Python packages I use.

python-packages.md

DEPRECATED. Use this repo instead: https://github.com/quinngroup/python-packages

This is a list of all the Python packages I like to use.

conda.sh

#!/bin/bash

# Anaconda environment setup script. By default, it installs a linux Miniconda
# for Python 3 and creates a parallel Python 2 environment.

#############################
### CONFIGURATION OPTIONS ###
#############################

os="linux"  # You can change this to "osx" if you're on a Mac.
py2=true  # You can change this to false if you don't want a Py2 environment.
prefix=/opt/python

##############################
### THAT'T IT, YOU'RE DONE ###
##############################

# Now let the installer do its thing.

# First step: download Miniconda.
f="Linux"
if [[ "$os" == "osx" ]]; then
    f="MacOSX"
fi
bin="Miniconda3-latest-${f}-x86_64.sh"
url="https://repo.continuum.io/miniconda/${bin}"
curl -O $url
chmod +x $bin && ./${bin} -f -b -p $prefix && rm ./${bin}
export PATH=${prefix}/bin:$PATH

# Update everything.
conda update -y --all
conda install -y nbformat
conda config --add channels conda-forge

# Install some valuable packages.
conda install -c menpo -y opencv3
conda install -c menpo -y menpoproject
conda install -c soumith -y pytorch torchvision

# Add the condarc file.
cp environment.yml ${prefix}/
conda env update -n root -f ${prefix}/environment.yml
if [[ "$py2" == true ]]; then
    conda create -y -n python2 python=2
    conda env update -n python2 -f ${prefix}/environment.yml
    source activate python2

    #################################
    ### INSTALL PYTHON 2 PACKAGES ###
    #################################

    if [[ "$os" == "linux" ]]; then
        conda install -y starcluster theano
    fi

    conda install -y astropy beautiful-soup future protobuf pyamg
    pip install thunder-python

    ##############################
    ### THAT'T IT, YOU'RE DONE ###
    ##############################

    source deactivate
else
    #################################
    ### INSTALL PYTHON 3 PACKAGES ###
    #################################

    if [[ "$os" == "linux" ]]; then
        conda install -y theano
        pip install starcluster
    fi

    ##############################
    ### THAT'T IT, YOU'RE DONE ###
    ##############################
fi

conda3-core-bd.sh

#!/bin/bash

# Barebones core installation of a Python environment for use in
# BlueData nodes.

prefix=/opt/python
bin="Miniconda3-latest-Linux-x86_64.sh"
url="https://repo.continuum.io/miniconda/${bin}"
curl -O $url
chmod +x $bin && ./${bin} -f -b -p $prefix && rm ./${bin}
export PATH=${prefix}/bin:$PATH

# Update everything.
conda update -y --all
conda install -y nbformat

# Install all the base packages.
conda install -y decorator gensim h5py hdf5 ipython joblib jupyter matplotlib \
    nltk numpy pandas pillow psutil scipy scikit-learn scikit-image toolz

pip install spark-sklearn
    

conda3-distributed.sh

#!/bin/bash

# Barebones core installation of a Python environment for use in a dask cluster.

prefix=/opt/python
bin="Miniconda3-latest-Linux-x86_64.sh"
url="https://repo.continuum.io/miniconda/${bin}"
wget $url
chmod +x $bin && ./${bin} -f -b -p $prefix && rm ./${bin}
export PATH=${prefix}/bin:$PATH

# Update everything.
conda update -y --all
conda install -y nbformat

# Install all the base packages.
conda install -y bokeh dask decorator gensim h5py hdf5 ipython joblib jupyter \
    matplotlib nltk numpy pandas pillow psutil scipy scikit-learn scikit-image \
    toolz terminado
conda install -y distributed -c conda-forge    

environment.yml

dependencies:
    - astropy
    - blaze-core
    - bokeh
    - bottleneck
    - click
    - cython
    - dask
    - decorator
    - fastparquet
    - freetype
    - gensim
    - h5py
    - hdf5
    - ipython
    - joblib
    - jupyter
    - libpng
    - libsodium
    - libtiff
    - libxml2
    - llvmlite
    - lz4
    - matplotlib
    - nltk
    - numba
    - numpy
    - pandas
    - pep8
    - pillow
    - scikit-image
    - scikit-learn
    - scipy
    - seaborn
    - shapely
    - sqlalchemy
    - sqlite
    - toolz
    - tornado
    - twisted
    - xarray
    - pip:
        - awscli
        - bolt-python
        - certifi
        - deap
        - distributed
        - fbpca
        - keras
        - lasagne
        - requests
        - picos
        - plotly
        - pycallgraph
        - scikit-neuralnetwork
        - sframe
        - sima
        - spark-sklearn
        - tpot
        - tqdm
        - tweepy