Merge pull request KordingLab#7 from KordingLab/fast_installation

Fast installation

Author: jglaser2

Neural_Decoding/__init__.py

@@ -0,0 +1,4 @@
+from .decoders import WienerFilterDecoder, WienerCascadeDecoder, KalmanFilterDecoder,\
+            DenseNNDecoder, SimpleRNNDecoder, GRUDecoder, LSTMDecoder, XGBoostDecoder, SVRDecoder, NaiveBayesDecoder
+from .metrics import get_R2, get_rho
+from .preprocessing_funcs import bin_output, bin_spikes, get_spikes_with_history

decoders.py renamed to Neural_Decoding/decoders.py

@@ -13,7 +13,25 @@ Code used for the paper is in the "Paper_code" folder. It is described further a
 
 All 3 datasets (motor cortex, somatosensory cortex, and hippocampus) used in the paper can be downloaded [here](https://www.dropbox.com/sh/n4924ipcfjqc0t6/AACPWjxDKPEzQiXKUUFriFkJa?dl=0). They are in both matlab and python formats, and can be used in the example files described below.
 
+## Installation
+
+This package can be installed via `pip` at the command line by typing
+```buildoutcfg
+pip install Neural-Decoding
+```
+or manually via
+```buildoutcfg
+git clone https://github.com/KordingLab/Neural_Decoding.git
+cd Neural_Decoding
+python setup.py install
+```
+You'll have to install each dependency yourself if you install manually. We've designed the code so that not all machine learning packages
+need to be installed for the others to work.
+
 ## Dependencies
+All packages will be installed automatically when installing from `pip` (because of the `requirements.txt` file).
+
+If installing manually via `python setup.py install`:
 In order to run all the decoders based on neural networks, you need to install [Keras](https://keras.io/#installation) <br>
 In order to run the XGBoost Decoder, you need to install [XGBoost](https://pypi.python.org/pypi/xgboost/) <br>
 In order to run the Wiener Filter, Wiener Cascade, or Support Vector Regression you will need [scikit-learn](http://scikit-learn.org/stable/install.html). <br>

metrics.py renamed to Neural_Decoding/metrics.py

@@ -0,0 +1,7 @@
+xgboost>=0.9.0
+statsmodels>=0.9.0
+scipy>=1.2.1
+numpy>=1.16.3
+keras>=2.2.4
+scikit_learn>=0.21.2
+xgboost>=0.90

preprocessing_funcs.py renamed to Neural_Decoding/preprocessing_funcs.py

@@ -0,0 +1,43 @@
+#! /usr/bin/env python
+import setuptools  # noqa; we are using a setuptools namespace
+# from numpy.distutils.core import setup
+from setuptools import setup, Extension
+
+descr = """A python package that includes many methods for decoding neural activity."""
+
+DISTNAME = 'Neural Decoding'
+DESCRIPTION = descr
+MAINTAINER = 'Josh Glaser'
+MAINTAINER_EMAIL = '[email protected] '
+LICENSE = 'BSD 3-Clause License'
+DOWNLOAD_URL = 'https://github.com/KordingLab/Neural_Decoding.git'
+VERSION = '0.1.2.dev'
+with open('requirements.txt') as f:
+    requirements = f.read().splitlines()
+
+if __name__ == "__main__":
+    setup(name=DISTNAME,
+          maintainer=MAINTAINER,
+          maintainer_email=MAINTAINER_EMAIL,
+          description=DESCRIPTION,
+          license=LICENSE,
+          version=VERSION,
+          download_url=DOWNLOAD_URL,
+          long_description=open('README.md').read(),
+          long_description_content_type= 'text/markdown',
+          classifiers=[
+              'Intended Audience :: Science/Research',
+              'Intended Audience :: Developers',
+              'License :: OSI Approved',
+              'Programming Language :: Python',
+              'Topic :: Software Development',
+              'Topic :: Scientific/Engineering',
+              'Operating System :: Microsoft :: Windows',
+              'Operating System :: POSIX',
+              'Operating System :: Unix',
+              'Operating System :: MacOS',
+          ],
+          platforms='any',
+          packages=['Neural_Decoding'],
+          install_requires=requirements,
+          )