Pyphi

------------------
_2016-02-06_

API changes
- Mechanisms and purviews are now passed to all functions and methods in node
index form (e.g. `(0, 1, 3)`). Previously, many functions took these
arguments as `Node` objects. Since nodes belong to a specific `Subsystem` it
was possible to pass nodes from one subsystem to another subsystem's methods,
leading to incorrect results.
- `constellation_distance` no longer takes a `subsystem` argument because
concepts in a constellation already reference their subsystems.
- Moved `utils.cut_mechanism_indices` and `utils.mechanism_split_by_cut` to
to `Cut.all_cut_mechanisms` and `Cut.splits_mechanism`, respectively;
moved `utils.cut_mice` to `Mice.damaged_by_cut`.
- `Concept.__eq__`: when comparing concepts for equality, we no longer directly
check equality of their subsystems. Concept equality is now defined as
follows:
- Same φ
- Same mechanism node indices cause/effect purview node indices
- Same mechanism state
- Same cause/effect repertoires
- Same networks
This allows two concepts to be equal when _e.g._ the only difference between
them is that one's subsystem is a superset of the other's subsystem.
- `Concept.__hash__`: the above notion of concept equality is also implemented
for concept hashing, so two concepts that differ only in that way will have
the same hash value.
- Disabled concept caching; removed the `config.CACHE_CONCEPTS` option.

API Additions
- Added `config.REPR_VERBOSITY` to control whether `__reprs__` of PyPhi models
use pretty string formatting and control the verbosity of the output.
- Added a `Constellation` object.
- Added `utils.submatrix` and `utils.relevant_connections` functions.
- Added the `macro.effective_info` function.
- Added the `utils.state_of` function.
- Added the `Subsystem.proper_state` attribute. This is the state of the
subsystem's nodes, rather than the entire network state.
- Added an optional Redis-backed cache for Mice objects. This is enabled with
`config.REDIS_CACHE` and configured with `config.REDIS_CONFIG`.
- Enabled parallel concept evaluation with `config.PARALLEL_CONCEPT_EVALUATION`.

Fixes
- `Concept.eq_repertoires` no longer fails when the concept has no cause or
effect.
- Fixed the `Subsystem.proper_state` attribute.

Refactor
- Subsystem Mice and cause/effect repertoire caches; Network purview caches.
Cache logic is now handled by decorators and custom cache objects.
- Block reducibility tests and Mice connection computations.
- Rich object comparisons on phi-objects.

Documentation
- Updated documentation and examples to reflect node-to-index conversion.

------------------
_2015-11-02_

API changes
- Subsystem states are now validated rather than network states. Previously,
network states were validated, but in some cases there can be a
globally-impossible network state that is locally possible for a subsystem
(or vice versa) when considering the subsystem's TPM, which is conditioned
on the external nodes (i.e., background conditions). It is now impossible to
create a subsystem in an impossible state (a `StateUnreachableError` is
thrown), and accordingly no 𝚽 values are calculated for such subsystems; this
may change results from older versions, since in some cases the calculated
main complex was in fact in an impossible. This functionality is enabled by
default but can be disabled via the `VALIDATE_SUBSYSTEM_STATES` option.

------------------
_2015-10-12_

Fixes
- Fixed a caching bug where the subsystem's state was not included in its hash
value, leading to collisions.

------------------
_2015-09-08_

API changes
- Heavily refactored the `pyphi.json` module and renamed it to `pyphi.jsonify`.

------------------
_2015-07-01_

API additions
- Added `convert.nodes2state` function.
- Added `constrained_nodes` keyword argument to `validate.state_reachable`.

API changes
- Concept equality is now more permissive. For two concepts to be considered
equal, they must only have the same φ, the same mechanism and purviews (in
the same state), and the same repertoires.

------------------
_2015-06-30_

API additions
- Added `purviews`, `past_purviews`, `future_purviews` keyword arguments to
various concept-calculating methods. With these, the purviews that are
considered in the concept calculation can be restricted.

API changes
- States are now associated with subsystems rather than networks. Functions in
the `compute` module that operate on networks now also take a state.

Fixes
- Fixed a bug in `compute._constellation_distance_emd` where partitioned
concepts were unable to be moved to the null concept for the EMD calculation.
In some cases, the partitioned system has *greater* ∑φ than the unpartitioned
system; therefore it must be possible for the φ of partitioned-constellation
concepts to be moved to the null concept, not just vice versa.
- Fixed a bug in `compute._constellation_distance_emd` where it was possible to
move concepts around within their own constellation; the distance matrix now
disallows any such intraconstellation paths. This is important because in
some cases paths from a concept in one constellation to a concept the other
can actually be shorter if a detour is taken through a different concept in
the same constellation.
- Fixed a bug in `validate.state_reachable` where network states were
incorrectly validated.
- `macro.emergence` now always returns a macro-network, even when 𝚽 = 0.
- Fixed a bug in `repr(Network)` where the perturbation vector and connectivity
matrix were switched.

Documentation
- Added example describing “magic cuts” that, counterintuitively, can create
more concepts.
- Updated existing documentation to the new subsystem-state association.