all (documentation): Switched docstrings from Doxygen style to Google style. Removed Doxygen documentation and switched to using Sphinx with sphinxcontrib-napoleon extension to implement Google style. Sphinx documentation included.

all (organization): Created Python package dictionary_learning within project for easy use. Created Netbeans project using the Python code.

advanced_debugging: Created a new file that contains a decorator to log entering and exiting functions (optionally can log arguments).

advanced_iterators: Created a few simple functions to ease construction of numpy.ndarray objects.

batch_learner: Broke up some longer commands. Changed a couple minor things due to features not present in NumPy version 1.7 vs. 1.8.

neuron_viewer: Restructured to properly call parent constructor (no more dictionary hack).

NeuronViewer: Fixed lines to properly call class from neuron_viewer (as hack was removed).

random_dictionary_learning_data: Created a new file that generates random images (like those seen in data) to allow for a regression test on batch_learner.
random_dictionary_learning_data: Moved to test directory where it was intended to be.
neuron_viewer: Manually wrapped a few doctrings that were a little long.
batch_learner: Manually wrapped a few doctrings that were a little long.
advanced_iterators: Added docstrings. Reran Sphinx to catch the changes.
advanced_iterators: Added comments. Reran Sphinx to catch the changes (as it has a code viewer, which shouldn't be affected).
random_dictionary_learning_data: As this was moved to tests, the documentation of it has been removed from Sphinx.
NeuronViewer: iPython checkpoints should not be part of the repository.
neuron_viewer: Removed compiled Python.
advanced_debugging: Removed compiled Python.
neuron_viewer: Added support for images without time.
NeuronViewer: Added max of dictionary to iPython notebook.
docs: Updated Sphinx.
Removed doc/_build.
advanced_debugging: Added __wrapped__ to the wrapped callable for easy access to the underlying layer.
batch_learner: Removed IOError in favor of Exception as IOError is misleading. Suggests it was a system error.
neuron_veiwer: Added support for arrays have no time dimension (just an image).
NeuronViewer: Added lines to view regression images (commented). Added support for viewing the maximum projection of the dictionary and image.
batch_learner: Broke up some lines into smaller lines. Cleaned up some comments and docstrings.
pathHelpers: Copied from ilastik code base. (Do not want to depend on ilastik while developing code for the Svoboda lab plugin. This will change in the future.)
make: Made sure the Windows bat file includes a line for building the RST files (untested though).
.gitignore: Added gitignore file to stop commits of temporary files (ending with ~), compile Python files (.pyc) files, special Mac directory files (.DS_Store), and the Sphinx build directory (docs/_build).
random_dictionary_learning_data: Created a constructor for DictionaryLearningRandomDataSample that clearly sets its values to None.
random_dictionary_learning_data: Added simple docstring.
.gitignore: Added newline.
random_dictionary_learning_data: Shortened code lines and clarified ambiguous sections.