dit 1.5__tar.gz → 2.2__tar.gz

dit-2.2/.gitignore

@@ -0,0 +1,63 @@
+# Python related
+*.pyc
+*.pyo
+*.so
+
+# Creating during installation
+MANIFEST
+build/
+dist/
+dit.egg-info/
+
+# gedit
+*.*~
+
+# known autogenerated .c files
+*.o
+
+dit/math/_close.c
+dit/math/_samplediscrete.c
+dit/math/_*.html
+
+# ignore coverage information
+.coverage*
+coverage.xml
+
+# ignore project files for various IDEs
+
+# komodo
+*.kpf
+*.komodoproject
+.komodotools
+
+# geany
+*.geany
+
+# ignore rope's project directory...
+.ropeproject
+
+# vscode
+.vscode
+
+# cursor
+.cursor/
+
+# vim
+*.swp
+*.swo
+
+# ignore the documentation build directory
+docs/_build/
+docs/images/idiagrams.pdf
+docs/images/*.png
+.idea/
+.cache/
+.hypothesis/
+.pypirc
+.pytest_cache/
+.vscode
+dit/inference/pycounts.c
+.mypy_cache
+dit.code-workspace
+newrelic_agent.log
+__marimo__

dit-2.2/PKG-INFO

@@ -0,0 +1,494 @@
+Metadata-Version: 2.4
+Name: dit
+Version: 2.2
+Summary: Python package for information theory on discrete random variables.
+Project-URL: Homepage, http://dit.io
+Project-URL: Repository, https://github.com/dit/dit
+Project-URL: Documentation, http://docs.dit.io
+Author-email: chebee7i <admin@dit.io>, "Ryan G. James" <dit@autoplectic.com>
+License-Expression: BSD-3-Clause
+License-File: LICENSE.txt
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.11
+Requires-Dist: boltons
+Requires-Dist: debtcollector
+Requires-Dist: lattices>=0.5
+Requires-Dist: loguru
+Requires-Dist: networkx>=2.6
+Requires-Dist: numpy>=1.22
+Requires-Dist: pltable
+Requires-Dist: scipy>=1.7
+Requires-Dist: xarray
+Provides-Extra: broja
+Requires-Dist: ecos; extra == 'broja'
+Provides-Extra: dev
+Requires-Dist: colorama; extra == 'dev'
+Requires-Dist: hypothesis; extra == 'dev'
+Requires-Dist: hypothesis>=6.0; extra == 'dev'
+Requires-Dist: hypothesis[numpy]; extra == 'dev'
+Requires-Dist: ipython; extra == 'dev'
+Requires-Dist: jax; extra == 'dev'
+Requires-Dist: jaxlib; extra == 'dev'
+Requires-Dist: matplotlib; extra == 'dev'
+Requires-Dist: nbconvert; extra == 'dev'
+Requires-Dist: numdifftools; extra == 'dev'
+Requires-Dist: optimistix; extra == 'dev'
+Requires-Dist: pint; extra == 'dev'
+Requires-Dist: pycddlib-standalone; extra == 'dev'
+Requires-Dist: pypoman; extra == 'dev'
+Requires-Dist: pytensor; extra == 'dev'
+Requires-Dist: pytest-cov; extra == 'dev'
+Requires-Dist: pytest-rerunfailures; extra == 'dev'
+Requires-Dist: pytest-sugar; extra == 'dev'
+Requires-Dist: pytest-xdist; extra == 'dev'
+Requires-Dist: pytest>=9.0.3; extra == 'dev'
+Requires-Dist: python-ternary; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Requires-Dist: scikit-learn; extra == 'dev'
+Requires-Dist: slsqp-jax; extra == 'dev'
+Requires-Dist: sphinx; extra == 'dev'
+Requires-Dist: sphinx-rtd-theme; extra == 'dev'
+Requires-Dist: sphinxcontrib-bibtex; extra == 'dev'
+Requires-Dist: sympy; extra == 'dev'
+Requires-Dist: torch; extra == 'dev'
+Requires-Dist: ty; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: colorama; extra == 'docs'
+Requires-Dist: hypothesis; extra == 'docs'
+Requires-Dist: ipython; extra == 'docs'
+Requires-Dist: matplotlib; extra == 'docs'
+Requires-Dist: nbconvert; extra == 'docs'
+Requires-Dist: numdifftools; extra == 'docs'
+Requires-Dist: pint; extra == 'docs'
+Requires-Dist: pycddlib-standalone; extra == 'docs'
+Requires-Dist: python-ternary; extra == 'docs'
+Requires-Dist: scikit-learn; extra == 'docs'
+Requires-Dist: sphinx; extra == 'docs'
+Requires-Dist: sphinx-rtd-theme; extra == 'docs'
+Requires-Dist: sphinxcontrib-bibtex; extra == 'docs'
+Requires-Dist: sympy; extra == 'docs'
+Provides-Extra: jax
+Requires-Dist: jax; extra == 'jax'
+Requires-Dist: jaxlib; extra == 'jax'
+Requires-Dist: optimistix; extra == 'jax'
+Requires-Dist: slsqp-jax; extra == 'jax'
+Provides-Extra: music
+Requires-Dist: music21; extra == 'music'
+Provides-Extra: optional
+Requires-Dist: colorama; extra == 'optional'
+Requires-Dist: matplotlib; extra == 'optional'
+Requires-Dist: numdifftools; extra == 'optional'
+Requires-Dist: pint; extra == 'optional'
+Requires-Dist: pycddlib-standalone; extra == 'optional'
+Requires-Dist: pypoman; extra == 'optional'
+Requires-Dist: scikit-learn; extra == 'optional'
+Provides-Extra: pytensor
+Requires-Dist: pytensor; extra == 'pytensor'
+Provides-Extra: symbolic
+Requires-Dist: sympy; extra == 'symbolic'
+Provides-Extra: test
+Requires-Dist: hypothesis>=6.0; extra == 'test'
+Requires-Dist: hypothesis[numpy]; extra == 'test'
+Requires-Dist: pytest-cov; extra == 'test'
+Requires-Dist: pytest-rerunfailures; extra == 'test'
+Requires-Dist: pytest-sugar; extra == 'test'
+Requires-Dist: pytest-xdist; extra == 'test'
+Requires-Dist: pytest>=9.0.3; extra == 'test'
+Provides-Extra: torch
+Requires-Dist: torch; extra == 'torch'
+Description-Content-Type: text/x-rst
+
+``dit`` is a Python package for information theory.
+
+|build| |codecov| |docs| |conda|
+
+|joss| |zenodo| |slack|
+
+Introduction
+------------
+
+Information theory is a powerful extension to probability and statistics, quantifying dependencies
+among arbitrary random variables in a way that is consistent and comparable across systems and
+scales. Information theory was originally developed to quantify how quickly and reliably information
+could be transmitted across an arbitrary channel. The demands of modern, data-driven science have
+been coopting and extending these quantities and methods into unknown, multivariate settings where
+the interpretation and best practices are not known. For example, there are at least four reasonable
+multivariate generalizations of the mutual information, none of which inherit all the
+interpretations of the standard bivariate case. Which is best to use is context-dependent. ``dit``
+implements a vast range of multivariate information measures in an effort to allow information
+practitioners to study how these various measures behave and interact in a variety of contexts. We
+hope that having all these measures and techniques implemented in one place will allow the
+development of robust techniques for the automated quantification of dependencies within a system
+and concrete interpretation of what those dependencies mean.
+
+Citing
+------
+
+If you use `dit` in your research, please cite it as::
+
+   @article{dit,
+     Author = {James, R. G. and Ellison, C. J. and Crutchfield, J. P.},
+     Title = {{dit}: a {P}ython package for discrete information theory},
+     Journal = {The Journal of Open Source Software},
+     Volume = {3},
+     Number = {25},
+     Pages = {738},
+     Year = {2018},
+     Doi = {https://doi.org/10.21105/joss.00738}
+   }
+
+Basic Information
+-----------------
+
+Documentation
+*************
+
+http://docs.dit.io
+
+Downloads
+*********
+
+https://pypi.org/project/dit/
+
+https://anaconda.org/conda-forge/dit
+
++-------------------------------------------------------------------+
+| Dependencies                                                      |
++===================================================================+
+| * Python 3.11+                                                    |
+| * `boltons <https://boltons.readthedocs.io>`_                     |
+| * `debtcollector <https://docs.openstack.org/debtcollector/>`_    |
+| * `lattices <https://github.com/dit/lattices>`_                   |
+| * `loguru <https://loguru.readthedocs.io>`_                       |
+| * `networkx <https://networkx.github.io/>`_                       |
+| * `numpy <http://www.numpy.org/>`_                                |
+| * `PLTable <https://github.com/platomav/PLTable>`_                |
+| * `scipy <https://www.scipy.org/>`_                               |
+| * `xarray <https://docs.xarray.dev/>`_                            |
++-------------------------------------------------------------------+
+
+Optional Dependencies
+~~~~~~~~~~~~~~~~~~~~~
+* colorama: colored column heads in PID indicating failure modes
+* cython: faster sampling from distributions
+* hypothesis: random sampling of distributions
+* jax, jaxlib: JAX-based optimization backend with autodiff support
+* matplotlib, python-ternary: plotting of various information-theoretic expansions
+* numdifftools: numerical evaluation of gradients and hessians during optimization
+* pint: add units to informational values
+* pycddlib-standalone, pypoman: polytope vertex enumeration for convex-maximization-based measures
+* pytensor: PyTensor-based optimization backend with autodiff support
+* scikit-learn: faster nearest-neighbor lookups during entropy/mutual information estimation from samples
+* torch: PyTorch-based optimization backend with autodiff and GPU support
+
+Install
+*******
+
+The easiest way to install is:
+
+.. code-block:: bash
+
+  pip install dit
+
+If you want to install ``dit`` within a conda environment, you can simply do:
+
+.. code-block:: bash
+
+  conda install -c conda-forge dit
+
+For development, we recommend `uv <https://docs.astral.sh/uv/>`_:
+
+.. code-block:: bash
+
+  git clone https://github.com/dit/dit.git
+  cd dit
+  uv sync --extra dev
+
+This installs ``dit`` in editable mode with all development dependencies
+(tests, docs, linting, type checking, and optional backends).
+
+Testing
+*******
+
+.. code-block:: bash
+
+  # Using uv (recommended)
+  uv run pytest
+
+  # Or with pip
+  pip install -e ".[test]"
+  pytest
+
+Code and bug tracker
+********************
+
+https://github.com/dit/dit
+
+License
+*******
+
+BSD 3-Clause, see LICENSE.txt for details.
+
+Implemented Measures
+--------------------
+
+``dit`` implements the following information measures. Most of these are implemented in multivariate & conditional
+generality, where such generalizations either exist in the literature or are relatively obvious --- for example,
+though it is not in the literature, the multivariate conditional exact common information is implemented here.
+
++------------------------------------------+-----------------------------------------+-----------------------------------+
+| Entropies                                | Mutual Informations                     | Divergences                       |
+|                                          |                                         |                                   |
+| * Shannon Entropy                        | * Co-Information                        | * Variational Distance            |
+| * Renyi Entropy                          | * Interaction Information               | * Kullback-Leibler Divergence /   |
+| * Tsallis Entropy                        | * Total Correlation / Multi-Information |   Relative Entropy                |
+| * Necessary Conditional Entropy          | * Dual Total Correlation / Binding      | * Cross Entropy                   |
+| * Residual Entropy / Independent         |   Information                           | * Jensen-Shannon Divergence       |
+|   Information / Variation of Information | * CAEKL Multivariate Mutual Information | * Earth Mover's Distance          |
++------------------------------------------+ * O-Information                         +-----------------------------------+
+| Common Informations                      | * Cohesion                              | Other Measures                    |
+|                                          | * Transmission                          |                                   |
+| * Gacs-Korner Common Information         | * Union Information                     | * Channel Capacity                |
+| * Wyner Common Information               | * Logarithmic Decomposition             | * Complexity Profile              |
+| * Exact Common Information               | * Delta^k / Gamma^k                     | * Connected Informations          |
+| * Functional Common Information          | * DeWeese Mutual Information            | * Copy Mutual Information         |
+| * MSS Common Information                 +-----------------------------------------+ * Cumulative Residual Entropy     |
+| * Kamath-Anantharam Dual Common          | Partial Information Decomposition       | * Extropy                         |
+|   Information                            |                                         | * Hypercontractivity Coefficient  |
+| * Beta Common Information                | * :math:`I_{min}`                       | * Information Bottleneck          |
+| * Salamatian-Cohen-Medard Maximum Entropy| * :math:`I_{\wedge}`                    | * Information Diagrams            |
+|   Function                               | * :math:`I_{RR}`                        | * Information Trimming            |
++------------------------------------------+ * :math:`I_{\downarrow}`                | * Lautum Information              |
+| Secret Key Agreement Bounds              | * :math:`I_{proj}`                      | * LMPR Complexity                 |
+|                                          | * :math:`I_{BROJA}`                     | * Marginal Utility of Information |
+| * Secrecy Capacity                       | * :math:`I_{ccs}`                       | * Maximum Correlation             |
+| * Intrinsic Mutual Information           | * :math:`I_{\pm}`                       | * Maximum Entropy Distributions   |
+| * Reduced Intrinsic Mutual Information   | * :math:`I_{sx}`                        | * Perplexity                      |
+| * Minimal Intrinsic Mutual Information   | * :math:`I_{dep}`                       | * Rate-Distortion Theory          |
+| * Necessary Intrinsic Mutual Information | * :math:`I_{RAV}`                       | * TSE Complexity                  |
+| * Two-Part Intrinsic Mutual Information  | * :math:`I_{mmi}`                       | * Gray-Wyner Network              |
+|                                          | * :math:`I_{\prec}`                     |                                   |
+|                                          | * :math:`I_{RA}`                        |                                   |
+|                                          | * :math:`I_{SKAR}`                      |                                   |
+|                                          | * :math:`I_{IG}`                        |                                   |
+|                                          | * :math:`I_{RDR}`                       |                                   |
+|                                          | * :math:`I_{do}`                        |                                   |
++------------------------------------------+-----------------------------------------+-----------------------------------+
+
+Quickstart
+----------
+
+The basic usage of ``dit`` corresponds to creating distributions, modifying them
+if need be, and then computing properties of those distributions. First, we
+import:
+
+.. code:: python
+
+   >>> import dit
+
+Suppose we have a really thick coin, one so thick that there is a reasonable
+chance of it landing on its edge. Here is how we might represent the coin in
+``dit``.
+
+.. code:: python
+
+   >>> d = dit.Distribution(['H', 'T', 'E'], [.4, .4, .2])
+   >>> print(d)
+   Class:          Distribution
+   Alphabet:       ('E', 'H', 'T') for all rvs
+   Base:           linear
+   Outcome Class:  str
+   Outcome Length: 1
+   RV Names:       None
+
+   x   p(x)
+   E   0.2
+   H   0.4
+   T   0.4
+
+Calculate the probability of ``H`` and also of the combination ``H or T``.
+
+.. code:: python
+
+   >>> d['H']
+   0.4
+   >>> d.event_probability(['H','T'])
+   0.8
+
+Calculate the Shannon entropy and extropy of the joint distribution.
+
+.. code:: python
+
+   >>> dit.shannon.entropy(d)
+   1.5219280948873621
+   >>> dit.other.extropy(d)
+   1.1419011889093373
+
+Create a distribution where ``Z = xor(X, Y)``.
+
+.. code:: python
+
+   >>> import dit.example_dists
+   >>> d = dit.example_dists.Xor()
+   >>> d.set_rv_names(['X', 'Y', 'Z'])
+   >>> print(d)
+   Class:          Distribution
+   Alphabet:       ('0', '1') for all rvs
+   Base:           linear
+   Outcome Class:  str
+   Outcome Length: 3
+   RV Names:       ('X', 'Y', 'Z')
+
+   x     p(x)
+   000   0.25
+   011   0.25
+   101   0.25
+   110   0.25
+
+Calculate the Shannon mutual informations ``I[X:Z]``, ``I[Y:Z]``, and
+``I[X,Y:Z]``.
+
+.. code:: python
+
+   >>> dit.shannon.mutual_information(d, ['X'], ['Z'])
+   0.0
+   >>> dit.shannon.mutual_information(d, ['Y'], ['Z'])
+   0.0
+   >>> dit.shannon.mutual_information(d, ['X', 'Y'], ['Z'])
+   1.0
+
+Calculate the marginal distribution ``P(X,Z)``.
+Then print its probabilities as fractions, showing the mask.
+
+.. code:: python
+
+   >>> d2 = d.marginal(['X', 'Z'])
+   >>> print(d2.to_string(show_mask=True, exact=True))
+   Class:          Distribution
+   Alphabet:       ('0', '1') for all rvs
+   Base:           linear
+   Outcome Class:  str
+   Outcome Length: 2 (mask: 3)
+   RV Names:       ('X', 'Z')
+
+   x     p(x)
+   0*0   1/4
+   0*1   1/4
+   1*0   1/4
+   1*1   1/4
+
+Convert the distribution probabilities to log (base 3.5) probabilities, and
+access its probability mass function.
+
+.. code:: python
+
+   >>> d2.set_base(3.5)
+   >>> d2.pmf
+   array([-1.10658951, -1.10658951, -1.10658951, -1.10658951])
+
+Draw 5 random samples from this distribution.
+
+.. code:: python
+
+   >>> dit.math.prng.seed(1)
+   >>> d2.rand(5)
+   ['01', '10', '00', '01', '00']
+
+Source and Channel Coding
+-------------------------
+
+Beyond measures, ``dit`` builds explicit codes and ships a catalog of channels.
+
+The ``dit.coding`` module constructs lossless *source codes* (Shannon, Fano,
+Shannon-Fano-Elias, Huffman, length-limited Huffman, Golomb/Rice, Tunstall, and
+the universal integer codes) and reports their code-theoretic properties (rate,
+redundancy, efficiency, the Kraft sum, and whether the code is prefix-free /
+uniquely decodable / optimal).
+
+.. code:: python
+
+   >>> from dit.coding import huffman
+   >>> d = dit.Distribution(['a', 'b', 'c', 'd', 'e'], [0.4, 0.2, 0.2, 0.1, 0.1])
+   >>> code = huffman(d)
+   >>> code.average_length()
+   2.2
+   >>> float(code.source_entropy())
+   2.1219280948873624
+   >>> code.is_optimal(), code.is_prefix_free()
+   (True, True)
+
+It also builds binary (GF(2)) *channel codes* --- linear block codes
+(repetition, parity-check, Hamming, Reed-Muller, Golay) as well as LDPC, polar,
+and convolutional codes --- and evaluates them against a noisy channel supplied
+as a conditional ``Distribution`` ``p(Y|X)``.
+
+.. code:: python
+
+   >>> from dit.coding import hamming
+   >>> code = hamming(3)
+   >>> code.length, code.dimension, code.minimum_distance()
+   (7, 4, 3)
+   >>> bsc = dit.example_channels.binary_symmetric_channel(0.05)
+   >>> float(code.probability_of_error(bsc, method='exact'))
+   0.04438054218749993
+
+The ``dit.example_channels`` module is a catalog of canonical discrete
+memoryless channels (binary symmetric, binary erasure, Z-channel, q-ary
+symmetric/erasure, noisy typewriter, ...). Each constructor returns a
+conditional ``Distribution`` ``p(Y|X)`` ready for
+``dit.algorithms.channel_capacity`` or the coding layer above.
+
+.. code:: python
+
+   >>> from dit.algorithms import channel_capacity
+   >>> bec = dit.example_channels.binary_erasure_channel(0.25)
+   >>> float(channel_capacity(bec)[0])
+   0.75
+
+Contributions & Help
+--------------------
+
+If you'd like to feature added to ``dit``, please file an issue. Or, better yet, open a pull request. Ideally, all code should be tested and documented, but please don't let this be a barrier to contributing. We'll work with you to ensure that all pull requests are in a mergable state.
+
+If you'd like to get in contact about anything, you can reach us through our `slack channel <https://dit-python.slack.com/>`_.
+
+
+.. badges:
+
+.. |build| image:: https://github.com/dit/dit/actions/workflows/build.yml/badge.svg
+   :target: https://github.com/dit/dit/actions/workflows/build.yml
+   :alt: Continuous Integration Status
+
+.. |codecov| image:: https://codecov.io/gh/dit/dit/branch/main/graph/badge.svg
+   :target: https://codecov.io/gh/dit/dit
+   :alt: Test Coverage Status
+
+.. |docs| image:: https://readthedocs.org/projects/dit/badge/?version=latest
+   :target: http://dit.readthedocs.org/en/latest/?badge=latest
+   :alt: Documentation Status
+
+.. |conda| image:: https://anaconda.org/conda-forge/dit/badges/installer/conda.svg
+   :target: https://anaconda.org/conda-forge/dit
+   :alt: Conda installation
+
+.. |zenodo| image:: https://zenodo.org/badge/13201610.svg
+   :target: https://zenodo.org/badge/latestdoi/13201610
+   :alt: DOI
+
+.. |slack| image:: https://img.shields.io/badge/Slack-dit--python-lightgrey.svg
+   :target: https://dit-python.slack.com/
+   :alt: dit chat
+
+.. |joss| image:: http://joss.theoj.org/papers/10.21105/joss.00738/status.svg
+   :target: https://doi.org/10.21105/joss.00738
+   :alt: JOSS Status