copying to personal repo

doc/source/an_model.rst

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+an_model
+--------
+
+.. automodule:: cnmodel.an_model
+    :members:
+    :undoc-members:
+    :show-inheritance:
+ 
+
+cnmodel.an_model.cache
+======================
+
+.. automodule:: cnmodel.an_model.cache
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.an_model.wrapper
+========================
+
+.. automodule:: cnmodel.an_model.wrapper
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+

doc/source/architecture.rst

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+Architecture of CNModel
+=======================
+
+CNModel is built in a layered architecture that provides both high-level tools 
+for constructing and simulating networks, as well as low-level access to the 
+individual components. The model consists of three major pieces: *cell types*,
+which describe the morphology and membrane physiology of the various cell types
+in the cochlear nucleus; *synapse types*, which describe the strength, kinetics,
+and short-term plasticity of the many synaptic connections; and *populations*,
+which describe the aggregate organization of cell types, including their
+distribution within the nucleus and their patterns of connectivity. 
+
+    .. figure:: architecture.svg
+
+
+Cells
+-----
+
+The cell types found in the cochlear nucleus (bushy, t-stellate, etc.) are each
+represented in CNModel as classes that inherit from the base `Cell` class. One 
+instance of any of these classes represents exactly one neuron, and internally
+manages any number of NEURON sections and mechanisms.
+
+Each class is responsible for determining the morphology and intrinsic membrane
+properties of the cell it represents. Additionally, cell classes define the
+properties of their synapses in a cooperative manner: the pre- snd postsynaptic 
+cells each create half of the synapse.
+
+Morphology can be procedurally generated (usually a single somatic section,
+perhaps with another for a dendrite and/or axon), or it can be loaded from an
+SWC file. After the cell morphology is established, the membrane is "decorated"
+with channels using a `ChannelDecorator` object. 
+
+Cell classes may be further divided into a class hierarchy. For example, the
+base `DStellate` class is further inherited by `DStellateRothman` and 
+`DStellateEager` classes that each implement different D-stellate models that
+have been published previously. To simplify (and in many cases to automate) the
+creation of cells each base cell class (`Bushy`, `SGC`, `TStellate`, etc.) 
+implements a `create` method that can be used to generate instances from any of
+the subclasses.
+
+
+Synapses
+--------
+
+Every synapse in CNModel is represented by an instance of the `Synapse` class.
+This class contains two objects: a `Terminal`, and a `PSD`. Synapses are created
+by calling the `connect` method of the presynaptic cell with the postsynaptic
+cell as an argument::
+    
+    pre_cell.connect(post_cell)
+    
+When `connect` is called, the presynaptic terminal is created by calling 
+``pre_cell.make_terminal()``, and the postsynaptic receptors are created by
+calling ``post_cell.make_psd()``. In this way, both pre- and postsynaptic
+cells are given a chance to influence the creation of the synapse.
+
+CNModel implements most synapses in two different ways. The first is a simple 
+synapse that implements variable amplitude, short-term plasticity, and double-
+exponential rise/fall kinetics. This synapse is relatively efficient to compute
+and simple to configure. The second synapse implementation is a much more
+physiologically detailed model that includes stochastic release from multiple
+release zones per terminal, synaptic cleft diffusion, and state models of 
+postsynaptic receptors. This synapse is computationally expensive but may capture
+important behaviors that are not possible with the simpler implementation.
+
+
+Populations
+-----------
+
+Populations are objects that encapsulate a group of cells sharing a common cell
+class. Each base `Cell` class has a corresponding `Population` class that
+implements the organization of many cells within the nucleus and the patterns
+of connectivity between populations.
+
+Conceptually, a `Population` represents *all* cells of a particular type within
+the nucleus. When a population is created, it initially decides how many cells
+is will represent and how to distribute properties across those cells. For
+example, an `SGC` population describes 10k cells distributed uniformly across
+the tonotopic axis. Initially, none of these 10k cells are created; rather, 
+each cell is simply represented as a virtual placeholder, and only instantiated
+when it is explicitly requested or when it is required to satisfy the input 
+requirements for another cell.
+
+Populations are connected to each other in much the same way cells are::
+    
+    pre_pop.connect(post_pop)
+
+Like the virtual cells, however, this connection does not create any synapses,
+but instead merely records the fact that one population of cells projects to
+another. Once the populations of interest are created and connected, the user
+then manually instantiates only the cells that they wish to record from, and 
+finally the entire network of presynaptic inputs is automatically instantiated.
+
+Because populations manage the creation of synaptic connections between large
+groups of neurons, they are also responsible for ensuring that the appropriate
+patterns of connectivity are followed. For example, this allows us to ensure 
+that bushy cells are automatically connected to auditory nerve fibers coming
+from a relatively narrow window across the tonotopic axis, whereas D-stellate
+cells integrate the same inputs across a broader window.
+
+
+Physiological parameters
+------------------------
+
+Throughout the model we use physiological parameters (channel kinetics, 
+synaptic strengths, convergence ratios, etc.) that are often derived
+from published reports. In an attempt to make the provenance of these
+parameters clear, we have separated them from the source code and embedded
+them in annotated tables. These tables are found in `cnmodel/data`, and are
+automatically parsed by the model as they are needed.
+
+Morphology
+----------
+
+The model implements the ability to use morphological reconstructions of
+cells, as rendered in hoc files, the native NEURON format. These reconstructions
+can be decorated with ion channels and synapses according to pre-specified
+tables or pre-defined rules. 
+
+Unit testing
+------------
+
+CNModel attempts to reproduce several specific published observations.
+The complexity of the model makes it quite fragile--small modifications to one
+physiological parameter may have unexpected (and sometimes unnoticed) 
+consequences in the output of the model. 
+
+To combat this unavoidable fragility, CNModel includes a large battery of unit
+tests that are used to ensure the model output is stable across modifications
+and platforms, and that it does reproduce our target observations within
+reasonable limits. As such, any modification to the model should usually be
+followed soon after by running the unit tests (these depend on the py.test
+package and may be invoked by running the included `test.py` script).
+
+
+Auditory nerve input
+--------------------
+
+CNModel builds from the auditory periphery model developed by Zilany et al. 
+(2014). The periphery model converts auditory stimuli into 
+spike trains for auditory nerve fibers of a specific CF and SR group. 
+
+CNModel uses the Python version of the auditory periphery model
+as implemented by Rudnicki and Hemmert (available from https://github.com/mrkrd/cochlea).
+This version does not require MATLAB, and in some simulations may run slightly faster
+because there is no delay associated with loading (and unloading) MATLAB. The
+interface is otherwise exactly the same, and the model type can be selected
+at runtime.
+
+An alternative approach is to use the original auditory periphery model. Because
+this model was developed in MATLAB, CNModel uses a Python-to-MATLAB bridge
+that transparently invokes the periphery model in a background process.
+When using CNModel, is is generally not necessary to manually interact with
+MATLAB in any way; this interaction is wrapped within functions in the
+`cnmodel/an_model` subpackage.
+
+At present, there is no mechanism for feedback from the cochlear nucleus model
+back into the auditory periphery model. As such, the output of the periphery
+model is a convenient place to do some caching--we can precompute auditory
+nerve spike trains in response to various sound stimuli and reuse those spike
+trains to improve the computational performance of the nucleus model. This
+caching is performed automatically, but relies on the use of `Sound` objects
+(described below) as a mechanism for storing and retrieving cached spike trains.
+
+
+Generating sound stimuli
+------------------------
+
+Sound stimuli are defined as subclasses of `cnmodel.util.sound.Sound`. Each 
+subclass (for example, `TonePip` and `NoisePip`) defines the function for
+generating a sound waveform, but also provides a unique key that is used to
+store and retrieve auditory nerve spike trains that were generated with
+a particular stimulus. 
+
+`Sound` objects may be passed directly to `SGC` cells or populations, and the
+necessary spike trains will be automatically computed (or read from cache).
+
+
+

doc/source/cells.rst

@@ -0,0 +1,106 @@
+Cell classes
+------------
+
+.. automodule:: cnmodel.cells
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. autoclass:: Cell
+   :members:
+
+Individual cell subclasses
+--------------------------
+
+cnmodel.cells.bushy
+===================
+
+.. automodule:: cnmodel.cells.bushy
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.cells.cartwheel
+=======================
+
+.. automodule:: cnmodel.cells.cartwheel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+.. cnmodel.cells.cell class
+.. -------------------------
+..
+.. .. automodule:: cnmodel.cells.cell
+..     :members:
+..     :undoc-members:
+..     :show-inheritance:
+..     :noindex:
+
+cnmodel.cells.dstellate
+=======================
+
+.. automodule:: cnmodel.cells.dstellate
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.cells.hh
+================
+
+.. automodule:: cnmodel.cells.hh
+    :members:
+    :undoc-members:
+    :noindex:
+    :show-inheritance:
+
+cnmodel.cells.octopus
+=====================
+
+.. automodule:: cnmodel.cells.octopus
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.cells.pyramidal
+=======================
+
+.. automodule:: cnmodel.cells.pyramidal
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.cells.sgc
+=================
+
+.. automodule:: cnmodel.cells.sgc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.cells.tstellate
+=======================
+
+.. automodule:: cnmodel.cells.tstellate
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.cells.tuberculoventral
+==============================
+
+.. automodule:: cnmodel.cells.tuberculoventral
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+
+

doc/source/conf.py

@@ -0,0 +1,167 @@
+# -*- coding: utf-8 -*-
+#
+# CNModel documentation build configuration file, created by
+# sphinx-quickstart on Sun Apr  2 15:20:59 2017.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# 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.
+#
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../.."))
+
+
+# -- 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.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = ".rst"
+
+# The master toctree document.
+master_doc = "index"
+autoclass_content = "both"
+
+# General information about the project.
+project = u"CNModel"
+copyright = u"2017, 2018, Paul B. Manis and Luke Campagnola"
+author = u"Paul B. Manis and Luke Campagnola"
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = u"0"
+# The full version, including alpha/beta/rc tags.
+release = u"0.2"
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "sphinx"
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+# html_theme = 'alabaster'
+html_theme = "classic"
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = "CNModeldoc"
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (
+        master_doc,
+        "CNModel.tex",
+        u"CNModel Documentation",
+        u"Paul B. Manis and Luke Campagnola",
+        "manual",
+    )
+]
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [(master_doc, "cnmodel", u"CNModel Documentation", [author], 1)]
+
+
+# -- 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 = [
+    (
+        master_doc,
+        "CNModel",
+        u"CNModel Documentation",
+        author,
+        "CNModel",
+        "One line description of project.",
+        "Miscellaneous",
+    )
+]

doc/source/data.rst

@@ -0,0 +1,37 @@
+cnmodel.data package
+--------------------
+
+.. autofunction:: cnmodel.data.get
+
+.. autofunction:: cnmodel.data.get_source
+
+.. autofunction:: cnmodel.data.add_table_data
+
+cnmodel.data.connectivity
+=========================
+
+.. literalinclude:: ../../cnmodel/data/connectivity.py
+   :language: python
+   :linenos:
+
+cnmodel.data.synapses
+=====================
+
+.. literalinclude:: ../../cnmodel/data/synapses.py
+   :language: python
+   :linenos:
+
+cnmodel.data.populations
+========================
+
+.. literalinclude:: ../../cnmodel/data/populations.py
+   :language: python
+   :linenos:
+    
+cnmodel.data.ionchannels
+========================
+
+.. literalinclude:: ../../cnmodel/data/ionchannels.py
+   :language: python
+   :linenos:
+    

doc/source/decorator.rst

@@ -0,0 +1,16 @@
+cnmodel.decorator package
+-------------------------
+
+.. automodule:: cnmodel.decorator
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+cnmodel.decorator.decorator
+============================
+
+.. automodule:: cnmodel.decorator.decorator
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:

doc/source/examples.rst

@@ -0,0 +1,31 @@
+
+Examples
+========
+
+
+Contents:
+
+.. toctree::
+    :maxdepth: 0
+
+    examples/test_circuit
+    examples/test_mechanisms
+    examples/test_an_model
+    examples/test_bushy_variation
+    examples/test_simple_synapses
+    examples/test_mso_inputs
+    examples/test_sgc_input_phaselocking
+    examples/test_populations
+    examples/test_sgc_input
+    examples/test_cells
+    examples/test_physiology
+    examples/figures
+    examples/test_ccstim
+    examples/test_sounds
+    examples/toy_model
+    examples/test_sound_stim
+    examples/test_sgc_input_PSTH
+    examples/test_synapses
+    examples/test_decorator
+    examples/plot_hcno_kinetics
+    examples/play_test_sounds

doc/source/examples/figures.rst

@@ -0,0 +1,22 @@
+
+examples.figures
+----------------
+
+Plot selected figures from paper, Manis and Campagnola, Hearing Research, 2018.
+To obtain the original results, this should be run after checking out the 
+"hearing-research-2018" tag available in the repository on github.
+
+From the main cnmodel directory::
+
+    $ ./examples figures.sh fignum
+
+where fignum is one of 2a, 2b, 2c, 3, 4, 5, 6a, 6b, or 7.
+
+Note that Figure 7 may take several **hours** to generate.
+
+
+
+
+.. literalinclude:: ../../../examples/figures.py
+   :language: python
+   :linenos:

doc/source/examples/play_test_sounds.rst

@@ -0,0 +1,10 @@
+
+examples.play_test_sounds
+-------------------------
+
+.. automodule:: examples.play_test_sounds
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+

doc/source/examples/plot_hcno_kinetics.rst

@@ -0,0 +1,10 @@
+
+examples.plot_hcno_kinetics
+---------------------------
+
+.. automodule:: examples.plot_hcno_kinetics
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+

doc/source/examples/test_an_model.rst

@@ -0,0 +1,10 @@
+
+examples.test_an_model
+----------------------
+
+.. automodule:: examples.test_an_model
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+

doc/source/examples/test_bushy_variation.rst

@@ -0,0 +1,10 @@
+
+examples.test_bushy_variation
+-----------------------------
+
+.. automodule:: examples.test_bushy_variation
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+

doc/source/examples/test_ccstim.rst

@@ -0,0 +1,10 @@
+
+examples.test_ccstim
+--------------------
+
+.. automodule:: examples.test_ccstim
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+

doc/source/examples/test_cells.rst

@@ -0,0 +1,10 @@
+
+examples.test_cells
+-------------------
+
+.. automodule:: examples.test_cells
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+

doc/source/examples/test_circuit.rst

@@ -0,0 +1,10 @@
+
+examples.test_circuit
+---------------------
+
+.. automodule:: examples.test_circuit
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+

doc/source/examples/test_decorator.rst

@@ -0,0 +1,10 @@
+
+examples.test_decorator
+-----------------------
+
+.. automodule:: examples.test_decorator
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+

doc/source/examples/test_mechanisms.rst

@@ -0,0 +1,10 @@
+
+examples.test_mechanisms
+------------------------
+
+.. automodule:: examples.test_mechanisms
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+

doc/source/examples/test_mso_inputs.rst

@@ -0,0 +1,10 @@
+
+examples.test_mso_inputs
+------------------------
+
+.. automodule:: examples.test_mso_inputs
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+

doc/source/examples/test_physiology.rst

@@ -0,0 +1,10 @@
+
+examples.test_physiology
+------------------------
+
+.. automodule:: examples.test_physiology
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+

doc/source/examples/test_populations.rst

@@ -0,0 +1,10 @@
+
+examples.test_populations
+-------------------------
+
+.. automodule:: examples.test_populations
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+

doc/source/examples/test_sgc_input.rst

@@ -0,0 +1,10 @@
+
+examples.test_sgc_input
+-----------------------
+
+.. automodule:: examples.test_sgc_input
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+

doc/source/examples/test_sgc_input_PSTH.rst

@@ -0,0 +1,10 @@
+
+examples.test_sgc_input_PSTH
+----------------------------
+
+.. automodule:: examples.test_sgc_input_PSTH
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+

doc/source/examples/test_sgc_input_phaselocking.rst

@@ -0,0 +1,10 @@
+
+examples.test_sgc_input_phaselocking
+------------------------------------
+
+.. automodule:: examples.test_sgc_input_phaselocking
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+

doc/source/examples/test_simple_synapses.rst

@@ -0,0 +1,10 @@
+
+examples.test_simple_synapses
+-----------------------------
+
+.. automodule:: examples.test_simple_synapses
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+

doc/source/examples/test_sound_stim.rst

@@ -0,0 +1,10 @@
+
+examples.test_sound_stim
+------------------------
+
+.. automodule:: examples.test_sound_stim
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+

doc/source/examples/test_sounds.rst

@@ -0,0 +1,10 @@
+
+examples.test_sounds
+--------------------
+
+.. automodule:: examples.test_sounds
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+

doc/source/examples/test_synapses.rst

@@ -0,0 +1,10 @@
+
+examples.test_synapses
+----------------------
+
+.. automodule:: examples.test_synapses
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+

doc/source/examples/toy_model.rst

@@ -0,0 +1,10 @@
+
+examples.toy_model
+------------------
+
+.. automodule:: examples.toy_model
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+

doc/source/index.rst

@@ -0,0 +1,32 @@
+.. CNModel documentation master file, created by
+   sphinx-quickstart on Sun Apr  2 15:20:59 2017.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to CNModel's documentation!
+===================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   readme
+   architecture
+
+.. toctree::
+   :maxdepth: 1
+   
+   examples
+   modules
+
+Indices and tables
+==================
+
+* :ref:`modindex`
+* :ref:`genindex`
+* :ref:`search`
+
+.. automodule:: cnmodel
+    :members:
+    :show-inheritance:
+    :undoc-members:

doc/source/modules.rst

@@ -0,0 +1,18 @@
+API Reference
+=============
+
+Contents:
+
+.. toctree::
+    :maxdepth: 0
+
+    an_model
+    cells
+    data
+    decorator
+    morphology
+    synapses
+    populations
+    protocols
+    util
+

doc/source/morphology.rst

@@ -0,0 +1,26 @@
+cnmodel.morphology package
+--------------------------
+
+.. automodule:: cnmodel.morphology
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+cnmodel.morphology.hoc_reader
+=============================
+
+.. automodule:: cnmodel.morphology.hoc_reader
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.morphology.morphology
+=============================
+
+.. automodule:: cnmodel.morphology.morphology
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+

doc/source/populations.rst

@@ -0,0 +1,54 @@
+cnmodel.populations package
+---------------------------
+
+
+.. automodule:: cnmodel.populations
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+cnmodel.populations.population
+===============================
+
+.. automodule:: cnmodel.populations.population
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+    
+cnmodel.populations.bushy
+=========================
+
+.. automodule:: cnmodel.populations.bushy
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.populations.dstellate
+=============================
+
+.. automodule:: cnmodel.populations.dstellate
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.populations.sgc
+=======================
+
+.. automodule:: cnmodel.populations.sgc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+    
+cnmodel.populations.tstellate
+=============================
+
+.. automodule:: cnmodel.populations.tstellate
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:

doc/source/protocols.rst

@@ -0,0 +1,72 @@
+cnmodel.protocols package
+=========================
+
+.. automodule:: cnmodel.protocols
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+cnmodel.protocols.cc
+--------------------
+
+.. automodule:: cnmodel.protocols.cc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.protocols.iv_curve
+--------------------------
+
+.. automodule:: cnmodel.protocols.iv_curve
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.protocols.population_test
+---------------------------------
+
+.. automodule:: cnmodel.protocols.population_test
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.protocols.protocol
+--------------------------
+
+.. automodule:: cnmodel.protocols.protocol
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.protocols.simple_synapse_test
+-------------------------------------
+
+.. automodule:: cnmodel.protocols.simple_synapse_test
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.protocols.synapse_test
+------------------------------
+
+.. automodule:: cnmodel.protocols.synapse_test
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.protocols.vc_curve
+--------------------------
+
+.. automodule:: cnmodel.protocols.vc_curve
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+

doc/source/readme.rst

@@ -0,0 +1 @@
+.. include:: ../../README.rst

doc/source/synapses.rst

@@ -0,0 +1,83 @@
+cnmodel.synapses package
+========================
+
+.. automodule:: cnmodel.synapses
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+cnmodel.synapses.exp2_psd
+-------------------------
+
+.. automodule:: cnmodel.synapses.exp2_psd
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.synapses.glu_psd
+------------------------
+
+.. automodule:: cnmodel.synapses.glu_psd
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.synapses.gly_psd
+-------------------------
+
+.. automodule:: cnmodel.synapses.gly_psd
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.synapses.psd
+--------------------
+
+.. automodule:: cnmodel.synapses.psd
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.synapses.simple_terminal
+--------------------------------
+
+.. automodule:: cnmodel.synapses.simple_terminal
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.synapses.stochastic_terminal
+------------------------------------
+
+.. automodule:: cnmodel.synapses.stochastic_terminal
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.synapses.synapse
+------------------------
+
+.. automodule:: cnmodel.synapses.synapse
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.synapses.terminal
+-------------------------
+
+.. automodule:: cnmodel.synapses.terminal
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+
+

doc/source/util.rst

@@ -0,0 +1,147 @@
+cnmodel.util package
+--------------------
+
+Utility routines used within cnmodel
+
+.. automodule:: cnmodel.util
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+    
+cnmodel.util.Params
+====================
+
+.. automodule:: cnmodel.util.Params
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.util.ccstim
+===================
+
+.. automodule:: cnmodel.util.ccstim
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.util.expfitting
+=======================
+
+.. automodule:: cnmodel.util.expfitting
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.util.filelock
+=====================
+
+.. automodule:: cnmodel.util.filelock
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.util.find_point
+=======================
+
+.. automodule:: cnmodel.util.find_point
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.util.fitting
+====================
+
+.. automodule:: cnmodel.util.fitting
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.util.get_anspikes
+=========================
+
+.. automodule:: cnmodel.util.get_anspikes
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.util.matlab_proc
+========================
+
+.. automodule:: cnmodel.util.matlab_proc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.util.nrnutils
+=====================
+
+.. automodule:: cnmodel.util.nrnutils
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.util.process
+====================
+
+.. automodule:: cnmodel.util.process
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.util.pynrnutilities
+===========================
+
+.. automodule:: cnmodel.util.pynrnutilities
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.util.random_seed 
+========================
+
+.. automodule:: cnmodel.util.random_seed
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.util.sound
+==================
+
+.. automodule:: cnmodel.util.sound
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.util.stim
+=================
+
+.. automodule:: cnmodel.util.stim
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+cnmodel.util.user_tester
+========================
+
+.. automodule:: cnmodel.util.user_tester
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :noindex:
+
+