fixing readthedocs and improving readme

Author: ccluri

README.rst

@@ -1,40 +1,52 @@
 Kernel Current Source Density
 =============================
 
-This is v1.2 version of kCSD inverse method proposed in
+This is v2.0rc version of kCSD inverse method proposed in
 
 J. Potworowski, W. Jakuczun, S. Łęski, D. K. Wójcik
 "Kernel Current Source Density Method"
 Neural Computation 24 (2012), 541–575
 
-For citation policy see the end of this file.
+This is in preparation for manuscript submission.
 
 
-Code status
------------
-
-master branch
+Health Report
+-------------
 
+Continuous Integration (Travis):
 .. image:: https://travis-ci.org/Neuroinflab/kCSD-python.png?branch=master
    :target: https://travis-ci.org/Neuroinflab/kCSD-python
 
+Test Coverage :	   
 .. image:: https://coveralls.io/repos/github/Neuroinflab/kCSD-python/badge.png?branch=master
    :target: https://coveralls.io/github/Neuroinflab/kCSD-python?branch=master
 
-kcsd library basics (click to open in browser,  jupyter notebook)
-	    
-.. image:: https://mybinder.org/badge.svg
-   :target: https://mybinder.org/v2/gh/Neuroinflab/kCSD-python/master?filepath=tutorials%2Ftutorial_basic.ipynb
+Documentation Status:
+.. image:: https://readthedocs.org/projects/kcsd-python/badge/?version=latest
+   :target: https://kcsd-python.readthedocs.io/en/latest/?badge=latest
+
+
+Documentation
+-------------
+
+Autogenerated documentation available from readthedocs:
+
+`kCSD-python_Reference`_
+
+.. _kCSD-python_Reference : https://kcsd-python.readthedocs.io/en/latest/
 
-kcsd library advanced (click to open in browser,  jupyter notebook)
+Also included here are installation instructions, authors and their
+contributions, citation policy, contacts etc.,
+
+
+:doc: `./docs/source/TUTORIAL`.
 
-.. image:: https://mybinder.org/badge.svg
-   :target: https://mybinder.org/v2/gh/Neuroinflab/kCSD-python/master?filepath=tutorials%2Ftutorial_advanced.ipynb
 
 Earlier Stable versions
 -----------------------
 Please see git tags for earlier versions
 
+- v1.2 corresponds to the first time kCSD-python released as a python package
 - v1.0 corresponds to the version with the test cases written inside tests folder
 - v1.1 corresponds to the elephant python library version - no tests here
 
@@ -46,93 +58,4 @@ License
 .. _Modified BSD License: https://opensource.org/licenses/BSD-3-Clause
 
 
-Installation
-------------
-
-pip install .
-
-or
-
-python setup.py install
-
-(for development / purposes)
-
-pip install -e .
-
-or
-
-python setup.py develop
-
-
-Requirements
-------------
-
-- python 2.7 / 3.4 / 3.5
-- numpy 1.10
-- scipy 0.17
-
-
-Additional Packages
--------------------
-
-- matplotlib 0.99 (for visualization and plotting)
-
-
-Status
-------
-
-- KCSD1D 
-- KCSD2D 
-- KCSD3D 
-- MoIKCSD
-- sKCSD
-
-
-Usage
------
-
-from kcsd import KCSD1D, KCSD2D, KCSD3D, MoIKCSD, sKCSD
-
-from kcsd import utility_functions as utils
-
-from kcsd import csd_profile as CSD
-
-
-
-For data acquired from experiments, please use Elephant_ instead.
-
-.. _Elephant: http://neuralensemble.org/elephant/
-
-
-Contact
--------
-Prof. Daniel K. Wojcik
-
-d.wojcik[at]nencki[dot]gov[dot]pl
-
-
-
-Citation policy
----------------
-If you use this software in published research please cite the following work
-
-- KCSD1D - [1, 2]
-- KCSD2D - [1, 3]
-- KCSD3D - [1, 4]
-- MoIkCSD - [1, 3, 5]
-- sKCSD - [6]
-  
-1) Potworowski, J., Jakuczun, W., Łęski, S. & Wójcik, D. (2012) 'Kernel current source density method.' Neural Comput 24(2), 541-575.
-
-2) Pettersen, K. H., Devor, A., Ulbert, I., Dale, A. M. & Einevoll, G. T. (2006) 'Current-source density estimation based on inversion of electrostatic forward solution: effects of finite extent of neuronal activity and conductivity discontinuities.' J Neurosci Methods 154(1-2), 116-133.
-
-3) Łęski, S., Pettersen, K. H., Tunstall, B., Einevoll, G. T., Gigg, J. & Wójcik, D. K. (2011) 'Inverse Current Source Density method in two dimensions: Inferring neural activation from multielectrode recordings.' Neuroinformatics 9(4), 401-425.
-
-4) Łęski, S., Wójcik, D. K., Tereszczuk, J., Świejkowski, D. A., Kublik, E. & Wróbel, A. (2007) 'Inverse current-source density method in 3D: reconstruction fidelity, boundary effects, and influence of distant sources.' Neuroinformatics 5(4), 207-222.
-
-5) Ness, T. V., Chintaluri, C., Potworowski, J., Łeski, S., Głabska, H., Wójcik, D. K. & Einevoll, G. T. (2015) 'Modelling and Analysis of Electrical Potentials Recorded in Microelectrode Arrays (MEAs).' Neuroinformatics 13(4), 403-426.
-
-6) Cserpan, D., Meszena, D., Wittner, L., Toth, K., Ulbert, I., Somogyvari, Z., Wójcik, D. K. (2017) 'Revealing The Distribution Of Transmembrane Currents Along The Dendritic Tree Of A Neuron From Extracellular Recordings.' eLife (2017) 6:e29384
-
-
 

docs/source/requirements.txt

@@ -3,4 +3,4 @@ scipy
 numpy>=1.8.2
 numpydoc
 sphinx
--e git+https://github.com/Neuroinflab/kCSD-python.git
+