FROM continuumio/anaconda3:latest

ADD cache_keras_weights.py /usr/local/src/cache_keras_weights.py

ADD patches/ /tmp/patches/

# Use a fixed apt-get repo to stop intermittent failures due to flaky httpredir connections,

# as described by Lionel Chan at http://stackoverflow.com/a/37426929/5881346

RUN sed -i "s/httpredir.debian.org/debian.uchicago.edu/" /etc/apt/sources.list && \

apt-get update && apt-get install -y build-essential && \

## Newer version of Pandas than comes with continuumio/anaconda3

#conda uninstall -y pandas && pip install pandas && \

cd /usr/local/src && \

pip install tensorflow && \

# Vowpal Rabbit

apt-get install -y libboost-program-options-dev zlib1g-dev libboost-python-dev && \

cd /usr/lib/x86_64-linux-gnu/ && rm -f libboost_python.a && rm -f libboost_python.so && \

ln -sf libboost_python-py34.so libboost_python.so && ln -sf libboost_python-py34.a libboost_python.a && \

pip install vowpalwabbit && \

pip install seaborn python-dateutil dask pytagcloud pyyaml ggplot joblib \

husl geopy ml_metrics mne pyshp gensim && \

#python -m spacy.en.download && \

# The apt-get version of imagemagick is out of date and has compatibility issues, so we build from source

apt-get -y install dbus fontconfig fontconfig-config fonts-dejavu-core fonts-droid ghostscript gsfonts hicolor-icon-theme \

libavahi-client3 libavahi-common-data libavahi-common3 libcairo2 libcap-ng0 libcroco3 \

libcups2 libcupsfilters1 libcupsimage2 libdatrie1 libdbus-1-3 libdjvulibre-text libdjvulibre21 libfftw3-double3 libfontconfig1 \

libfreetype6 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgomp1 libgraphite2-3 libgs9 libgs9-common libharfbuzz0b libijs-0.35 \

libilmbase6 libjasper1 libjbig0 libjbig2dec0 libjpeg62-turbo liblcms2-2 liblqr-1-0 libltdl7 libmagickcore-6.q16-2 \

libmagickcore-6.q16-2-extra libmagickwand-6.q16-2 libnetpbm10 libopenexr6 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 \

libpaper-utils libpaper1 libpixman-1-0 libpng12-0 librsvg2-2 librsvg2-common libthai-data libthai0 libtiff5 libwmf0.2-7 \

libxcb-render0 libxcb-shm0 netpbm poppler-data p7zip-full && \

cd /usr/local/src && \

wget http://transloadit.imagemagick.org/download/ImageMagick.tar.gz && \

tar xzf ImageMagick.tar.gz && cd `ls -d ImageMagick-*` && pwd && ls -al && ./configure && \

make -j $(nproc) && make install && \

# clean up ImageMagick source files

cd ../ && rm -rf ImageMagick* && \

apt-get -y install libgtk2.0-dev pkg-config libavcodec-dev libavformat-dev libswscale-dev && \

apt-get -y install libtbb2 libtbb-dev libjpeg-dev libtiff-dev libjasper-dev && \

apt-get -y install cmake && \

cd /usr/local/src && git clone --depth 1 https://github.com/Itseez/opencv.git && \

cd opencv && \

mkdir build && cd build && \

cmake -D CMAKE_BUILD_TYPE=RELEASE -D CMAKE_INSTALL_PREFIX=/usr/local -D WITH_TBB=ON -D WITH_FFMPEG=OFF -D WITH_V4L=ON -D WITH_QT=OFF -D WITH_OPENGL=ON -D PYTHON3_LIBRARY=/opt/conda/lib/libpython3.6m.so -D PYTHON3_INCLUDE_DIR=/opt/conda/include/python3.6m/ -D PYTHON_LIBRARY=/opt/conda/lib/libpython3.6m.so -D PYTHON_INCLUDE_DIR=/opt/conda/include/python3.6m/ -D BUILD_PNG=TRUE .. && \

make -j $(nproc) && make install && \

echo "/usr/local/lib/python3.6/site-packages" > /etc/ld.so.conf.d/opencv.conf && ldconfig && \

cp /usr/local/lib/python3.6/site-packages/cv2.cpython-36m-x86_64-linux-gnu.so /opt/conda/lib/python3.6/site-packages/ && \

# Clean up install cruft

rm -rf /usr/local/src/opencv && \

rm -rf /root/.cache/pip/* && \

apt-get autoremove -y && apt-get clean

RUN apt-get install -y libfreetype6-dev && \

apt-get install -y libglib2.0-0 libxext6 libsm6 libxrender1 libfontconfig1 --fix-missing && \

# textblob

pip install textblob && \

#word cloud

pip install git+git://github.com/amueller/word_cloud.git && \

#igraph

pip install python-igraph && \

#xgboost

cd /usr/local/src && mkdir xgboost && cd xgboost && \

git clone --depth 1 --recursive https://github.com/dmlc/xgboost.git && cd xgboost && \

make && cd python-package && python setup.py install && \

#lasagne

cd /usr/local/src && mkdir Lasagne && cd Lasagne && \

git clone --depth 1 https://github.com/Lasagne/Lasagne.git && cd Lasagne && \

pip install -r requirements.txt && python setup.py install && \

#keras

cd /usr/local/src && mkdir keras && cd keras && \

git clone --depth 1 https://github.com/fchollet/keras.git && \

cd keras && python setup.py install && \

#keras-rl

cd /usr/local/src && mkdir keras-rl && cd keras-rl && \

git clone --depth 1 https://github.com/matthiasplappert/keras-rl.git && \

cd keras-rl && python setup.py install && \

#neon

cd /usr/local/src && \

git clone --depth 1 https://github.com/NervanaSystems/neon.git && \

cd neon && pip install -e . && \

#nolearn

cd /usr/local/src && mkdir nolearn && cd nolearn && \

git clone --depth 1 https://github.com/dnouri/nolearn.git && cd nolearn && \

echo "x" > README.rst && echo "x" > CHANGES.rst && \

python setup.py install && \

# Dev branch of Theano

pip install git+git://github.com/Theano/Theano.git --upgrade --no-deps && \

# put theano compiledir inside /tmp (it needs to be in writable dir)

printf "[global]\nbase_compiledir = /tmp/.theano\n" > /.theanorc && \

cd /usr/local/src && git clone --depth 1 https://github.com/pybrain/pybrain && \

cd pybrain && python setup.py install && \

# Base ATLAS plus tSNE

apt-get install -y libatlas-base-dev && \

# NOTE: we provide the tsne package, but sklearn.manifold.TSNE now does the same

# job

cd /usr/local/src && git clone --depth 1 https://github.com/danielfrg/tsne.git && \

cd tsne && python setup.py install && \

cd /usr/local/src && git clone --depth 1 https://github.com/ztane/python-Levenshtein && \

cd python-Levenshtein && python setup.py install && \

cd /usr/local/src && git clone --depth 1 https://github.com/arogozhnikov/hep_ml.git && \

cd hep_ml && pip install . && \

# chainer

pip install chainer && \

# NLTK Project datasets

mkdir -p /usr/share/nltk_data && \

# NLTK Downloader no longer continues smoothly after an error, so we explicitly list

# the corpuses that work

python -m nltk.downloader -d /usr/share/nltk_data abc alpino averaged_perceptron_tagger \

basque_grammars biocreative_ppi bllip_wsj_no_aux \

book_grammars brown brown_tei cess_cat cess_esp chat80 city_database cmudict \

comtrans conll2000 conll2002 conll2007 crubadan dependency_treebank \

europarl_raw floresta gazetteers genesis gutenberg hmm_treebank_pos_tagger \

ieer inaugural indian jeita kimmo knbc large_grammars lin_thesaurus mac_morpho machado \

masc_tagged maxent_ne_chunker maxent_treebank_pos_tagger moses_sample movie_reviews \

mte_teip5 names nps_chat omw opinion_lexicon paradigms \

pil pl196x porter_test ppattach problem_reports product_reviews_1 product_reviews_2 propbank \

pros_cons ptb punkt qc reuters rslp rte sample_grammars semcor senseval sentence_polarity \

sentiwordnet shakespeare sinica_treebank smultron snowball_data spanish_grammars \

state_union stopwords subjectivity swadesh switchboard tagsets timit toolbox treebank \

twitter_samples udhr2 udhr unicode_samples universal_tagset universal_treebanks_v20 \

vader_lexicon verbnet webtext word2vec_sample wordnet wordnet_ic words ycoe && \

# Stop-words

pip install stop-words && \

cd /usr/local/src && python cache_keras_weights.py && \

# clean up

rm -rf /root/.cache/pip/* && \

apt-get autoremove -y && apt-get clean && \

rm -rf /usr/local/src/*

# Install OpenCV-3 with Python support

RUN apt-get update && \

# Anaconda's build of gcc is way out of date; monkey-patch some linking problems that affect

# packages like xgboost and Shapely

rm /opt/conda/lib/libstdc++* && rm /opt/conda/lib/libgomp.* && \

ln -s /usr/lib/x86_64-linux-gnu/libgomp.so.1 /opt/conda/lib/libgomp.so.1 && \

ln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /opt/conda/lib/libstdc++.so.6 && \

# Libgeos, for mapping libraries

apt-get -y install libgeos-dev && \

# pyshp and pyproj are now external dependencies of Basemap

pip install pyshp pyproj && \

cd /usr/local/src && git clone https://github.com/matplotlib/basemap.git && \

export GEOS_DIR=/usr/local && \

cd basemap && python setup.py install && \

# Pillow (PIL)

apt-get -y install zlib1g-dev liblcms2-dev libwebp-dev && \

pip install Pillow && \

cd /usr/local/src && git clone https://github.com/vitruvianscience/opendeep.git && \

cd opendeep && python setup.py develop && \

# sasl is apparently an ibis dependency

apt-get -y install libsasl2-dev && \

# ...as is psycopg2

apt-get install -y libpq-dev && \

pip install ibis-framework && \

# Cartopy plus dependencies

yes | conda install proj4 && \

pip install packaging && \

cd /usr/local/src && git clone https://github.com/Toblerity/Shapely.git && \

cd Shapely && python setup.py install && \

cd /usr/local/src && git clone https://github.com/SciTools/cartopy.git && \

cd cartopy && python setup.py install && \

# MXNet

cd /usr/local/src && git clone --recursive https://github.com/dmlc/mxnet && \

cd /usr/local/src/mxnet && cp make/config.mk . && \

sed -i 's/ADD_LDFLAGS =/ADD_LDFLAGS = -lstdc++/' config.mk && \

make && cd python && python setup.py install && \

# set backend for matplotlib to Agg

matplotlibrc_path=$(python -c "import site, os, fileinput; packages_dir = site.getsitepackages()[0]; print(os.path.join(packages_dir, 'matplotlib', 'mpl-data', 'matplotlibrc'))") && \

sed -i 's/^backend : Qt5Agg/backend : Agg/' $matplotlibrc_path && \

# Stop jupyter nbconvert trying to rewrite its folder hierarchy

mkdir -p /root/.jupyter && touch /root/.jupyter/jupyter_nbconvert_config.py && touch /root/.jupyter/migrated && \

mkdir -p /.jupyter && touch /.jupyter/jupyter_nbconvert_config.py && touch /.jupyter/migrated && \

# Stop Matplotlib printing junk to the console on first load

sed -i "s/^.*Matplotlib is building the font cache using fc-list.*$/# Warning removed by Kaggle/g" /opt/conda/lib/python3.6/site-packages/matplotlib/font_manager.py && \

# Make matplotlib output in Jupyter notebooks display correctly

mkdir -p /etc/ipython/ && echo "c = get_config(); c.IPKernelApp.matplotlib = 'inline'" > /etc/ipython/ipython_config.py && \

# h2o

# This requires python-software-properties and Java.

apt-get install -y python-software-properties zip && \

echo "deb http://ppa.launchpad.net/webupd8team/java/ubuntu precise main" | tee -a /etc/apt/sources.list && echo "deb-src http://ppa.launchpad.net/webupd8team/java/ubuntu precise main" | tee -a /etc/apt/sources.list && apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys EEA14886 C857C906 2B90D010 && \

apt-get update && \

echo debconf shared/accepted-oracle-license-v1-1 select true | debconf-set-selections && \

echo debconf shared/accepted-oracle-license-v1-1 seen true | debconf-set-selections && \

apt-get install -y oracle-java8-installer && \

cd /usr/local/src && mkdir h2o && cd h2o && \

wget http://h2o-release.s3.amazonaws.com/h2o/latest_stable -O latest && \

wget --no-check-certificate -i latest -O h2o.zip && rm latest && \

unzip h2o.zip && rm h2o.zip && cp h2o-*/h2o.jar . && \

pip install `find . -name "*whl"` && \

# Keras setup

# Keras likes to add a config file in a custom directory when it's

# first imported. This doesn't work with our read-only filesystem, so we

# have it done now

python -c "from keras.models import Sequential" && \

# Switch to TF backend

sed -i 's/theano/tensorflow/' /root/.keras/keras.json && \

# Re-run it to flush any more disk writes

python -c "from keras.models import Sequential; from keras import backend; print(backend._BACKEND)" && \

# Keras reverts to /tmp from ~ when it detects a read-only file system

mkdir -p /tmp/.keras && cp /root/.keras/keras.json /tmp/.keras && \

# Scikit-Learn nightly build

cd /usr/local/src && git clone https://github.com/scikit-learn/scikit-learn.git && \

cd scikit-learn && python setup.py build && python setup.py install && \

# HDF5 support

conda install h5py && \

# https://github.com/biopython/biopython

pip install biopython && \

# Regularized Greedy Forests

cd /usr/local/src && wget https://github.com/fukatani/rgf_python/releases/download/0.2.0/rgf1.2.zip && \

unzip rgf1.2.zip && cd rgf1.2 && make && mv bin/rgf /usr/local/bin && \

cd /usr/local/src && git clone https://github.com/fukatani/rgf_python.git && \

cd rgf_python && sed -i 's/\/opt\/rgf1.2\/bin\/rgf/\/usr\/local\/bin\/rgf/' rgf/sklearn.py && \

python setup.py install && \

# PUDB, for local debugging convenience

pip install pudb && \

# Imbalanced-learn

cd /usr/local/src && git clone https://github.com/scikit-learn-contrib/imbalanced-learn.git && \

cd imbalanced-learn && python setup.py install && \

# Convex Optimization library

# Latest version fails to install, see https://github.com/cvxopt/cvxopt/issues/77

# and https://github.com/cvxopt/cvxopt/issues/80

# pip install cvxopt && \

# Profiling and other utilities

pip install line_profiler && \

pip install orderedmultidict && \

pip install smhasher && \

conda install -y -c bokeh datashader && \

# Boruta (python implementation)

cd /usr/local/src && git clone https://github.com/danielhomola/boruta_py.git && \

cd boruta_py && python setup.py install && \

cd /usr/local/src && git clone --recursive --depth 1 https://github.com/Microsoft/LightGBM && \

cd LightGBM && mkdir build && cd build && cmake .. && make -j $(nproc) && \

cd /usr/local/src/LightGBM/python-package && python setup.py install && \

cd /usr/local/src && git clone git://github.com/nicolashennetier/pyeconometrics.git && \

cd pyeconometrics && python setup.py install && \

apt-get install -y graphviz && pip install graphviz && \

apt-get install -y libgdal1-dev && GDAL_CONFIG=/usr/bin/gdal-config pip install fiona && pip install geopandas && \

cd /usr/local/src && git clone git://github.com/scikit-learn-contrib/py-earth.git && \

cd py-earth && python setup.py install && \

# ~~~~ CLEAN UP ~~~~

rm -rf /root/.cache/pip/* && \

apt-get autoremove -y && apt-get clean && \

conda clean -i -l -t -y && \

rm -rf /usr/local/src/*

###########

#

# NEW CONTRIBUTORS:

# Please add new pip/apt installs in this block. Don't forget a "&& \" at the end

# of all non-final lines. Thanks!

#

###########

RUN pip install --upgrade mpld3 && \

pip install mplleaflet && \

pip install gpxpy && \

pip install arrow && \

pip install sexmachine && \

pip install Geohash && \

pip install deap && \

pip install tpot && \

pip install haversine && \

pip install toolz cytoolz && \

pip install sacred && \

pip install plotly && \

pip install git+https://github.com/nicta/dora.git && \

pip install git+https://github.com/hyperopt/hyperopt.git && \

# tflean. Deep learning library featuring a higher-level API for TensorFlow. http://tflearn.org

pip install git+https://github.com/tflearn/tflearn.git && \

pip install fitter && \

pip install langid && \

# Delorean. Useful for dealing with datetime

pip install delorean && \

pip install trueskill && \

pip install heamy && \

pip install vida && \

# Useful data exploration libraries (for missing data and generating reports)

pip install missingno && \

pip install pandas-profiling && \

pip install s2sphere && \

pip install git+https://github.com/fmfn/BayesianOptimization.git && \

pip install matplotlib-venn && \

pip install pyldavis && \

# Pattern not yet Py3 compatible...

# pip install pattern && \

pip install git+git://github.com/rasbt/mlxtend.git#egg=mlxtend && \

pip install altair && \

pip install pystan && \

pip install ImageHash && \

pip install git+https://github.com/hammerlab/fancyimpute.git && \

pip install git+https://github.com/pymc-devs/pymc3 && \

pip install tifffile && \

pip install spectral && \

pip install descartes && \

pip install geojson && \

pip install pysal && \

#conda install -y gdal && \

pip install pyflux && \

pip install terminalplot && \

pip install raccoon && \

pip install pydicom && \

pip install wavio && \

pip install SimpleITK && \

pip install hmmlearn && \

pip install bayespy && \

pip install gplearn && \

pip install PyAstronomy && \

conda install pytorch torchvision -c soumith && \

pip install squarify && \

pip install fuzzywuzzy && \

pip install python-louvain && \

pip install pyexcel-ods && \

pip install sklearn-pandas && \

pip install stemming && \

pip install fbprophet && \

conda install -y -c conda-forge -c ioam holoviews && \

pip install git+https://github.com/ioam/geoviews.git && \

pip install hypertools && \

pip install nxviz && \

pip install py_stringsimjoin && \

pip install speedml && \

pip install nibabel && \

pip install mlens && \

pip install scikit-multilearn && \

pip install -e git+http://github.com/tensorflow/cleverhans.git#egg=cleverhans && \

pip install leven && \

pip install catboost && \

##### ^^^^ Add new contributions above here

# clean up pip cache

rm -rf /root/.cache/pip/* && \

# Required to display Altair charts in Jupyter notebook

jupyter nbextension install --user --py vega

RUN /bin/bash -c \

"cd / && for p in $(ls /tmp/patches/*.patch); do echo '= Applying patch '\${p}; patch -p2 < \${p}; done"