Merge branch 'release/0.9.0'

.coveragerc

@@ -6,6 +6,9 @@ branch = True
 [report]
 # Regexes for lines to exclude from consideration
 exclude_lines =
+    # Match pylint syntax
+    coverage: disable
+
     # Have to re-enable the standard pragma
     pragma: no cover
 
@@ -18,7 +21,6 @@ exclude_lines =
     def print_
     def dprint
 
-
     # Don't complain if tests don't hit defensive assertion code:
     raise AssertionError
     raise NotImplementedError

.flake8

@@ -0,0 +1,15 @@
+[flake8]
+
+ignore = F401
+
+exclude =
+  __pycache__,
+  __pyphi_cache__,
+  .cache,
+  .git,
+  .coverage,
+  build,
+  dist,
+  docs,
+  htmlcov,
+  benchmarks,

.gitignore

@@ -1,23 +1,29 @@
 __pycache__
+.cache
 .ropeproject
-node_modules
 .venv
 .env
 .pythonrc*
 .agignore
+.projectile
 **/*.pyc
 **/*.egg-info
 **/*.log
 **/*.BACKUP
 pyphi/data/hamming_matrices/10.npy
-
 __pyphi_cache__
 dist
 build
+profiling
 docs/_build
-github-docs
 .coverage
 htmlcov
 results
 html
 env
+benchmarks/pyphi_config.yml
+profiling/pyphi_config.yml
+ignore
+.ignore
+startup.py
+my_requirements.txt

.pylintrc

@@ -0,0 +1,19 @@
+[MASTER]
+
+ignore=
+  __pycache__,
+  __pyphi_cache__,
+  .cache,
+  .git,
+  .coverage,
+  build,
+  dist,
+  docs,
+  htmlcov,
+  benchmarks,
+
+[MESSAGES CONTROL]
+
+disable=
+  no-member,
+  invalid-name

.travis.yml

@@ -14,23 +14,22 @@ services:
 
 python:
   - "3.4"
+  - "3.5"
+  - "3.6"
 
 # Setup miniconda
 before_install:
-  - wget http://repo.continuum.io/miniconda/Miniconda3-3.3.0-Linux-x86_64.sh -O miniconda.sh
+  - wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
   - chmod +x miniconda.sh
   - ./miniconda.sh -b
   - export PATH=/home/travis/miniconda3/bin:$PATH
   # Update conda itself
   - conda update --yes conda
-  # The next couple lines fix a crash with multiprocessing on Travis and are
-  # not specific to using Miniconda
-  # - sudo rm -rf /dev/shm
-  # - sudo ln -s /run/shm /dev/shm
 
 # Install packages
 install:
-  - conda install --yes python=$TRAVIS_PYTHON_VERSION pip numpy scipy
+  - conda create --yes --name=$TRAVIS_PYTHON_VERSION python=$TRAVIS_PYTHON_VERSION numpy scipy
+  - source activate $TRAVIS_PYTHON_VERSION
   - pip install -r requirements.txt
   - pip install coveralls
   - pip freeze

CACHING.rst

@@ -0,0 +1,57 @@
+Caching
+~~~~~~~
+
+PyPhi can optionally store the results of |Phi| calculations as they're
+computed in order to avoid expensive re-computation. These results can be
+stored locally on the filesystem (the default setting), or in a full-fledged
+database.
+
+Caching is configured either in the ``pyphi_config.yml`` file or at runtime by
+modifying ``pyphi.config``. See the `configuration documentation
+<http://pyphi.readthedocs.io/en/stable/configuration.html>`_ for more
+information.
+
+
+Caching with MongoDb
+````````````````````
+
+Using the default caching system is easier and works out of the box, but using
+a database is more robust.
+
+To use the database-backed caching system, you must install `MongoDB
+<http://www.mongodb.org/>`_. Please see their `installation guide
+<http://docs.mongodb.org/manual/installation/>`_ for instructions.
+
+Once you have MongoDB installed, use ``mongod`` to start the MongoDB server.
+Make sure the ``mongod`` configuration matches the PyPhi's database
+configuration settings in ``pyphi_config.yml`` (see the `configuration section
+<https://pythonhosted.org/pyphi/index.html#configuration>`_ of PyPhi's
+documentation).
+
+You can also check out MongoDB's `Getting Started guide
+<http://docs.mongodb.org/manual/tutorial/getting-started/>`_ or the full
+`manual <http://docs.mongodb.org/manual/>`_.
+
+
+Caching with Redis
+``````````````````
+
+PyPhi can also use Redis as a fast in-memory global LRU cache to store Mice
+objects, reducing the memory load on PyPhi processes.
+
+`Install Redis <http://redis.io/download>`_. The `redis.conf` file provided
+with PyPhi includes the minimum settings needed to run Redis as an LRU cache:
+
+.. code:: bash
+
+    redis-server /path/to/pyphi/redis.conf
+
+Once the server is running you can enable Redis caching by setting
+``REDIS_CACHE: true`` in your ``pyphi_config.yml``.
+
+**Note:** PyPhi currently flushes the connected Redis database at the start of
+every execution. If you are running Redis for another application be sure PyPhi
+connects to its own Redis server.
+
+
+.. |phi| unicode:: U+1D6BD .. mathematical bold capital phi

CHANGELOG.md

@@ -1,6 +1,110 @@
 Changelog
 =========
 
+0.9.0
+-----
+_2017-12-04_
+
+### API changes:
+- Many functions have been refactored to different modules; see the "Refactor"
+  section for details.
+- `compute.possible_complexes` no longer includes the empty subsystem.
+- Made `is_cut` a property.
+- Renamed `macro.list_all_partitions` and `macro.list_all_groupings` to
+  `all_partitions` and `all_groupings`. Both are now generators and return
+  nested tuples instead of lists.
+- Moved `macro.make_mapping` to `CoarseGrain.make_mapping`.
+- Moved `macro.make_macro_tpm` to `CoarseGrain.macro_tpm`.
+- Added blackbox functionality to `macro.emergence`. Blackboxing and coarse-
+  graining are now parametrized with the `blackbox` and `coarse_grain`
+  arguments.
+- Removed `utils.submatrix`.
+- Made `Network.tpm` and `Network.cm` immutable properties.
+- Removed the `purview` argument from `Subsystem.expand_repertoire`.
+- Moved `validate.StateUnreachableError` and `macro.ConditionallyDependentError`
+  to the `exceptions` module.
+- Removed perturbation vector support.
+- Changed `tpm.marginalize_out` to take a list of indices.
+- Fixed `macro.effective_info` to use the algorithm from the macro-micro paper.
+- Replace `constants.DIRECTIONS`, `constants.PAST`, and `constants.FUTURE` with
+  a proper `Enum` class: `constants.Direction`. Past and future are now
+  represented by `constants.Direction.PAST` and `constants.Direction.FUTURE`.
+- Simplifed logging config to use `config.LOG_STDOUT_LEVEL`,
+  `config.LOG_FILE_LEVEL` and `config.LOG_FILE`.
+- Removed the `location` property of `Concept`.
+
+### API Additions
+- Added `subsystem.evaluate_partition`. This returns the φ for a particular
+  partition.
+- Added `config.MEASURE` to choose between EMD, KLD, or L1 for distance
+  computations.
+- Added `macro.MacroSubsystem`. This subclass of `Subsystem` is used to performs
+  macro computations.
+- Added `macro.CoarseGrain` to represent coarse-grainings of a system.
+- Added `macro.Blackbox` to represent system blackboxes.
+- Added `validate.blackbox` and `validate.coarse_grain`.
+- Added `macro.all_coarse_grains` and `macro.all_blackboxes` generators.
+- Added `Subsystem.cut_indices` property.
+- Added `Subsystem.cm` connectivity matrix alias.
+- Added `utils.all_states`, a generator over all states of an `n`-element
+  system.
+- Added `tpm.is_state_by_state` for testing whether a TPM is in state-by-state
+  format.
+- `Network` now takes an optional `node_labels`  argument, allowing nodes to be
+  referenced by a canonical name other than their indices. The nodes of a
+  `Subsystem` can now be specified by either their index or their label.
+- Added `models.normalize_constellation` for deterministically ordering a
+  constellation.
+- Added a `Makefile`.
+- Added an `exceptions` module.
+- Added `distribution.purview` for computing the purview of a repertoire.
+- Added `distribution.repertoire_shape`.
+- Added `config.PARTITION_TYPE` to control the ways in which φ-partitions are
+  generated.
+- Added more functions to the `convert` module:
+  - `holi2loli` and `loli2holi` convert decimal indices between **HOLI** and
+    **LOLI** formats.
+  - `holi2loli_state_by_state` and `loli2holi_state_by_state` convert between
+    **HOLI** and **LOLI** formats for state-by-state TPMs.
+  - Added short aliases for some functions:
+    - `h2l` is `holi2loli`
+    - `l2h` is `loli2holi`
+    - `l2s` is `loli_index2state`
+    - `h2s` is `holi_index2state`
+    - `s2h` is `state2loli_index`
+    - `s2l` is `state2holi_index`
+    - `h2l_sbs` is `holi2loli_state_by_state`
+    - `l2h_sbs` is `loli2holi_state_by_state`
+    - `sbn2sbs` is `state_by_node2state_by_state`
+    - `sbs2sbn` is `state_by_state2state_by_node`
+- Added the `Constellation.mechanisms`, `Constellation.labeled_mechanisms`, and
+  `Constellation.phis` properties.
+- Add `BigMip.print` method with optional `constellations` argument that allows
+  omitting the constellations.
+
+### Refactor
+- Refactored the `utils` module into the `connectivity`, `distance`,
+  `distribution`, `partition`, `timescale`, and `tpm` modules.
+- Existing macro coarse-grain logic to use `MacroSubsystem` and `CoarseGrain`.
+- Improved string representations of PyPhi objects.
+- Refactored JSON support. The `jsonify` module now dumps PyPhi models to a
+  a format which can be loaded to reproduce the full object graph of PyPhi
+  objects. This causes backwards incompatible changes to the JSON format of
+  some model representations.
+- Refactored `pyphi.config` to be an object. Added validation and callbacks for
+  config options.
+
+### Optimizations
+- Added an analytic solution for the EMD computation between effect
+  repertoires.
+- Improved the time complexity of `directed_bipartition_of_one` from
+  exponential to linear.
+
+### Documentation
+- Updated documentation and examples to reflect changes made to the `macro` API
+  and usage.
+- Added documentation pages for new modules.
+
 
 0.8.1
 ------------------
@@ -41,8 +145,8 @@ _2016-02-06_
 - Disabled concept caching; removed the `config.CACHE_CONCEPTS` option.
 
 ### API Additions
-- Added `config.READABLE_REPRS` to control whether `__reprs__` of PyPhi models
-  default to using pretty string formatting.
+- 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.
@@ -68,7 +172,7 @@ _2016-02-06_
 - Updated documentation and examples to reflect node-to-index conversion.
 
 
-0.7.5
+0.7.5 [unreleased]
 ------------------
 _2015-11-02_
 
@@ -85,7 +189,7 @@ _2015-11-02_
   default but can be disabled via the `VALIDATE_SUBSYSTEM_STATES` option.
 
 
-0.7.4
+0.7.4 [unreleased]
 ------------------
 _2015-10-12_
 
@@ -94,15 +198,15 @@ _2015-10-12_
   value, leading to collisions.
 
 
-0.7.3
+0.7.3 [unreleased]
 ------------------
 _2015-09-08_
 
 ### API changes
 - Heavily refactored the `pyphi.json` module and renamed it to `pyphi.jsonify`.
 
 
-0.7.2
+0.7.2 [unreleased]
 ------------------
 _2015-07-01_