Merge branch 'release/0.7.0'

CHANGELOG.md

@@ -2,6 +2,30 @@ Changelog
 =========
 
 
+0.7.0
+------------------
+_2015-05-08_
+
+### API additions
+- `pyphi.macro` provides several functions to analyze networks over different
+  spatial scales.
+- `.convert.conditionally_independent(tpm)` checks if a TPM is conditionally
+  independent.
+
+### API changes
+- Φ and φ values are now rounded to `config.PRECISION` when stored on objects.
+
+### Fixes
+- Tests for `Subsystem_find_mip_parallel` and `Subsystem_find_mip_sequential`.
+- Slow tests for `compute.big_mip`.
+
+### Refactor
+- Subsystem cause and effect repertoire caching.
+
+### Documentation
+- Added XOR and Macro examples.
+
+
 0.6.0
 ------------------
 _2015-04-20_

docs/api/config.rst

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

docs/api/index.rst

@@ -6,9 +6,11 @@ PyPhi API documentation, autogenerated from the source code.
 .. toctree::
     :maxdepth: 2
 
+    config
     compute
     network
     subsystem
+    macro
     convert
     examples
     models

docs/api/macro.rst

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

docs/api/validate.rst

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

docs/conf.py

@@ -120,6 +120,13 @@
 .. |CD| replace:: :math:`CD`
 .. |ABC| replace:: :math:`ABC`
 .. |CDE| replace:: :math:`CDE`
+.. |n0| replace:: :math:`n_{0}`
+.. |n1| replace:: :math:`n_{1}`
+.. |n2| replace:: :math:`n_{2}`
+.. |n0, n1| replace:: :math:`n_{0}n_{1}`
+.. |n0, n2| replace:: :math:`n_{0}n_{2}`
+.. |n1, n2| replace:: :math:`n_{1}n_{2}`
+.. |n0, n1, n2| replace:: :math:`n_{0}n_{1}n_{2}`
 .. |(AB / DE) x ([] / C)| replace:: :math:`\\frac{AB}{DE} \\times \\frac{\left[\\;\\right]}{C}`
 .. |(A / CD) x ([] / E)| replace:: :math:`\\frac{A}{CD} \\times \\frac{\left[\\;\\right]}{E}`
 .. |([] / C) x (A / D)| replace:: :math:`\\frac{\\left[\\;\\right]}{C} \\times \\frac{A}{D}`
@@ -146,8 +153,30 @@
 .. |PRECISION| replace:: :const:`constants.PRECISION`
 .. |EPSILON| replace:: :const:`constants.EPSILON`
 .. |CM[i][j] = 1| replace:: :math:`CM_{i,j} = 1`
-.. |BigMip| replace:: :class:`pyphi.models.BigMip`
-.. |Concept| replace:: :class:`pyphi.models.Concept`
+.. |compute| replace:: :mod:`~pyphi.compute`
+.. |network| replace:: :mod:`~pyphi.network`
+.. |subsystem| replace:: :mod:`~pyphi.subsystem`
+.. |macro| replace:: :mod:`~pyphi.macro`
+.. |convert| replace:: :mod:`~pyphi.convert`
+.. |examples| replace:: :mod:`~pyphi.examples`
+.. |node| replace:: :mod:`~pyphi.node`
+.. |concept_caching| replace:: :mod:`~pyphi.concept_caching`
+.. |memory| replace:: :mod:`~pyphi.memory`
+.. |db| replace:: :mod:`~pyphi.db`
+.. |utils| replace:: :mod:`~pyphi.utils`
+.. |validate| replace:: :mod:`~pyphi.validate`
+.. |config| replace:: :mod:`~pyphi.config`
+.. |Subsystem| replace:: :class:`~pyphi.subsystem.Subsystem`
+.. |Network| replace:: :class:`~pyphi.network.Network`
+.. |BigMip| replace:: :class:`~pyphi.models.BigMip`
+.. |Concept| replace:: :class:`~pyphi.models.Concept`
+.. |Mip| replace:: :class:`~pyphi.models.Mip`
+.. |Mice| replace:: :class:`~pyphi.models.Mice`
+.. |find_mip| :func:`~pyphi.subsystem.find_mip`
+.. |find_mice| :func:`~pyphi.subsystem.find_mice`
+.. |loli_index2state| replace:: :class:`~pyphi.convert.loli_index2state`
+.. |holi_index2state| replace:: :class:`~pyphi.convert.holi_index2state`
+.. |big_phi > 0| replace:: :math:`\\Phi > 0`
 """
 
 # -- Options for Napoleon (docstring format extension) --------------------

docs/examples/2014paper.rst

@@ -228,7 +228,7 @@ been all on is 1:
     >>> cr[(1, 1, 1)]
     1.0
 
-Now the cause information specified by :math:`A = 1` is 1.5:
+Now the cause information specified by :math:`A = 1` is :math:`1.5`:
 
     >>> subsystem.cause_info((A,), (B, C, D))
     1.5
@@ -258,7 +258,7 @@ where :math:`B, C,` and :math:`D` were all on:
 And so we have less cause information:
 
     >>> subsystem.cause_info((A,), (B, C, D))
-    0.21428400000000067
+    0.214284
 
 Figure 4
 ~~~~~~~~
@@ -308,14 +308,14 @@ mechanism; they only take a purview):
 The Earth Mover's distance between them gives the cause and effect information:
 
     >>> subsystem.cause_info((A,), (A, B, C))
-    0.33333191666400036
+    0.333332
     >>> subsystem.effect_info((A,), (A, B, C))
-    0.24999975000000002
+    0.25
 
 And the minimum of those gives the cause-effect information:
 
     >>> subsystem.cause_effect_info((A,), (A, B, C))
-    0.24999975000000002
+    0.25
 
 
 Figure 5
@@ -338,7 +338,7 @@ Figure 5
            [[ 0. ,  0. ],
             [ 0. ,  0.5]]])
     >>> subsystem.cause_info((A,), (A, B, C))
-    0.9999997500000001
+    1.0
 
 But because it has no outputs, its effect repertoire no different from the unconstrained effect repertoire, so it has no effect information:
 
@@ -370,7 +370,7 @@ selective and it has effect information:
            [[ 0.,  0.],
             [ 0.,  1.]]])
     >>> subsystem.effect_info((A,), (A, B, C))
-    0.4999996875
+    0.5
 
 But because it now has no inputs, its cause repertoire is no different from the
 unconstrained effect repertoire, so it has no cause information:
@@ -408,11 +408,11 @@ These objects contain the :math:`\varphi^{\textrm{MIP}}_{\textrm{cause}}` and
 attributes:
 
     >>> mip_c.phi
-    0.499998999999
+    0.499999
     >>> mip_c.partition
     (Part(mechanism=(n0,), purview=()), Part(mechanism=(n1, n2), purview=(n0, n1, n2)))
     >>> mip_e.phi
-    0.24999975000000002
+    0.25
     >>> mip_e.partition
     (Part(mechanism=(), purview=(n1,)), Part(mechanism=(n0, n1, n2), purview=(n0, n2)))
 
@@ -548,7 +548,7 @@ Conceptual information can be computed using the function named, as you might
 expect, :func:`~pyphi.compute.conceptual_information`:
 
     >>> pyphi.compute.conceptual_information(subsystem)
-    2.1111091388868752
+    2.111109
 
 
 Figure 12
@@ -574,7 +574,7 @@ We can verify that the :math:`\Phi^{\textrm{MIP}}` value and minimal cut are as
 shown in the figure:
 
     >>> big_mip.phi
-    1.916662694926084
+    1.916663
     >>> big_mip.cut
     Cut(severed=(0, 1), intact=(2,))
 
@@ -649,18 +649,18 @@ into, use :func:`~pyphi.compute.condensed`:
 We find that there are 3 complexes: the major complex :math:`ABC` with
 :math:`\Phi \approx 1.92`, and the two minor complexes :math:`DE` with
 :math:`\Phi \approx 0.028` and :math:`FG` with :math:`\Phi \approx 0.069` (note
-that there is typo in the figure; :math:`\FG`'s :math:`\Phi` value should be
-:math:`\0.069`).
+that there is typo in the figure; :math:`FG`'s :math:`\Phi` value should be
+:math:`0.069`).
 
     >>> len(condensed)
     3
     >>> ABC, DE, FG = condensed
     >>> (ABC.subsystem.nodes, ABC.phi)
-    ((n0, n1, n2), 1.916662694926084)
+    ((n0, n1, n2), 1.916663)
     >>> (DE.subsystem.nodes, DE.phi)
-    ((n5, n6), 0.06944459259257413)
+    ((n5, n6), 0.069445)
     >>> (FG.subsystem.nodes, FG.phi)
-    ((n3, n4), 0.027777936507761905)
+    ((n3, n4), 0.027778)
 
 There are several other functions available for working with complexes; see the
 documentation for :func:`~pyphi.compute.subsystems`,

docs/examples/basic.rst

@@ -46,8 +46,8 @@ 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.config.PRECISION)
-    2.312495
+    >>> phi
+    2.312496
 
 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

docs/examples/conditional_independence.rst

@@ -1,5 +1,5 @@
-Conditional Independence Example
-================================
+Conditional Independence
+========================
 
 * :mod:`pyphi.examples.cond_depend_tpm()`
 * :mod:`pyphi.examples.cond_independ_tpm()`

docs/examples/index.rst

@@ -12,6 +12,8 @@ The relevant functions are listed at the beginning of each example.
     basic
     residue
     conditional_independence
+    xor
+    macro
     2014paper