Version 2.0.3

.github/workflows/python-unittest-ci.yml

@@ -26,46 +26,16 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install pytest
-        pip install mosek numba numpy scipy sympy tqdm
-#     - name: Set up MOSEK license
-#       env:
-#         MOSEK_LICENSE_KEY: ${{ secrets.MOSEK_LICENSE_KEY }}
-#       run: |
-#         mkdir -p $HOME/mosek
-#         echo "$MOSEK_LICENSE_KEY" > $HOME/mosek/mosek.lic
+        pip install mosek numba networkx numpy scipy sympy tqdm
+    - name: Set up MOSEK license
+      env:
+         MOSEK_LICENSE_KEY: ${{ secrets.MOSEK_LICENSE_KEY }}
+      run: |
+         mkdir -p $HOME/mosek
+         echo "$MOSEK_LICENSE_KEY" > $HOME/mosek/mosek.lic
     - name: Test with pytest
       run: |
-        pytest -v \
-        --ignore=test/test_writers.py \
-        --ignore=test/test_optimize.py \
-        --deselect=test/test_solvers.py::TestSDP::test_LP_with_SDP \
-        --deselect=test/test_solvers.py::TestSDP::test_SDP \
-        --deselect=test/test_solvers.py::TestSDP::test_SDP_equalities \
-        --deselect=test/test_solvers.py::TestSDP::test_SDP_inequalities \
-        --deselect=test/test_solvers.py::TestLP::test_LP_free_bounds \
-        --deselect=test/test_solvers.py::TestLP::test_LP_non_negative_bounds \
-        --deselect=test/test_solvers.py::TestLP::test_LP_lower_bounds_of_zero \
-        --deselect=test/test_solvers.py::TestLP::test_LP_free_bounds_of_zero_and_non_negative \
-        --deselect=test/test_solvers.py::TestLP::test_LP_negative_lower_bounds \
-        --deselect=test/test_solvers.py::TestLP::test_LP_negative_lower_bounds_and_non_negative \
-        --deselect=test/test_solvers.py::TestSolverProcesses::test_semiknown_constraints \
-        --deselect=test/test_solvers.py::TestSolverProcesses::test_partially_known_objective \
-        --deselect=test/test_pipeline.py::TestSDPOutput::test_bounds \
-        --deselect=test/test_pipeline.py::TestSDPOutput::test_CHSH \
-        --deselect=test/test_pipeline.py::TestSDPOutput::test_GHZ_commuting \
-        --deselect=test/test_pipeline.py::TestSDPOutput::test_GHZ_NC \
-        --deselect=test/test_pipeline.py::TestSDPOutput::test_instrumental \
-        --deselect=test/test_pipeline.py::TestSDPOutput::test_lpi \
-        --deselect=test/test_pipeline.py::TestSDPOutput::test_supports \
-        --deselect=test/test_pipeline.py::TestLPOutput::test_bounds \
-        --deselect=test/test_pipeline.py::TestLPOutput::test_instrumental \
-        --deselect=test/test_pipeline.py::TestLPOutput::test_supports \
-        --deselect=test/test_pipeline.py::TestInstrumental::test_instrumental_fanout \
-        --deselect=test/test_pipeline.py::TestInstrumental::test_instrumental_nonfanout \
-        --deselect=test/test_pipeline.py::TestBell::test_bell_fanout \
-        --deselect=test/test_pipeline.py::TestBell::test_bell_nonfanout \
-        --deselect=test/test_pipeline.py::TestTriangle::test_triangle_fanout \
-        --deselect=test/test_pipeline.py::TestTriangle::test_triangle_nonfanout \
-        --deselect=test/test_pipeline.py::TestEvans::test_evans_fanout \
-        --deselect=test/test_pipeline.py::TestEvans::test_evans_nonfanout \
-        --deselect=test/test_pipeline.py::TestFullNN::test_fullnetworknonlocality_3partite_line
+         pytest -v
+    - name: Clean up MOSEK license file
+      run: |
+         rm $HOME/mosek/mosek.lic

README.md

@@ -1,15 +1,17 @@
 [![DOI](https://zenodo.org/badge/500850617.svg)](https://zenodo.org/badge/latestdoi/500850617)
 
 # Inflation
-Inflation is a Python package that implements inflation algorithms for causal inference. In causal inference, the main task is to determine which causal relationships can exist between different observed random variables. Inflation algorithms are a class of techniques designed to solve the causal compatibility problem, that is, test compatibility between some observed data and a given causal relationship.
+Inflation is a package, written in Python, that implements inflation algorithms for causal inference. In causal inference, the main task is to determine which causal relationships can exist between different observed random variables. Inflation algorithms are a class of techniques designed to solve the causal compatibility problem, that is, test compatibility between some observed data and a given causal relationship.
 
-The first version of this package implements the inflation technique for quantum causal compatibility. For details, see [Physical Review X 11 (2), 021043 (2021)](https://journals.aps.org/prx/abstract/10.1103/PhysRevX.11.021043). The inflation technique for classical causal compatibility will be implemented in a future update.
+This package implements the inflation technique for classical, quantum, and post-quantum causal compatibility. By relaxing independence constraints to symmetries on larger graphs, it develops hierarchies of relaxations of the causal compatibility problem that can be solved using linear and semidefinite programming. For details, see [Wolfe et al. “The inflation technique for causal inference with latent variables.” Journal of Causal Inference 7 (2), 2017-0020 (2019)](https://www.degruyter.com/document/doi/10.1515/jci-2017-0020/html), [Wolfe et al. “Quantum inflation: A general approach to quantum causal compatibility.” Physical Review X 11 (2), 021043 (2021)](https://journals.aps.org/prx/abstract/10.1103/PhysRevX.11.021043), and references therein.
 
 Examples of use of this package include:
 
+- Causal compatibility with classical, quantum, non-signaling, and hybrid models.
 - Feasibility problems and extraction of certificates.
 - Optimization of Bell operators.
-- Optimisation over classical distributions.
+- Optimization over classical distributions.
+- Handling of bilayer (i.e., networks) and multilayer causal structures.
 - Standard [Navascués-Pironio-Acín hierarchy](https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.98.010401).
 - Scenarios with partial information.
 - Possibilistic compatibility with a causal network.

docs/_build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 5ac241c6c147f17086ae747d1ca39b93
+config: 3499f0084671aa32dd3b76f6907174da
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/html/_modules/index.html

@@ -1,24 +1,24 @@
+
+
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Overview: module code &mdash; Inflation 2.0.2 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/copybutton.css" type="text/css" />
-  <!--[if lt IE 9]>
-    <script src="../_static/js/html5shiv.min.js"></script>
-  <![endif]-->
+  <title>Overview: module code &mdash; Inflation 2.0.1 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=92fd9be5" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
+
 
-        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
-        <script src="../_static/jquery.js"></script>
-        <script src="../_static/underscore.js"></script>
-        <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
-        <script src="../_static/doctools.js"></script>
-        <script src="../_static/clipboard.min.js"></script>
-        <script src="../_static/copybutton.js"></script>
-        <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
+      <script src="../_static/jquery.js?v=5d32c60e"></script>
+      <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+      <script src="../_static/documentation_options.js?v=f5cff4aa"></script>
+      <script src="../_static/doctools.js?v=9a2dae69"></script>
+      <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+      <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
+      <script src="../_static/copybutton.js?v=a56c686a"></script>
+      <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" /> 
@@ -33,7 +33,7 @@
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" />
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
     <input type="hidden" name="check_keywords" value="yes" />
     <input type="hidden" name="area" value="default" />
   </form>
@@ -64,8 +64,8 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="../contents.html" class="icon icon-home"></a> &raquo;</li>
-      <li>Overview: module code</li>
+      <li><a href="../contents.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li class="breadcrumb-item active">Overview: module code</li>
       <li class="wy-breadcrumbs-aside">
       </li>
   </ul>

docs/_build/html/_modules/inflation/InflationProblem.html

@@ -92,6 +92,7 @@ <h1>Source code for inflation.InflationProblem</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Tuple</span><span class="p">,</span> <span class="n">List</span><span class="p">,</span> <span class="n">Union</span><span class="p">,</span> <span class="n">Dict</span>
 <span class="kn">from</span> <span class="nn">warnings</span> <span class="kn">import</span> <span class="n">warn</span>
 
+<span class="kn">import</span> <span class="nn">networkx</span> <span class="k">as</span> <span class="nn">nx</span>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="kn">import</span> <span class="nn">sympy</span>
 <span class="kn">from</span> <span class="nn">tqdm</span> <span class="kn">import</span> <span class="n">tqdm</span>

docs/_build/html/_static/_sphinx_javascript_frameworks_compat.js

@@ -1,20 +1,9 @@
-/*
- * _sphinx_javascript_frameworks_compat.js
- * ~~~~~~~~~~
- *
- * Compatability shim for jQuery and underscores.js.
- *
- * WILL BE REMOVED IN Sphinx 6.0
- * xref RemovedInSphinx60Warning
+/* Compatability shim for jQuery and underscores.js.
  *
+ * Copyright Sphinx contributors
+ * Released under the two clause BSD licence
  */
 
-/**
- * select a different prefix for underscore
- */
-$u = _.noConflict();
-
-
 /**
  * small helper function to urldecode strings
  *

docs/_build/html/_static/copybutton.css

@@ -35,7 +35,8 @@ div.highlight  {
     position: relative;
 }
 
-.highlight:hover button.copybtn {
+/* Show the copybutton */
+.highlight:hover button.copybtn, button.copybtn.success {
 	opacity: 1;
 }
 

docs/_build/html/_static/copybutton.js

@@ -20,7 +20,7 @@ const messages = {
   },
   'fr' : {
     'copy': 'Copier',
-    'copy_to_clipboard': 'Copié dans le presse-papier',
+    'copy_to_clipboard': 'Copier dans le presse-papier',
     'copy_success': 'Copié !',
     'copy_failure': 'Échec de la copie',
   },
@@ -102,18 +102,25 @@ const clearSelection = () => {
   }
 }
 
-// Changes tooltip text for two seconds, then changes it back
+// Changes tooltip text for a moment, then changes it back
+// We want the timeout of our `success` class to be a bit shorter than the
+// tooltip and icon change, so that we can hide the icon before changing back.
+var timeoutIcon = 2000;
+var timeoutSuccessClass = 1500;
+
 const temporarilyChangeTooltip = (el, oldText, newText) => {
   el.setAttribute('data-tooltip', newText)
   el.classList.add('success')
-  setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000)
-  setTimeout(() => el.classList.remove('success'), 2000)
+  // Remove success a little bit sooner than we change the tooltip
+  // So that we can use CSS to hide the copybutton first
+  setTimeout(() => el.classList.remove('success'), timeoutSuccessClass)
+  setTimeout(() => el.setAttribute('data-tooltip', oldText), timeoutIcon)
 }
 
 // Changes the copy button icon for two seconds, then changes it back
 const temporarilyChangeIcon = (el) => {
   el.innerHTML = iconCheck;
-  setTimeout(() => {el.innerHTML = iconCopy}, 2000)
+  setTimeout(() => {el.innerHTML = iconCopy}, timeoutIcon)
 }
 
 const addCopyButtonToCodeCells = () => {
@@ -125,7 +132,8 @@ const addCopyButtonToCodeCells = () => {
   }
 
   // Add copybuttons to all of our code cells
-  const codeCells = document.querySelectorAll('div.highlight pre')
+  const COPYBUTTON_SELECTOR = 'div.highlight pre';
+  const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR)
   codeCells.forEach((codeCell, index) => {
     const id = codeCellId(index)
     codeCell.setAttribute('id', id)
@@ -141,10 +149,25 @@ function escapeRegExp(string) {
     return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string
 }
 
+/**
+ * Removes excluded text from a Node.
+ *
+ * @param {Node} target Node to filter.
+ * @param {string} exclude CSS selector of nodes to exclude.
+ * @returns {DOMString} Text from `target` with text removed.
+ */
+function filterText(target, exclude) {
+    const clone = target.cloneNode(true);  // clone as to not modify the live DOM
+    if (exclude) {
+        // remove excluded nodes
+        clone.querySelectorAll(exclude).forEach(node => node.remove());
+    }
+    return clone.innerText;
+}
+
 // Callback when a copy button is clicked. Will be passed the node that was clicked
 // should then grab the text and replace pieces of text that shouldn't be used in output
 function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") {
-
     var regexp;
     var match;
 
@@ -199,7 +222,12 @@ function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onl
 
 var copyTargetText = (trigger) => {
   var target = document.querySelector(trigger.attributes['data-clipboard-target'].value);
-  return formatCopyText(target.innerText, '$ ', false, true, true, true, '', '')
+
+  // get filtered text
+  let exclude = '.linenos';
+
+  let text = filterText(target, exclude);
+  return formatCopyText(text, '$ ', false, true, true, true, '', '')
 }
 
   // Initialize with a callback so we can modify the text before copy

docs/_build/html/_static/copybutton_funcs.js

@@ -2,10 +2,25 @@ function escapeRegExp(string) {
     return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string
 }
 
+/**
+ * Removes excluded text from a Node.
+ *
+ * @param {Node} target Node to filter.
+ * @param {string} exclude CSS selector of nodes to exclude.
+ * @returns {DOMString} Text from `target` with text removed.
+ */
+export function filterText(target, exclude) {
+    const clone = target.cloneNode(true);  // clone as to not modify the live DOM
+    if (exclude) {
+        // remove excluded nodes
+        clone.querySelectorAll(exclude).forEach(node => node.remove());
+    }
+    return clone.innerText;
+}
+
 // Callback when a copy button is clicked. Will be passed the node that was clicked
 // should then grab the text and replace pieces of text that shouldn't be used in output
 export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") {
-
     var regexp;
     var match;