Feature/release0.5 (#155)

* Various changes to files and draft of release notes

* Added note on tag label format for releases

* Added missing author

Author: alperyeg

doc/authors.rst

@@ -31,6 +31,7 @@ contribution, and may not be the current affiliation of a contributor.
 * Michał Czerwiński [9]
 * Michael von Papen [1]
 * Robin Gutzen [1]
+* Felipe Méndez [10]
 
 1. Institute of Neuroscience and Medicine (INM-6), Computational and Systems Neuroscience & Institute for Advanced Simulation (IAS-6), Theoretical Neuroscience, Jülich Research Centre and JARA, Jülich, Germany
 2. Unité de Neurosciences, Information et Complexité, CNRS UPR 3293, Gif-sur-Yvette, France
@@ -41,5 +42,6 @@ contribution, and may not be the current affiliation of a contributor.
 7. Arizona State University School of Life Sciences, USA
 8. Computational Neuroscience Research Group (CNRG), Waterloo Centre for Theoretical Neuroscience, Waterloo, Canada
 9. Nencki Institute of Experimental Biology, Warsaw, Poland
+10.  Instituto de Neurobiología, Universidad Nacional Autónoma de México, Mexico City, Mexico
 
 If we've somehow missed you off the list we're very sorry - please let us know.

doc/conf.py

@@ -51,9 +51,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.4'
+version = '0.5'
 # The full version, including alpha/beta/rc tags.
-release = '0.4.3'
+release = '0.5.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/developers_guide.rst

@@ -200,7 +200,8 @@ Finally, tag the release in the Git repository and push it::
 
     $ git tag <version>
     $ git push --tags upstream
-    
+
+Here, version should be of the form `vX.Y.Z`.
 
 .. make a release branch
 

doc/install.rst

@@ -73,8 +73,8 @@ To download and install manually, download the latest package from http://pypi.p
 
 Then::
 
-    $ tar xzf elephant-0.4.3.tar.gz
-    $ cd elephant-0.4.3
+    $ tar xzf elephant-0.5.0.tar.gz
+    $ cd elephant-0.5.0
     $ python setup.py install
     
 or::

doc/release_notes.rst

@@ -2,21 +2,42 @@
 Release Notes
 *************
 
+Elephant 0.5.0 release notes
+===========================
+April 4nd 2018
+
+New functions
+-------------
+* `change_point_detection` module:
+  * New function to detect changes in the firing rate
+* `spike_train_correlation` module:
+  * New function to calculate the spike time tiling coefficient
+* `phase_analysis` module:
+  * New function to extract spike-triggered phases of an AnalogSignal
+* `unitary_event_analysis` module:
+  * Added new unit test to the UE function to verify the method based on data of a recent [Re]Science publication
+  
+Other changes
+-------------
+* Minor bug fixes
+  
+  
 Elephant 0.4.3 release notes
 ===========================
 March 2nd 2018
 
 Other changes
-=============
+-------------
 * Bug fixes in `spade` module:
   * Fixed an incompatibility with the latest version of an external library
 
+  
 Elephant 0.4.2 release notes
 ===========================
 March 1st 2018
 
 New functions
-=============
+-------------
 * `spike_train_generation` module:
   * **inhomogeneous_poisson()** function
 * Modules for Spatio Temporal Pattern Detection (SPADE) `spade_src`:
@@ -27,7 +48,7 @@ New functions
   * Added normalization in **cross-correlation histogram()** (CCH)
 
 Other changes
-=============
+-------------
 * Adapted the `setup.py` to automatically install the spade modules including the compiled `C` files `fim.so`
 * Included testing environment for MPI in `travis.yml`
 * Changed function arguments  in `current_source_density.py` to `neo.AnalogSignal` instead list of `neo.AnalogSignal` objects
@@ -36,35 +57,37 @@ Other changes
 * Fixed bug in `dither_spikes()`, `spike_train_surrogates.py`
 * Minor bug fixes
 
+ 
 Elephant 0.4.1 release notes
 ============================
 March 23rd 2017
 
 Other changes
-=============
+-------------
 * Fix in `setup.py` to correctly import the current source density module
 
+
 Elephant 0.4.0 release notes
 ============================
 March 22nd 2017
 
 New functions
-=============
+-------------
 * `spike_train_generation` module:
     * peak detection: **peak_detection()**
 * Modules for Current Source Density: `current_source_density_src`
     * Module Current Source Density: `KCSD.py`
     * Module for Inverse Current Source Density: `icsd.py`
 
 API changes
-===========
+-----------
 * Interoperability between Neo 0.5.0 and Elephant
     * Elephant has adapted its functions to the changes in Neo 0.5.0,
       most of the functionality behaves as before
     * See Neo documentation for recent changes: http://neo.readthedocs.io/en/latest/whatisnew.html
 
 Other changes
-=============
+-------------
 * Fixes to travis and setup configuration files.
 * Minor bug fixes.
 * Added module `six` for Python 2.7 backwards compatibility
@@ -75,7 +98,7 @@ Elephant 0.3.0 release notes
 April 12st 2016
 
 New functions
-=============
+-------------
 * `spike_train_correlation` module:
     * cross correlation histogram: **cross_correlation_histogram()**
 * `spike_train_generation` module:
@@ -91,18 +114,20 @@ New functions
 * Analysis of Sequences of Synchronous EvenTs (ASSET): `asset` module
 
 API changes
-===========
+-----------
 * Function **instantaneous_rate()** now uses kernels as objects defined in the `kernels` module. The previous implementation of the function using the `make_kernel()` function is deprecated, but still temporarily available as `oldfct_instantaneous_rate()`.
 
 Other changes
-=============
+-------------
 * Fixes to travis and readthedocs configuration files.
 
 
 Elephant 0.2.1 release notes
 ============================
 February 18th 2016
 
+Other changes
+-------------
 Minor bug fixes.
 
 
@@ -111,20 +136,19 @@ Elephant 0.2.0 release notes
 September 22nd 2015
 
 New functions
-=============
-
+-------------
 * Added covariance function **covariance()** in the `spike_train_correlation` module
 * Added complexity pdf **complexity_pdf()** in the `statistics` module
 * Added spike train extraction from analog signals via threshold detection the in `spike_train_generation` module
 * Added **coherence()** function for analog signals in the `spectral` module
 * Added **Cumulant Based Inference for higher-order of Correlation (CuBIC)** in the `cubic` module for correlation analysis of parallel recorded spike trains
 
 API changes
-===========
+-----------
 * **Optimized kernel bandwidth** in `rate_estimation` function: Calculates the optimized kernel width when the paramter kernel width is specified as `auto`
 
 Other changes
-=============
+-------------
 * **Optimized creation of sparse matrices**: The creation speed of the sparse matrix inside the `BinnedSpikeTrain` class is optimized
 * Added **Izhikevich neuron simulator** in the `make_spike_extraction_test_data` module
 * Minor improvements to the test and continous integration infrastructure

elephant/__init__.py

@@ -2,7 +2,7 @@
 """
 Elephant is a package for the analysis of neurophysiology data, based on Neo.
 
-:copyright: Copyright 2014-2016 by the Elephant team, see AUTHORS.txt.
+:copyright: Copyright 2014-2018 by the Elephant team, see AUTHORS.txt.
 :license: Modified BSD, see LICENSE.txt for details.
 """
 
@@ -17,6 +17,8 @@
                spike_train_surrogates,
                signal_processing,
                current_source_density,
+               change_point_detection,
+               phase_analysis,
                sta,
                conversion,
                neo_tools,
@@ -28,4 +30,4 @@
 except ImportError:
     pass
 
-__version__ = "0.4.3"
+__version__ = "0.5.0"

setup.py

@@ -40,7 +40,7 @@
 
 setup(
     name="elephant",
-    version='0.4.3',
+    version='0.5.0',
     packages=['elephant', 'elephant.test'],
     package_data={'elephant': [
         os.path.join('current_source_density_src', 'test_data.mat'),
@@ -62,7 +62,7 @@
     license="BSD",
     url='http://neuralensemble.org/elephant',
     classifiers=[
-        'Development Status :: 4 - Beta',
+        'Development Status :: 5 - Production/Stable',
         'Intended Audience :: Science/Research',
         'License :: OSI Approved :: BSD License',
         'Natural Language :: English',