Merge pull request #51 from baccuslab/dev

Pulling in dev changes: documentation, pep8 compliance, bug fixes, no more underscores
baccuslab · Jun 26, 2015 · 5c7239f · 5c7239f
2 parents dfe37c9 + bc0b883
commit 5c7239f
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Showing 17 changed files with 5,356 additions and 4,194 deletions.
diff --git a/.gitignore b/.gitignore
@@ -7,6 +7,8 @@
 *.o
 *.so
 *.pyc
+build/
+dist/
 
 # Packages #
 ############

diff --git a/__init__.py b/__init__.py
@@ -6,23 +6,24 @@
 
 Modules
 -------
-    binary          - Interact with *.bin raw experiment data files
-    spiketools      - Tools for manipulating spike trains
-    filtertools     - Analysis of linear filters
-    stimulustools   - Tools for getting stimulus history and statistics
-    visualizations  - Tools for plotting receptive fields, filters, etc.
-    nonlinearities  - Methods for estimating nonlinearities
+spiketools      - Tools for manipulating spike trains
+filtertools     - Analysis of linear filters
+stimulustools   - Tools for getting stimulus history and statistics
+visualizations  - Tools for plotting receptive fields, filters, etc.
+nonlinearities  - Methods for estimating nonlinearities
 
 For more information, see the accompanying README.md
 
 """
 
 __all__ = [
-        'spiketools', 
-        'filtertools', 
-        'stimulustools', 
-        'visualizations', 
-        'nonlinearities']
-__version__ = '0.2'
+        'spiketools',
+        'nonlinearities',
+        'stimulustools',
+        'visualizations',
+        'filtertools'
+        ]
+__version__ = '0.3'
 
 from pyret import *
+
diff --git a/demo/.gitattributes b/demo/.gitattributes
diff --git a/demo/.ipynb_checkpoints/Demo of pyret utilities-checkpoint.ipynb b/demo/.ipynb_checkpoints/Demo of pyret utilities-checkpoint.ipynb
diff --git a/demo/Demo of pyret utilities.html b/demo/Demo of pyret utilities.html
diff --git a/demo/Demo of pyret utilities.ipynb b/demo/Demo of pyret utilities.ipynb
diff --git a/doc/Makefile b/doc/Makefile
@@ -5,7 +5,7 @@
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
 PAPER         =
-BUILDDIR      = ../../pyret-doc
+BUILDDIR      = ../../pyret-docs
 
 # User-friendly check for sphinx-build
 ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
@@ -52,7 +52,7 @@ clean:
 html:
 	$(SPHINXBUILD) -ab html $(ALLSPHINXOPTS) $(BUILDDIR)
 	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)."
 
 dirhtml:
 	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml

diff --git a/doc/changelog.rst b/doc/changelog.rst
@@ -3,4 +3,5 @@ Changelog
 
 A list of new features, improvements, and bug-fixes in each release.
 
-.. include:: releases/v0.2.0.rst
+.. include:: releases/v0.3.rst
+.. include:: releases/v0.2.rst
diff --git a/doc/install.rst b/doc/install.rst
@@ -16,10 +16,20 @@ The fastest way to install is by grabbing the code from Github:
 Dependencies
 ------------
 
-Pyret requires that you have ``numpy``, ``scipy``, ``matplotlib``, and ``seaborn`` installed.
+Pyret requires the following dependencies:
+
+- ``numpy`` 
+
+- ``scipy``
+
+- ``scikit-image``
+
+- ``matplotlib``
+
+- ``seaborn``
 
 Development
 -----------
 
-To contribute to ``pyret``, you'll need to also install ``sphinx`` for documentation and
+To contribute to ``pyret``, you'll need to also install ``sphinx`` and ``numpydoc`` for documentation and
 ``nose`` for testing. We adhere to the `NumPy/SciPy documentation standards <https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt#docstring-standard>`_.
diff --git a/doc/releases/v0.2.0.rst → doc/releases/v0.2.rst b/doc/releases/v0.2.0.rst → doc/releases/v0.2.rst
@@ -1,6 +1,6 @@
-
-v0.2.0 (February 2015)
-----------------------
+====================
+v0.2 (February 2015)
+====================
 
 This is a major release with a number of API changes, enhancements, and bug fixes.
 

diff --git a/doc/releases/v0.3.rst b/doc/releases/v0.3.rst
@@ -0,0 +1,13 @@
+==================
+v0.3 (In Progress)
+==================
+
+API changes
+-----------
+
+General package changes
+-----------------------
+
+Known issues
+------------
+