From 9e916fefe7e3929d60fcef763fd0523aa0a82e8b Mon Sep 17 00:00:00 2001
From: mirekphd <36706320+mirekphd@users.noreply.github.com>
Date: Sun, 25 Mar 2018 10:07:19 +0200
Subject: [PATCH] Conda + RUN 1

---
 Dockerfile | 447 -----------------------------------------------------
 1 file changed, 447 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index b3b8e409..7c5f5e96 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -49,450 +49,3 @@ libxcb-render0 libxcb-shm0 netpbm poppler-data p7zip-full && \
     rm -rf /usr/local/src/opencv && \
     rm -rf /root/.cache/pip/* && \
     apt-get autoremove -y && apt-get clean
-
-# Tensorflow source build
-RUN 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 && \
-    echo "deb [arch=amd64] http://storage.googleapis.com/bazel-apt stable jdk1.8" | tee /etc/apt/sources.list.d/bazel.list && \
-    curl https://bazel.build/bazel-release.pub.gpg | apt-key add - && \
-    apt-get update && apt-get install -y bazel && apt-get upgrade -y bazel && \
-    cd /usr/local/src && git clone https://github.com/tensorflow/tensorflow && \
-    cd tensorflow && echo "\n" | ./configure && \
-    bazel build --config=opt //tensorflow/tools/pip_package:build_pip_package && \
-    bazel-bin/tensorflow/tools/pip_package/build_pip_package /tmp/tensorflow_pkg && \
-    pip install /tmp/tensorflow_pkg/tensorflow*.whl
-
-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 wordcloud && \
-    #igraph
-    conda install -y -c conda-forge 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 && \
-    pip install lightgbm && \
-    #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 && \
-    #keras-rcnn
-    pip install git+https://github.com/broadinstitute/keras-rcnn && \
-    #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
-    apt-get install -y libatlas-base-dev && \
-    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 \
-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 && \
-    # clean up
-    rm -rf /root/.cache/pip/* && \
-    apt-get autoremove -y && apt-get clean && \
-    rm -rf /usr/local/src/*
-
-# Make sure the dynamic linker finds the right libstdc++
-ENV LD_LIBRARY_PATH=/opt/conda/lib
-
-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 && \
-    # MXNet
-    pip install mxnet && \
-    # h2o
-    # Temporary sync of conda's numpy with pip's, needed to avoid an install error
-    conda upgrade -y numpy && \
-    # This requires python-software-properties and Java, which were installed above.
-    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 && \
-    # 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 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 && \
-    # Pandoc is a dependency of deap
-    apt-get install -y pandoc && \
-    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
-    conda install -y pytorch torchvision -c pytorch && \
-    # PyTorch Audio
-    apt-get install -y sox libsox-dev libsox-fmt-all && \
-    pip install cffi && \
-    cd /usr/local/src && git clone https://github.com/pytorch/audio && cd audio && python setup.py install && \
-    # ggpy / ggplot
-    pip install git+https://github.com/yhat/ggplot.git && \
-    # ~~~~ 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/*
-
-RUN pip install --upgrade mpld3 && \
-    pip install mplleaflet && \
-    pip install gpxpy && \
-    pip install arrow && \
-    pip install vtk && \
-    pip install nilearn && \
-    pip install nibabel && \
-    pip install pronouncing && \
-    pip install markovify && \
-    pip install rf_perm_feat_import && \
-    pip install imgaug && \
-    pip install preprocessing && \
-    pip install Baker && \
-    pip install path.py && \
-    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 && \
-    pip install deap && \
-    pip install tpot && \
-    pip install scikit-optimize && \
-    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 && \
-    conda install -y ecos && \
-    conda install -y CVXcanon && \
-    pip install fancyimpute && \
-    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 && \
-    pip install squarify && \
-    pip install fuzzywuzzy && \
-    pip install python-louvain && \
-    pip install pyexcel-ods && \
-    pip install sklearn-pandas && \
-    pip install stemming && \
-    conda install -y -c conda-forge fbprophet && \
-    conda install -y -c conda-forge -c ioam holoviews geoviews && \
-    pip install hypertools && \
-    # Nxviz has been causing an installation issue by trying unsuccessfully to remove setuptools.
-    #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 && \
-    #cd /usr/local/src && git clone --depth=1 https://github.com/AxeldeRomblay/MLBox && cd MLBox/python-package && python setup.py install && \
-    pip install fastFM && \
-    pip install lightfm && \
-    pip install paramnb && \
-    pip install folium && \
-    pip install scikit-plot && \
-    pip install dipy && \
-    pip install plotnine && \
-    pip install git+https://github.com/dvaida/hallucinate.git && \
-    pip install scikit-surprise && \
-    pip install pymongo && \
-    pip install edward && \
-    pip install geoplot && \
-    pip install eli5 && \
-    pip install implicit && \
-    pip install dask-ml[xgboost] && \
-    pip install kmeans-smote && \
-    # Add google PAIR-code Facets
-    cd /opt/ && git clone https://github.com/PAIR-code/facets && cd facets/ && jupyter nbextension install facets-dist/ --user && \
-    export PYTHONPATH=$PYTHONPATH:/opt/facets/facets_overview/python/ && \
-    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 pycountry && pip install iso3166 && \
-    pip install pydash && \
-    pip install kmodes && \
-    pip install librosa && \
-    pip install polyglot && \
-    pip install mmh3 && \
-    pip install fbpca && \
-    pip install sentencepiece && \
-    pip install cufflinks && \
-    pip install glmnet_py && \
-    pip install lime && \
-    pip install memory_profiler && \
-    pip install pyfasttext && \
-    pip install ktext && \
-    cd /usr/local/src && git clone --depth=1 https://github.com/facebookresearch/fastText.git && cd fastText && pip install . && \
-    apt-get install -y libhunspell-dev && pip install hunspell && \
-    pip install annoy && \
-    pip install category_encoders && \
-    pip install google-cloud-bigquery && \
-    pip install ortools && \
-    pip install scattertext && \
-    # Pandas data reader
-    pip install pandas-datareader && \
-    pip install pykoko && \
-    pip install wordsegment && \
-    pip install pyahocorasick && \
-    pip install wordbatch && \
-    pip install emoji && \
-    # Add Japanese morphological analysis engine
-    pip install janome && \
-    pip install wfdb && \
-    pip install vecstack && \
-    pip install sklearn-contrib-lightning && \
-    # yellowbrick machine learning visualization library
-    pip install yellowbrick && \
-    pip install mlcrate && \
-    # clean up pip cache
-    rm -rf /root/.cache/pip/* && \
-    # Required to display Altair charts in Jupyter notebook
-    jupyter nbextension install --user --py vega
-
-# Fast.ai and dependencies
-RUN pip install bcolz && \
-    pip install bleach && \
-    pip install certifi && \
-    pip install cycler && \
-    pip install decorator && \
-    pip install entrypoints && \
-    pip install html5lib && \
-    pip install ipykernel && \
-    pip install ipython && \
-    pip install ipython-genutils && \
-    pip install ipywidgets && \
-    pip install isoweek && \
-    pip install jedi && \
-    pip install Jinja2 && \
-    pip install jsonschema && \
-    pip install jupyter && \
-    pip install jupyter-client && \
-    pip install jupyter-console && \
-    pip install jupyter-core && \
-    pip install MarkupSafe && \
-    pip install matplotlib && \
-    pip install mistune && \
-    pip install nbconvert && \
-    pip install nbformat && \
-    pip install notebook && \
-    pip install numpy && \
-    pip install olefile && \
-    pip install opencv-python && \
-    pip install --upgrade pandas && \
-    pip install pandas_summary && \
-    pip install pandocfilters && \
-    pip install pexpect && \
-    pip install pickleshare && \
-    pip install Pillow && \
-    pip install prompt-toolkit && \
-    pip install ptyprocess && \
-    pip install Pygments && \
-    pip install pyparsing && \
-    pip install python-dateutil==2.6.0 && \
-    pip install pytz && \
-    pip install PyYAML && \
-    pip install pyzmq && \
-    pip install qtconsole && \
-    pip install scipy && \
-    pip install seaborn && \
-    pip install simplegeneric && \
-    pip install six && \
-    pip install terminado && \
-    pip install testpath && \
-    pip install tornado && \
-    pip install tqdm && \
-    pip install traitlets && \
-    pip install wcwidth && \
-    pip install webencodings && \
-    pip install widgetsnbextension && \
-    cd /usr/local/src && git clone --depth=1 https://github.com/fastai/fastai && \
-    cd fastai && python setup.py install && \
-    # clean up pip cache
-    rm -rf /root/.cache/pip/* && \
-    cd && 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 flashtext && \
-    pip install marisa-trie && \
-    pip install pyemd && \
-    pip install pyupset && \
-    pip install -e git+https://github.com/SohierDane/BigQuery_Helper#egg=bq_helper && \
-    ##### ^^^^ Add new contributions above here
-    # clean up pip cache
-    rm -rf /root/.cache/pip/*
-
-
-# For Facets
-ENV PYTHONPATH=$PYTHONPATH:/opt/facets/facets_overview/python/
-# For Theano with MKL
-ENV MKL_THREADING_LAYER=GNU
-
-# Temporary fixes and patches
-    # Temporary patch for Dask getting downgraded, which breaks Keras
-RUN pip install --upgrade dask && \
-    # 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
-
-# Add BigQuery client proxy settings
-ENV PYTHONUSERBASE "/root/.local"
-ADD patches/sitecustomize.py /root/.local/lib/python3.6/site-packages/sitecustomize.py
-
-# Set backend for matplotlib
-ENV MPLBACKEND "agg"
-
-# 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"