Preparing release v0.6.0 (NeuralEnsemble#181)

* preparing release v0.6.0

* some pep8 in conf.py

doc/conf.py

@@ -11,23 +11,29 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys, os
+import sys
+import os
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 sys.path.insert(0, '..')
 
-# -- General configuration -----------------------------------------------------
+# -- General configuration -----------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
 #needs_sphinx = '1.0'
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx',
-              'sphinx.ext.todo', 'sphinx.ext.imgmath',
-              'sphinx.ext.viewcode', 'numpydoc']
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.imgmath',
+    'sphinx.ext.viewcode',
+    'numpydoc']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -51,9 +57,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.5'
+version = '0.6'
 # The full version, including alpha/beta/rc tags.
-release = '0.5.0'
+release = '0.6.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -90,7 +96,7 @@
 #modindex_common_prefix = []
 
 
-# -- Options for HTML output ---------------------------------------------------
+# -- Options for HTML output ---------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
@@ -170,24 +176,24 @@
 htmlhelp_basename = 'elephantdoc'
 
 
-# -- Options for LaTeX output --------------------------------------------------
+# -- Options for LaTeX output --------------------------------------------
 
 latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
+    # The paper size ('letterpaper' or 'a4paper').
+    #'papersize': 'letterpaper',
 
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
+    # The font size ('10pt', '11pt' or '12pt').
+    #'pointsize': '10pt',
 
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
+    # Additional stuff for the LaTeX preamble.
+    #'preamble': '',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-  ('index', 'elephant.tex', u'Elephant Documentation',
-   authors, 'manual'),
+    ('index', 'elephant.tex', u'Elephant Documentation',
+     authors, 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -211,7 +217,7 @@
 #latex_domain_indices = True
 
 
-# -- Options for manual page output --------------------------------------------
+# -- Options for manual page output --------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
@@ -224,14 +230,18 @@
 #man_show_urls = False
 
 
-# -- Options for Texinfo output ------------------------------------------------
+# -- Options for Texinfo output ------------------------------------------
 
 # Grouping the document tree into Texinfo files. List of tuples
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    ('index', 'Elephant', u'Elephant Documentation',
-     authors, 'Elephant', 'Elephant is a package for the analysis of neurophysiology data.',
+    ('index',
+     'Elephant',
+     u'Elephant Documentation',
+     authors,
+     'Elephant',
+     'Elephant is a package for the analysis of neurophysiology data.',
      'Miscellaneous'),
 ]
 
@@ -245,7 +255,7 @@
 #texinfo_show_urls = 'footnote'
 
 
-# -- Options for Epub output ---------------------------------------------------
+# -- Options for Epub output ---------------------------------------------
 
 # Bibliographic Dublin Core info.
 epub_title = project
@@ -295,9 +305,11 @@
 mathjax_path = 'https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
 
 # Remove the copyright notice from docstrings:
+
+
 def process_docstring_remove_copyright(app, what, name, obj, options, lines):
     copyright_line = None
-    for i,line in enumerate(lines):
+    for i, line in enumerate(lines):
         if line.startswith(':copyright:'):
             copyright_line = i
             break
@@ -307,4 +319,5 @@ def process_docstring_remove_copyright(app, what, name, obj, options, lines):
 
 
 def setup(app):
-    app.connect('autodoc-process-docstring', process_docstring_remove_copyright)
+    app.connect('autodoc-process-docstring',
+                process_docstring_remove_copyright)

doc/install.rst

@@ -73,8 +73,8 @@ To download and install manually, download the latest package from http://pypi.p
 
 Then::
 
-    $ tar xzf elephant-0.5.0.tar.gz
-    $ cd elephant-0.5.0
+    $ tar xzf elephant-0.6.0.tar.gz
+    $ cd elephant-0.6.0
     $ python setup.py install
     
 or::

doc/release_notes.rst

@@ -2,50 +2,68 @@
 Release Notes
 *************
 
+Elephant 0.6.0 release notes
+============================
+October 12th 2018
+
+New functions
+-------------
+* `cell_assembly_detection` module
+    * New function to detect higher-order correlation structures such as patterns in parallel spike trains based on Russo et al, 2017.
+*  **wavelet_transform()** function in `signal_prosessing.py` module
+    * Function for computing wavelet transform of a given time series based on Le van Quyen et al. (2001)
+
+Other changes
+-------------
+* Switched to multiple `requirements.txt` files which are directly read into the `setup.py`
+* `instantaneous_rate()` accepts now list of spiketrains
+* Minor bug fixes  
+
+
 Elephant 0.5.0 release notes
-===========================
+============================
 April 4nd 2018
 
 New functions
 -------------
 * `change_point_detection` module:
-  * New function to detect changes in the firing rate
+    * New function to detect changes in the firing rate
 * `spike_train_correlation` module:
-  * New function to calculate the spike time tiling coefficient
+    * New function to calculate the spike time tiling coefficient
 * `phase_analysis` module:
-  * New function to extract spike-triggered phases of an AnalogSignal
+    * 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
+    * 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
+    * 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
+    * **inhomogeneous_poisson()** function
 * Modules for Spatio Temporal Pattern Detection (SPADE) `spade_src`:
-  * Module SPADE: `spade.py`
+    * Module SPADE: `spade.py`
 * Module `statistics.py`:
-  * Added CV2 (coefficient of variation for non-stationary time series)
+    * Added CV2 (coefficient of variation for non-stationary time series)
 * Module `spike_train_correlation.py`:
-  * Added normalization in **cross-correlation histogram()** (CCH)
+    * Added normalization in **cross-correlation histogram()** (CCH)
 
 Other changes
 -------------

elephant/__init__.py

@@ -31,4 +31,4 @@
 except ImportError:
     pass
 
-__version__ = "0.5.0"
+__version__ = "0.6.0"

setup.py

@@ -37,7 +37,7 @@
 
 setup(
     name="elephant",
-    version='0.5.0',
+    version='0.6.0',
     packages=['elephant', 'elephant.test'],
     package_data={'elephant': [
         os.path.join('current_source_density_src', 'test_data.mat'),