Merge branch 'release/1.2.0'

.flake8

@@ -1,7 +1,8 @@
 [flake8]
-
-ignore = F401
-
+ignore = E203, E501, W503
+max-line-length = 80
+max-complexity = 18
+select = B,C,E,F,W,T4,B9
 exclude =
   __pycache__,
   __pyphi_cache__,

.gitignore

@@ -1,30 +1,20 @@
 __pycache__
 .cache
-.ropeproject
 .venv
 .env
-.pythonrc*
 .agignore
-.projectile
-**/*.pyc
+.tox
+.coverage
 **/*.egg-info
 **/*.log
 **/*.BACKUP
-.tox
-pyphi/data/hamming_matrices/10.npy
 __pyphi_cache__
 dist
 build
-profiling
 docs/_build
-.coverage
 htmlcov
-results
-html
-env
+profiling
 benchmarks/pyphi_config.yml
-profiling/pyphi_config.yml
+benchmarks/env
+benchmarks/results
 ignore
-.ignore
-startup.py
-my_requirements.txt

.isort.cfg

@@ -1,5 +1,9 @@
 [settings]
-line_length=80
+multi_line_output=3
+include_trailing_comma=True
+force_grid_wrap=0
+use_parentheses=True
+line_length=88
 indent='    '
 default_section=THIRDPARTY
 known_first_party=pyphi

.pre-commit-config.yaml

@@ -0,0 +1,77 @@
+exclude: '^$'
+fail_fast: false
+repos:
+
+- repo: https://github.com/pre-commit/pre-commit-hooks.git
+  rev: v2.2.3
+  hooks:
+    - id: autopep8-wrapper
+    - id: check-added-large-files
+    - id: debug-statements
+    - id: double-quote-string-fixer
+    - id: end-of-file-fixer
+    - id: fix-encoding-pragma
+    - id: flake8
+      additional_dependencies: [
+      'flake8-blind-except',
+      'flake8-coding',
+      'flake8-comprehensions',
+      'flake8-debugger',
+      'flake8-deprecated',
+      'flake8-docstrings',
+      'flake8-meiqia',
+      'flake8-mutable',
+      'flake8-pep3101',
+      'flake8-print',
+      'flake8-quotes',
+      'flake8-string-format',
+      'flake8-tidy-imports',
+      'flake8-todo']
+      exclude: 'test_oauth.py'
+    - id: trailing-whitespace
+
+- repo: https://github.com/ambv/black
+  rev: 19.3b0
+  hooks:
+    - id: black
+      name: black
+      description: 'Black: The uncompromising Python code formatter'
+      entry: black
+      language: python
+      language_version: python3
+      require_serial: true
+      types: [python]
+
+# - repo: git@github.com:pre-commit/mirrors-yapf.git
+#   sha: v0.20.0
+#   hooks:
+#     - id: yapf
+#       exclude: 'migrations|settings|scripts'
+#       additional_dependencies: ['futures']
+#       args: ['--style=.style.yapf', '--parallel', '--in-place']
+
+# - repo: git@github.com:FalconSocial/pre-commit-python-sorter.git
+#   sha: b57843b0b874df1d16eb0bef00b868792cb245c2
+#   hooks:
+#     - id: python-import-sorter
+#       args: ['--silent-overwrite']
+
+# - repo: git@github.com:humitos/mirrors-docformatter.git
+#   sha: v0.0.1
+#   hooks:
+#     - id: docformatter
+#       args: ['--in-place', '--wrap-summaries=80', '--wrap-descriptions=80', '--pre-summary-newline', '--no-blank']
+
+# - repo: git@github.com:humitos/mirrors-autoflake.git
+#   sha: v1.0
+#   hooks:
+#     - id: autoflake
+#       args: ['--in-place', '--remove-all-unused-imports', '--remove-unused-variable']
+
+# - repo: git://github.com/guykisel/prospector-mirror
+#   sha: 'b27f281eb9398fc8504415d7fbdabf119ea8c5e1'
+#   hooks:
+#     - id: prospector
+#       # https://github.com/pre-commit/pre-commit/issues/178
+#       language: system
+#       args: ['--profile=prospector']

.pylintrc

@@ -60,6 +60,7 @@ disable =
     no-name-in-module,
     no-self-use,
     super-on-old-class,
+    bad-continuation,
 
 
 [REPORTS]

.travis.yml

@@ -1,3 +1,5 @@
+dist: xenial
+
 language: python
 
 sudo: false
@@ -14,14 +16,15 @@ services:
   - redis-server  # port 6379 (default)
 
 python:
-  - "3.4"
-  - "3.5"
-  - "3.6"
+  - 3.4
+  - 3.5
+  - 3.6
+  - 3.7
 
 # Install packages
 install:
   - pip install --upgrade pip setuptools wheel
-  - pip install --only-binary=numpy numpy==1.14
+  - if [[ $TRAVIS_PYTHON_VERSION == 3.4 ]]; then pip install --only-binary=numpy numpy==1.15.4; else pip install --only-binary=numpy numpy==1.16.4; fi
   - pip install --only-binary=scipy -r requirements.txt
   - pip install coveralls
   - pip freeze

CHANGELOG.md

@@ -1,8 +1,49 @@
 Changelog
 =========
 
+1.2.0
+-----
+_2019-06-21_
+
+### Fixes
+
+- Fixed a bug introduced into `pyphi.utils.load_data()` by a breaking change
+  in recent versions of NumPy that caused an error on import.
+- Fixed a bug where changing `config.PRECISION` dynamically did not change
+  `constants.EPSILON`, causing some comparisons that relied on
+  `constants.EPSILON` to not reflect the new precision.
+- Changing `config.FS_CACHE_DIRECTORY` and `config.FS_CACHE_VERBOSITY` now
+  causes a new `joblib.Memory` cache to be created. Previously, changing these
+  options dynamically had no effect.
+- Made test suite compatible with stricter usage of `pytest` fixtures
+  required by recent versions of `pytest`.
+
+### API additions
+
+- Added `pyphi.tpm.reconstitute_tpm()`.
+
+### API changes
+
+- Renamed `pyphi.partition.partition_registry` to
+  `pyphi.partition.partition_types`.
+- Renamed `pyphi.distance.bld()` to `pyphi.distance.klm()`.
+- Fixed the connectivity matrix of the `def
+  disjunction_conjunction_network()`.
+- Removed `'expanded_*_reperotire'` attributes of JSON-serialized `Concept`s.
+
+### Config
+
+- Added the `WELCOME_OFF` option to turn off the new welcome message.
+
+### Documentation
+
+- Added documentation for the `partition_types` registry.
+- Added documentation for the filesystem and database caches.
+
+
 1.1.0
 -----
+_2018-05-30_
 
 ### Fixes
 
@@ -15,6 +56,7 @@ Changelog
 - 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.
+- Fixed the connectivity matrix in `examples.disjunction_conjunction.network()`.
 
 ### API additions
 

INSTALLATION.rst

@@ -40,7 +40,7 @@ Now that we're using our shiny new Python versions, it is highly recommended to
 set up a **virtual environment** in which to install PyPhi. Virtual
 environments allow different projects to isolate their dependencies from one
 another, so that they don't interact in unexpected ways. Please see `this guide
-<http://docs.python-guide.org/page/dev/virtualenvs/>`__ for more information.
+<http://docs.python-guide.org/dev/virtualenvs/>`__ for more information.
 
 To do this, you must install ``virtualenvwrapper``, a `tool for manipulating
 virtual environments <http://virtualenvwrapper.readthedocs.org/>`__. This tool

Makefile

@@ -69,3 +69,6 @@ build-dist: clean-dist
 
 clean-dist:
 	rm -rf $(dist_dir)
+
+clean:
+	rm -rf **/__pycache__

README.md

@@ -13,18 +13,17 @@
 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:**
+**If you use this code, please cite the paper:**
 
 ---
 
-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 \[q-bio.NC\].
+Mayner WGP, Marshall W, Albantakis L, Findlay G, Marchman R, Tononi G. (2018)
+[PyPhi: A toolbox for integrated information
+theory](https://doi.org/10.1371/journal.pcbi.1006343). PLOS Computational
+Biology 14(7): e1006343. <https://doi.org/10.1371/journal.pcbi.1006343>
 
 ---
 
-The manuscript is available at <https://arxiv.org/abs/1712.09644>.
-
 
 ## Usage, Examples, and API documentation
 
@@ -113,25 +112,47 @@ before installing the requirements:
 sudo apt-get install python3-dev python3-scipy python3-numpy
 ```
 
+### Developing on Windows
+
+If you're just looking for an editable install, pip may work better than the conda develop utility included in the conda-build package. When using pip on Windows, the build of pyemd may fail. The simplest solution to this is to obtain pyemd through conda. 
+
+```bash
+conda create -n pyphi_dev
+conda activate pyphi_dev
+conda install -c wmayner pyemd
+cd path/to/local/editable/copy/of/pyphi
+pip install -e .
+```
+
+Unfortunately, pip isn't great at managing the DLLs that some packages (especially scipy) rely on. If you have missing DLL errors, try reinstalling the offending package (here, scipy) with conda. 
+
+```bash
+conda activate pyphi_dev
+pip uninstall scipy
+conda install scipy
+```
 
 ## 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 \[q-bio.NC\].
+Mayner WGP, Marshall W, Albantakis L, Findlay G, Marchman R, Tononi G. (2018)
+[PyPhi: A toolbox for integrated information
+theory](https://doi.org/10.1371/journal.pcbi.1006343). PLOS Computational
+Biology 14(7): e1006343. <https://doi.org/10.1371/journal.pcbi.1006343>
 
 ```
-@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}
+@article{mayner2018pyphi,
+  title={PyPhi: A toolbox for integrated information theory},
+  author={Mayner, William GP and Marshall, William and Albantakis, Larissa and Findlay, Graham and Marchman, Robert and Tononi, Giulio},
+  journal={PLoS Computational Biology},
+  volume={14},
+  number={7},
+  pages={e1006343},
+  year={2018},
+  publisher={Public Library of Science},
+  doi={10.1371/journal.pcbi.1006343},
+  url={https://doi.org/10.1371/journal.pcbi.1006343}
 }
 ```
 

docs/caching.rst

@@ -0,0 +1 @@
+.. include:: ../CACHING.rst

docs/conf.py

@@ -62,7 +62,7 @@
 
 # General information about the project.
 project = 'PyPhi'
-copyright = '2014--2017 {}'.format(__author__)
+copyright = '2014--2018 {}'.format(__author__)
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -121,7 +121,10 @@
 .. |big_phi_max| replace:: :math:`\Phi^{\textrm{max}}`
 .. |small_phi| replace:: :math:`\varphi`
 .. |small_phi > 0| replace:: :math:`\varphi > 0`
+.. |small_phi = 0| replace:: :math:`\varphi = 0`
 .. |small_phi_max| replace:: :math:`\varphi^{\textrm{max}}`
+.. |small_phi = 1/6| replace:: :math:`\varphi = \frac{1}{6}`
+.. |small_phi = 1/10| replace:: :math:`\varphi = \frac{1}{10}`
 .. |big_alpha| replace:: :math:`\mathcal{A}`
 .. |big_alpha > 0| replace:: :math:`\mathcal{A} > 0`
 .. |alpha| replace:: :math:`\alpha`
@@ -150,8 +153,6 @@
 .. |(AB / DE) x (∅ / C)| replace:: :math:`\frac{AB}{DE} \times \frac{\varnothing}{C}`
 .. |(A / CD) x (∅ / E)| replace:: :math:`\frac{A}{CD} \times \frac{\varnothing}{E}`
 .. |(∅ / C) x (A / D)| replace:: :math:`\frac{\varnothing}{C} \times \frac{A}{D}`
-.. |small_phi = 1/6| replace:: :math:`\varphi = \frac{1}{6}`
-.. |small_phi = 1/10| replace:: :math:`\varphi = \frac{1}{10}`
 .. |t| replace:: :math:`t`
 .. |t-1| replace:: :math:`t-1`
 .. |t+1| replace:: :math:`t+1`
@@ -168,6 +169,8 @@
 .. |N| replace:: :math:`N`
 .. |n x n| replace:: :math:`N \times N`
 .. |2^n x 2^n| replace:: :math:`2^N \times 2^N`
+.. |2^m x 2| replace:: :math:`2^m \times 2`
+.. |m| replace:: :math:`m`
 .. |i| replace:: :math:`i`
 .. |j| replace:: :math:`j`
 .. |i,jth| replace:: :math:`(i,j)^{\textrm{th}}`

docs/examples/actual_causation.rst

@@ -1,12 +1,16 @@
 Actual Causation
 ================
 
-This section demonstrates how to use PyPhi to evaluate actual causation as
+This section demonstrates how to use PyPhi to evaluate actual causation, as
 described in
 
-`Albantakis L, Marshall W, Hoel E, Tononi G (2017). What caused what? An
-irreducible account of actual causation. arXiv:1708.06716 [cs.AI]
-<https://arxiv.org/abs/1708.06716>`_.
+    Albantakis L, Marshall W, Hoel E, Tononi G (2019).
+    What Caused What? A quantitative Account of Actual Causation Using
+    Dynamical Causal Networks.
+    *Entropy*, 21 (5), pp. 459.
+    `<https://doi.org/10.3390/e21050459>`_
+
+First, we'll import the modules we need:
 
     >>> import pyphi
     >>> from pyphi import actual, config, Direction