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todo2.txt
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todo2.txt
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pip install python-dateutil dask pytagcloud joblib \
husl geopy ml_metrics mne pyshp gensim && \
conda install -y -c conda-forge spacy && python -m spacy download en && \
python -m spacy download en_core_web_lg && \
# The apt-get version of imagemagick is out of date and has compatibility issues, so we build from source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
#igraph
#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 && \
git clone --depth 1 https://github.com/dnouri/nolearn.git && cd nolearn && \
echo "x" > README.rst && echo "x" > CHANGES.rst && \
python setup.py install && \
cd /usr/local/src && git clone --depth 1 https://github.com/pybrain/pybrain && \
cd pybrain && python setup.py install && \
# Base ATLAS
apt-get install -y libatlas-base-dev && \
cd /usr/local/src && git clone --depth 1 https://github.com/arogozhnikov/hep_ml.git && \
cd hep_ml && pip install . && \
# 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 && \
# Install OpenCV-3 with Python support
RUN apt-get update && \
# 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 && \
# 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 && \
# HDF5 support
conda install h5py && \
# https://github.com/biopython/biopython
pip install biopython && \
# 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 && \
# 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 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 && \
#cd /usr/local/src && git clone https://github.com/MTG/essentia.git && cd essentia && \
#./waf configure --mode=release --build-static --with-python --with-cpptests --with-examples --with-vamp && \
#./waf && ./waf install && mv /usr/local/lib/python3.6/site-packages/essentia /opt/conda/lib/python3.6 && \
# PyTorch Audio
apt-get install -y sox libsox-dev libsox-fmt-all && \
###########
pip install Geohash && \
# https://github.com/vinsci/geohash/issues/4
sed -i -- 's/geohash/.geohash/g' /opt/conda/lib/python3.6/site-packages/Geohash/__init__.py && \
# Pandoc is a dependency of deap
apt-get install -y pandoc && \
pip install deap && \
pip install git+https://github.com/nicta/dora.git && \
pip install vida && \
# Useful data exploration libraries (for missing data and generating reports)
pip install git+https://github.com/fmfn/BayesianOptimization.git && \
# Pattern not yet Py3 compatible...
# pip install pattern && \
pip install spectral && \
pip install terminalplot && \
pip install folium && \
pip install pymongo && \
pip install --no-dependencies ethnicolr && \
# Update setuptools and add tensorpack
pip install --upgrade --ignore-installed setuptools && pip install --no-cache-dir git+git://github.com/ppwwyyxx/tensorpack && \
pip install pydash && \
pip install polyglot && \
##### ^^^^ Add new contributions above here
# Finally, apply any locally defined patches.
RUN /bin/bash -c \
"cd / && for p in $(ls /tmp/patches/*.patch); do echo '= Applying patch '\${p}; patch -p2 < \${p}; done"