cypher
-pip install yhat
-deactivate
-
 source /venv27/bin/activate
 pip install --upgrade setuptools pip
 pip install retry