Merge branch 'release/1.1.0'

.gitignore

@@ -10,6 +10,7 @@ __pycache__
 **/*.egg-info
 **/*.log
 **/*.BACKUP
+.tox
 pyphi/data/hamming_matrices/10.npy
 __pyphi_cache__
 dist

.isort.cfg

@@ -0,0 +1,7 @@
+[settings]
+line_length=80
+indent='    '
+default_section=THIRDPARTY
+known_first_party=pyphi
+known_third_party=
+sections=FUTURE,STDLIB,THIRDPARTY,FIRSTPARTY,LOCALFOLDER

.pylintrc

@@ -1,5 +1,5 @@
 # PyLint config for PyPhi code.
-# 
+#
 # Based on the PyLint config for Google's apitools:
 # https://github.com/google/apitools/blob/master/default.pylintrc
 
@@ -53,14 +53,13 @@ disable =
     cyclic-import,
     fixme,
     import-error,
+    invalid-name,
     locally-disabled,
     locally-enabled,
     no-member,
     no-name-in-module,
     no-self-use,
     super-on-old-class,
-    too-many-arguments,
-    too-many-function-args,
 
 
 [REPORTS]
@@ -330,6 +329,7 @@ max-branches=21
 
 # Maximum number of parents for a class (see R0901).
 # DEFAULT:  max-parents=7
+max-parents=10
 
 # Maximum number of attributes for a class (see R0902).
 # DEFAULT:  max-attributes=7
@@ -344,7 +344,7 @@ min-public-methods=0
 # Maximum number of public methods for a class (see R0904).
 # DEFAULT:  max-public-methods=20
 # RATIONALE:  API mapping
-max-public-methods=40
+max-public-methods=45
 
 [ELIF]
 max-nested-blocks=6

.travis.yml

@@ -4,8 +4,9 @@ sudo: false
 
 branches:
   only:
-      - master
-      - develop
+    - master
+    - develop
+    - scratch
 
 # Setup databases
 services:
@@ -17,20 +18,11 @@ python:
   - "3.5"
   - "3.6"
 
-# Setup miniconda
-before_install:
-  - 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:$PATH
-  # Update conda itself
-  - conda update --yes conda
-
 # Install packages
 install:
-  - conda create --yes --name=$TRAVIS_PYTHON_VERSION python=$TRAVIS_PYTHON_VERSION numpy scipy
-  - source activate $TRAVIS_PYTHON_VERSION
-  - pip install -r requirements.txt
+  - pip install --upgrade pip setuptools wheel
+  - pip install --only-binary=numpy numpy==1.14
+  - pip install --only-binary=scipy -r requirements.txt
   - pip install coveralls
   - pip freeze
 

CHANGELOG.md

@@ -1,8 +1,49 @@
 Changelog
 =========
 
+1.1.0
+-----
+
+### Fixes
+
+- Fixed a memory leaked when concepts returned by parallel CES computations
+  were returned with distinct subsystem objects. Now all objects in a CES share
+  the same subsystem reference.
+- Fixed a race condition caused by newly introduced `tqdm` synchronization.
+  Removed the existing `ProgressBar` implementation and pinned `tqdm` to
+  version >= 4.20.0.
+- Made model hashes deterministic (6b59061). This fixes an issue with the Redis
+  MICE cache in which cached values were not shared between processes and
+  program invokations.
+
+### API additions
+
+- Added a `NodeLabels` object for managing the labels of network elements. Most
+  models now carry a `NodeLabels` instance that is used for string formatting.
+- Added the `cut_node_labels` property to `Subsystem` and `MacroSubsystem`.
+- Added `utils.time_annotated` decorator to measure execution speed.
+
+### API changes
+
+- Specifying the nodes of a `Subsystem` is now optional. If not provided, the
+  subsystem will cover the entire network.
+- Removed the `labels2indices`, `indices2labels` and `parse_node_indices`
+  methods from `Network`, and the `indices2labels` method from `Subsystem`.
+- Renamed `config.load_config_file` to `config.load_file`, and
+  `config.load_config_dict` to `config.load_dict`
+- Removed backwards-compatible `Direction` import from `constants` module.
+- Renamed `macro.coarse_grain` to `coarse_graining`.
+- Exposed `coarse_grain`, `blackbox`, `time_scale`, `network_state` and
+  `micro_node_indices` as attributes of `MacroSubsystem`.
+
+### Config
+
+- Removed the `LOG_CONFIG_ON_IMPORT` configuration option.
+
+
 1.0.0 :tada:
 ------------
+_2017-12-21_
 
 ### API changes
 
@@ -65,7 +106,7 @@ modules.
 #### Constants
 
 - Renamed `Direction.PAST` to `Direction.CAUSE`
-- Renamed `Direction.CAUSE` to `Direction.EFFECT`
+- Renamed `Direction.FUTURE` to `Direction.EFFECT`
 
 ### API additions
 
@@ -107,6 +148,7 @@ modules.
 
 0.9.1
 -----
+_2017-12-21_
 
 ### Fixes
 - Refactored parallel processing support to fix an intermittent deadlock.

INSTALLATION.rst

@@ -136,6 +136,6 @@ like tab-completion. Once you've installed it, you can start the IPython
 interpreter with the command ``ipython``.
 
 Next, please see the documentation for some `examples
-<https://pyphi.readthedocs.io/page/examples>`__ of how to use PyPhi and
+<https://pyphi.readthedocs.io/page/examples/>`__ of how to use PyPhi and
 information on how to `configure
 <https://pyphi.readthedocs.io/page/configuration.html>`__ it.

MANIFEST.in

@@ -1,4 +1,8 @@
-include README.rst 
-include LICENSE.md 
-include pyphi_config.yml 
+include README.md
+include INSTALLATION.rst
+include CACHING.rst
+include LICENSE.md
+include CHANGELOG.md
+include pyphi_config.yml
 include redis.conf
+recursive-include pyphi/data *

Makefile

@@ -1,4 +1,3 @@
-
 .PHONY: test docs dist
 
 src = pyphi
@@ -17,6 +16,9 @@ coverage:
 	coverage html
 	open htmlcov/index.html
 
+lint:
+	pylint $(src)
+
 watch-tests:
 	watchmedo shell-command \
 		--command='make coverage' \
@@ -53,17 +55,17 @@ upload-docs: build-docs
 benchmark:
 	cd $(benchmarks) && asv continuous develop
 
-check-readme:
-	python setup.py check -r -s
+check-dist:
+	python setup.py check --strict
 
-dist: build-dist check-readme
-	twine upload dist/*
+dist: build-dist check-dist
+	twine upload $(dist_dir)/*
 
-test-dist: build-dist check-readme
-	twine upload --repository-url https://test.pypi.org/legacy/ dist/*
+test-dist: build-dist check-dist
+	twine upload --repository-url https://test.pypi.org/legacy/ $(dist_dir)/*
 
 build-dist: clean-dist
-	python setup.py sdist bdist_wheel
+	python setup.py sdist bdist_wheel --dist-dir=$(dist_dir)
 
 clean-dist:
-	rm -r $(dist_dir)
+	rm -rf $(dist_dir)

README.md

@@ -0,0 +1,167 @@
+<p>
+  <a href="http://pyphi.readthedocs.io/">
+    <img alt="PyPhi logo" src="https://github.com/wmayner/pyphi/raw/develop/docs/_static/pyphi-logo-text-760x180.png" height="90px" width="380px" style="max-width:100%">
+  </a>
+</p>
+
+[![Documentation badge](https://readthedocs.org/projects/pyphi/badge/?style=flat-square&maxAge=600)](https://pyphi.readthedocs.io/)
+[![Travis build badge](https://img.shields.io/travis/wmayner/pyphi.svg?style=flat-square&maxAge=600)](https://travis-ci.org/wmayner/pyphi)
+[![Coveralls.io badge](https://img.shields.io/coveralls/wmayner/pyphi/develop.svg?style=flat-square&maxAge=600)](https://coveralls.io/github/wmayner/pyphi?branch=develop)
+[![License badge](https://img.shields.io/github/license/wmayner/pyphi.svg?style=flat-square&maxAge=86400)](https://github.com/wmayner/pyphi/blob/master/LICENSE.md)
+[![Python versions badge](https://img.shields.io/pypi/pyversions/pyphi.svg?style=flat-square&maxAge=86400)](https://wiki.python.org/moin/Python2orPython3)
+
+PyPhi is a Python library for computing integrated information (𝚽), and the
+associated quantities and objects.
+
+**If you use this code, please cite the manuscript:**
+
+---
+
+Mayner WGP, Marshall W, Albantakis L, Findlay G, Marchman R, Tononi G (2017).
+[PyPhi: A toolbox for integrated
+information](https://arxiv.org/abs/1712.09644). arXiv:1712.09644 \[q-bio.NC\].
+
+---
+
+The manuscript is available at <https://arxiv.org/abs/1712.09644>.
+
+
+## Usage, Examples, and API documentation
+
+- [Documentation for the latest stable
+  release](http://pyphi.readthedocs.io/en/stable/)
+- [Documentation for the latest (potentially unstable) development
+  version](http://pyphi.readthedocs.io/en/latest/).
+- Documentation is also available within the Python interpreter with the `help`
+  function.
+
+
+## Installation
+
+Set up a Python 3 virtual environment and install with
+
+```bash
+pip install pyphi
+```
+
+To install the latest development version, which is a work in progress and may
+have bugs, run:
+
+```bash
+pip install "git+https://github.com/wmayner/pyphi@develop#egg=pyphi"
+```
+
+**Note:** this software is only supported on Linux and macOS. However, if you
+use Windows, you can run it by using the [Anaconda
+Python](https://www.anaconda.com/what-is-anaconda/) distribution and
+[installing PyPhi with conda](https://anaconda.org/wmayner/pyphi):
+
+```bash
+conda install -c wmayner pyphi
+```
+
+### Detailed installation guide for Mac OS X
+
+[See here](https://github.com/wmayner/pyphi/blob/develop/INSTALLATION.rst).
+
+
+## User group
+
+For discussion about the software or integrated information theory in general,
+you can join the [pyphi-users
+group](https://groups.google.com/forum/#!forum/pyphi-users).
+
+For technical issues with PyPhi or feature requests, please use the [issues
+page](https://github.com/wmayner/pyphi/issues).
+
+
+## Contributing
+
+To help develop PyPhi, fork the project on GitHub and install the requirements
+with
+
+```bash
+pip install -r requirements.txt
+```
+
+The `Makefile` defines some tasks to help with development:
+
+```bash
+make test
+```
+
+runs the unit tests every time you change the source code.
+
+```bash
+make benchmark
+```
+
+runs performance benchmarks.
+
+```bash
+make docs
+```
+
+builds the HTML documentation.
+
+### Developing on Linux
+
+Make sure you install the C headers for Python 3, SciPy, and NumPy
+before installing the requirements:
+
+```bash
+sudo apt-get install python3-dev python3-scipy python3-numpy
+```
+
+
+## Credit
+
+### Please cite these papers if you use this code:
+
+Mayner WGP, Marshall W, Albantakis L, Findlay G, Marchman R, Tononi G (2017).
+[PyPhi: A toolbox for integrated
+information](https://arxiv.org/abs/1712.09644). arXiv:1712.09644 \[q-bio.NC\].
+
+```
+@article{mayner2017pyphi,
+  title={PyPhi: A toolbox for integrated information},
+  author={Mayner, William, Gerald Paul AND Marshall, William AND 
+          Albantakis, Larissa AND Findlay, Graham AND 
+          Marchman, Robert AND Tononi, Giulio},
+  journal={arXiv:1712.09644 [q-bio.NC]},
+  year={2017},
+  month={12},
+  url={https://arxiv.org/abs/1712.09644}
+}
+```
+
+Albantakis L, Oizumi M, Tononi G (2014). [From the Phenomenology to the
+Mechanisms of Consciousness: Integrated Information Theory
+3.0](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003588).
+PLoS Comput Biol 10(5): e1003588. doi: 10.1371/journal.pcbi.1003588.
+
+```
+@article{iit3,
+    title={From the Phenomenology to the Mechanisms of Consciousness:
+    author={Albantakis, Larissa AND Oizumi, Masafumi AND Tononi, Giulio},
+    Integrated Information Theory 3.0},
+    journal={PLoS Comput Biol},
+    publisher={Public Library of Science},
+    year={2014},
+    month={05},
+    volume={10},
+    pages={e1003588},
+    number={5},
+    doi={10.1371/journal.pcbi.1003588},
+    url={http://dx.doi.org/10.1371%2Fjournal.pcbi.1003588}
+}
+```
+
+This project is inspired by a [previous
+project](https://github.com/albantakis/iit) written in Matlab by L. Albantakis,
+M. Oizumi, A. Hashmi, A. Nere, U. Olces, P. Rana, and B. Shababo.
+
+Correspondence regarding this code and the PyPhi paper should be directed to
+Will Mayner, at [<[email protected]>](mailto:[email protected]). Correspondence
+regarding the Matlab code and the IIT 3.0 paper should be directed to Larissa
+Albantakis, PhD, at [<[email protected]>](mailto:[email protected]).