Merge branch 'release/0.3.0'

Gruntfile.coffee

@@ -48,6 +48,10 @@ module.exports = (grunt) ->
           "<%= cfg.docDir %>/**/*"
           "!<%= cfg.docDir %>/_*/**/*"
           "<%= cfg.docDir %>/_static/**/*"
+          "!**/pyphi.log"
+          "!**/__pyphi_cache__"
+          "!**/__pyphi_cache__.BACKUP"
+          "!**/*.pyc"
         ]
         tasks: ["shell:buildDocs"]
       test:
@@ -71,12 +75,12 @@ module.exports = (grunt) ->
     "watch:test"
   ]
   grunt.registerTask "docs", [
-    "shell:openDocs"
     "shell:buildDocs"
+    "shell:openDocs"
   ]
   grunt.registerTask "watch-docs", [
-    "shell:openDocs"
     "shell:buildDocs"
+    "shell:openDocs"
     "watch:docs"
   ]
   grunt.registerTask "upload-github-docs", [

README.rst

@@ -142,7 +142,6 @@ Correspondence regarding the Matlab code and the IIT 3.0 paper (below) should
 be directed to Larissa Albantakis, PhD, at `albantakis@wisc.edu
 <mailto:albantakis@wisc.edu>`_.
 
-
 Please cite this paper if you use this code:
 ````````````````````````````````````````````
 

docs/_static/custom.css

@@ -18,16 +18,6 @@ div.highlight pre {
 div.highlight pre {
     font-size: 14px;
 }
-.rst-content tt.docutils.literal {
-    font-size: 90%;
-    padding: 2px 5px;
-    border: 1px solid #e1e4e5;
-    color: #099;
-    border-radius: 4px;
-}
-.rst-content dl:not(.docutils) tt.docutils.literal {
-    font-weight: normal;
-}
 .wy-table td p,
 .rst-content table.docutils td p,
 .rst-content table.field-list td p {

docs/api/compute.rst

@@ -0,0 +1,6 @@
+:mod:`compute`
+==============
+
+.. automodule:: pyphi.compute
+    :members:
+    :undoc-members:

docs/api/concept_caching.rst

@@ -0,0 +1,6 @@
+:mod:`concept_caching`
+======================
+
+.. automodule:: pyphi.concept_caching
+    :members:
+    :undoc-members:

docs/api/convert.rst

@@ -0,0 +1,6 @@
+:mod:`convert`
+==============
+
+.. automodule:: pyphi.convert
+    :members:
+    :undoc-members:

docs/api/db.rst

@@ -0,0 +1,6 @@
+:mod:`db`
+=========
+
+.. automodule:: pyphi.db
+    :members:
+    :undoc-members:

docs/api/examples.rst

@@ -0,0 +1,6 @@
+:mod:`examples`
+===============
+
+.. automodule:: pyphi.examples
+    :members:
+    :undoc-members:

docs/api/index.rst

@@ -0,0 +1,20 @@
+API Reference
+=============
+
+PyPhi API documentation, autogenerated from the source code.
+
+.. toctree::
+    :maxdepth: 2
+
+    compute
+    network
+    subsystem
+    convert
+    examples
+    models
+    node
+    concept_caching
+    memory
+    db
+    utils
+    validate

docs/api/memory.rst

@@ -0,0 +1,6 @@
+:mod:`memory`
+=============
+
+.. automodule:: pyphi.memory
+    :members:
+    :undoc-members:

docs/api/models.rst

@@ -0,0 +1,6 @@
+:mod:`models`
+=============
+
+.. automodule:: pyphi.models
+    :members:
+    :undoc-members:

docs/api/network.rst

@@ -0,0 +1,6 @@
+:mod:`network`
+==============
+
+.. automodule:: pyphi.network
+    :members:
+    :undoc-members:

docs/api/node.rst

@@ -0,0 +1,6 @@
+:mod:`node`
+===========
+
+.. automodule:: pyphi.node
+    :members:
+    :undoc-members:

docs/api/subsystem.rst

@@ -0,0 +1,6 @@
+:mod:`subsystem`
+================
+
+.. automodule:: pyphi.subsystem
+    :members:
+    :undoc-members:

docs/api/utils.rst

@@ -0,0 +1,6 @@
+:mod:`utils`
+============
+
+.. automodule:: pyphi.utils
+    :members:
+    :undoc-members:

docs/api/valiate.rst

@@ -0,0 +1,6 @@
+:mod:`validate`
+===============
+
+.. automodule:: pyphi.validate
+    :members:
+    :undoc-members:

docs/compute.rst

@@ -0,0 +1,3 @@
+.. automodule:: pyphi.compute
+    :members:
+    :undoc-members:

docs/conf.py

@@ -15,7 +15,6 @@
 
 import sys
 import os
-import sphinx_rtd_theme
 
 
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -166,7 +165,13 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'sphinx_rtd_theme'
+on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
+if not on_rtd:  # only import and set the theme if we're building docs locally
+    import sphinx_rtd_theme
+    html_theme = 'sphinx_rtd_theme'
+    # Add any paths that contain custom themes here, relative to this
+    # directory.
+    html_theme_path = ['_themes'] + [sphinx_rtd_theme.get_html_theme_path()]
 
 # (Optional) Logo. Should be small enough to fit the navbar (ideally 24x24).
 # Path should be relative to the ``_static`` files directory.
@@ -179,9 +184,6 @@
 
 html_sidebars = {'**': ['localtoc.html']}
 
-# Add any paths that contain custom themes here, relative to this directory.
-html_theme_path = ['_themes'] + [sphinx_rtd_theme.get_html_theme_path()]
-
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
 html_title = version + " documentation"

docs/configuration.rst

@@ -0,0 +1,6 @@
+Configuration
+=============
+
+.. automodule:: pyphi.constants
+    :members:
+    :undoc-members:

docs/examples/basic.rst

@@ -0,0 +1,74 @@
+Basic Usage
+===========
+
+* :func:`pyphi.examples.basic_network`
+* :func:`pyphi.examples.basic_subsystem`
+
+Let's make a simple 3-node network and compute its |big_phi|.
+
+To make a network, we need a TPM, current state, past state, and optionally a
+connectivity matrix. The TPM can be in more than one form; see the
+documentation for :class:`pyphi.network`. Here we'll use the 2-dimensional
+state-by-node form.
+
+    >>> import pyphi
+    >>> import numpy as np
+    >>> tpm = np.array([[0, 0, 0], [0, 0, 1], [1, 0, 1], [1, 0, 0], [1, 1, 0],
+    ...                 [1, 1, 1], [1, 1, 1], [1, 1, 0]])
+
+The current and past states should be |n|-tuples, where |n| is the number of
+nodes in the network, where the |ith| element is the state of the |ith| node in
+the network.
+
+    >>> current_state = (1, 0, 0)
+    >>> past_state = (1, 1, 0)
+
+The connectivity matrix is a square matrix such that the |i,jth| entry is 1 if
+there is a connection from node |i| to node |j|, and 0 otherwise.
+
+    >>> cm = np.array([[0, 0, 1], [1, 0, 1], [1, 1, 0]])
+
+Now we construct the network itself with the arguments we just created:
+
+    >>> network = pyphi.Network(tpm, current_state, past_state,
+    ...                         connectivity_matrix=cm)
+
+The next step is to define a subsystem for which we want to evaluate |big_phi|.
+To make a subsystem, we need the indices of subset of nodes which should be
+included in it and the network that the subsystem belongs to.
+
+In this case, we want the |big_phi| of the entire network, so we simply include
+every node in the network in our subsystem:
+
+    >>> subsystem = pyphi.Subsystem(range(network.size), network)
+
+Now we use :func:`pyphi.compute.big_phi` function to compute the |big_phi| of
+our subsystem:
+
+    >>> phi = pyphi.compute.big_phi(subsystem)
+    >>> round(phi, pyphi.constants.PRECISION)
+    2.312498
+
+If we want to take a deeper look at the integrated-information-theoretic
+properties of our network, we can access all the intermediate quantities and
+structures that are calculated in the course of arriving at a final |big_phi|
+value by using :func:`pyphi.compute.big_mip`. This returns a deeply nested
+object, |BigMip|, that contains data about the subsystem's constellation of
+concepts, cause and effect repertoires, etc.
+
+    >>> mip = pyphi.compute.big_mip(subsystem)
+
+For instance, we can see that this network has 4 concepts:
+
+    >>> len(mip.unpartitioned_constellation)
+    4
+
+The documentation for :mod:`pyphi.models` contains description of these
+structures.
+
+.. note::
+
+    The network and subsystem discussed here are returned by the
+    :func:`pyphi.examples.basic_network` and
+    :func:`pyphi.examples.basic_subsystem` functions.
+