Merged with previous version

docs/README.rst

@@ -3,7 +3,7 @@ piecewise-regression (aka segmented regression) in python
 ==========================================================
 :piecewise-regression: fitting straight line models with breakpoints
 :Author: Charlie Pilgrim
-:Version: 1.3.0
+:Version: 1.4.1
 :Github: https://github.com/chasmani/piecewise-regression
 :Documentation: https://piecewise-regression.readthedocs.io/en/master/index.html
 :Paper: https://joss.theoj.org/papers/10.21105/joss.03859
@@ -110,8 +110,9 @@ Example output: ::
 	----------------------------------------------------------------------------------------------------
 	alpha2              -2.03084       0.0218      -93.068    3.66e-164      -2.0739      -1.9878
 	====================================================================================================
+	Davies test for existence of at least 1 breakpoint: p=5.13032e-295 (e.g. p<0.05 means reject null hypothesis of no breakpoints at 5% significance)
 
-This includes estimates for all the model variables, along with confidence intervals. NOTE: The Davies hypothesis test for the existence of at least one breakpoint is not reported, and is under development and testing. 
+This includes estimates for all the model variables, along with confidence intervals. The Davies test is a hypothesis test for the existence of at least one breakpoint, against the null hypothesis of no breakpoints. Following Muggeo ("segmented: An R Package to Fit Regression Models with Broken-Line Relationships" 2008), this uses the Davies test with the Wald statistic on the breakpoint change in gradient. 
 
 3. Optional: Plotting the data and model results: ::
 
@@ -194,7 +195,7 @@ To get code coverage, run (requires pytest and pytest-cov libraries): ::
 
 	pytest --cov=./
 
-There are also a series of simulation tests that check the estimates have realistic confidence intervals. These can be found in the folder "tests-manual". 
+There are also a series of simulation tests that check the estimates have realistic confidence intervals, and the Davies test gives realistic p-values. These can be found in the folder "tests-manual". 
 
 Requirements
 =============

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: 02d290ccdd51d93ee81642fa219f16d1
+config: 5b909a9c30817d1108e3905be21db110
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/html/_sources/README.rst.txt

@@ -3,7 +3,7 @@ piecewise-regression (aka segmented regression) in python
 ==========================================================
 :piecewise-regression: fitting straight line models with breakpoints
 :Author: Charlie Pilgrim
-:Version: 1.3.0
+:Version: 1.4.1
 :Github: https://github.com/chasmani/piecewise-regression
 :Documentation: https://piecewise-regression.readthedocs.io/en/master/index.html
 :Paper: https://joss.theoj.org/papers/10.21105/joss.03859
@@ -110,8 +110,9 @@ Example output: ::
 	----------------------------------------------------------------------------------------------------
 	alpha2              -2.03084       0.0218      -93.068    3.66e-164      -2.0739      -1.9878
 	====================================================================================================
+	Davies test for existence of at least 1 breakpoint: p=5.13032e-295 (e.g. p<0.05 means reject null hypothesis of no breakpoints at 5% significance)
 
-This includes estimates for all the model variables, along with confidence intervals. NOTE: The Davies hypothesis test for the existence of at least one breakpoint is not reported, and is under development and testing. 
+This includes estimates for all the model variables, along with confidence intervals. The Davies test is a hypothesis test for the existence of at least one breakpoint, against the null hypothesis of no breakpoints. Following Muggeo ("segmented: An R Package to Fit Regression Models with Broken-Line Relationships" 2008), this uses the Davies test with the Wald statistic on the breakpoint change in gradient. 
 
 3. Optional: Plotting the data and model results: ::
 
@@ -194,7 +195,7 @@ To get code coverage, run (requires pytest and pytest-cov libraries): ::
 
 	pytest --cov=./
 
-There are also a series of simulation tests that check the estimates have realistic confidence intervals. These can be found in the folder "tests-manual". 
+There are also a series of simulation tests that check the estimates have realistic confidence intervals, and the Davies test gives realistic p-values. These can be found in the folder "tests-manual". 
 
 Requirements
 =============

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/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -236,17 +236,11 @@ div.body p, div.body dd, div.body li, div.body blockquote {
 a.headerlink {
     visibility: hidden;
 }
-a.brackets:before,
-span.brackets > a:before{
-    content: "[";
-}
 
-a.brackets:after,
-span.brackets > a:after {
-    content: "]";
+a:visited {
+    color: #551A8B;
 }
 
-
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -334,11 +328,17 @@ aside.sidebar {
 p.sidebar-title {
     font-weight: bold;
 }
+
+nav.contents,
+aside.topic,
 div.admonition, div.topic, blockquote {
     clear: left;
 }
 
 /* -- topics ---------------------------------------------------------------- */
+
+nav.contents,
+aside.topic,
 div.topic {
     border: 1px solid #ccc;
     padding: 7px;
@@ -377,13 +377,17 @@ div.body p.centered {
 
 div.sidebar > :last-child,
 aside.sidebar > :last-child,
+nav.contents > :last-child,
+aside.topic > :last-child,
 div.topic > :last-child,
 div.admonition > :last-child {
     margin-bottom: 0;
 }
 
 div.sidebar::after,
 aside.sidebar::after,
+nav.contents::after,
+aside.topic::after,
 div.topic::after,
 div.admonition::after,
 blockquote::after {
@@ -608,19 +612,27 @@ ol.simple p,
 ul.simple p {
     margin-bottom: 0;
 }
-dl.footnote > dt,
-dl.citation > dt {
+
+aside.footnote > span,
+div.citation > span {
     float: left;
-    margin-right: 0.5em;
 }
-
-dl.footnote > dd,
-dl.citation > dd {
+aside.footnote > span:last-of-type,
+div.citation > span:last-of-type {
+  padding-right: 0.5em;
+}
+aside.footnote > p {
+  margin-left: 2em;
+}
+div.citation > p {
+  margin-left: 4em;
+}
+aside.footnote > p:last-of-type,
+div.citation > p:last-of-type {
     margin-bottom: 0em;
 }
-
-dl.footnote > dd:after,
-dl.citation > dd:after {
+aside.footnote > p:last-of-type:after,
+div.citation > p:last-of-type:after {
     content: "";
     clear: both;
 }
@@ -636,10 +648,6 @@ dl.field-list > dt {
     padding-left: 0.5em;
     padding-right: 5px;
 }
-dl.field-list > dt:after {
-    content: ":";
-}
-
 
 dl.field-list > dd {
     padding-left: 0.5em;
@@ -666,6 +674,16 @@ dd {
     margin-left: 30px;
 }
 
+.sig dd {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
+.sig dl {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
 dl > dd:last-child,
 dl > dd:last-child > :last-child {
     margin-bottom: 0;
@@ -734,6 +752,14 @@ abbr, acronym {
     cursor: help;
 }
 
+.translated {
+    background-color: rgba(207, 255, 207, 0.2)
+}
+
+.untranslated {
+    background-color: rgba(255, 207, 207, 0.2)
+}
+
 /* -- code displays --------------------------------------------------------- */
 
 pre {

docs/_build/html/_static/doctools.js

@@ -4,7 +4,7 @@
  *
  * Base JavaScript utilities for all Sphinx HTML documentation.
  *
- * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

docs/_build/html/_static/documentation_options.js

@@ -1,5 +1,4 @@
-var DOCUMENTATION_OPTIONS = {
-    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
+const DOCUMENTATION_OPTIONS = {
     VERSION: '1',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,

docs/_build/html/_static/language_data.js

@@ -5,7 +5,7 @@
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
  *
- * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

docs/_build/html/_static/searchtools.js

@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for the full-text search.
  *
- * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -57,12 +57,12 @@ const _removeChildren = (element) => {
 const _escapeRegExp = (string) =>
   string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
 
-const _displayItem = (item, searchTerms) => {
+const _displayItem = (item, searchTerms, highlightTerms) => {
   const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
-  const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT;
   const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
   const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
   const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
+  const contentRoot = document.documentElement.dataset.content_root;
 
   const [docName, title, anchor, descr, score, _filename] = item;
 
@@ -75,20 +75,24 @@ const _displayItem = (item, searchTerms) => {
     if (dirname.match(/\/index\/$/))
       dirname = dirname.substring(0, dirname.length - 6);
     else if (dirname === "index/") dirname = "";
-    requestUrl = docUrlRoot + dirname;
+    requestUrl = contentRoot + dirname;
     linkUrl = requestUrl;
   } else {
     // normal html builders
-    requestUrl = docUrlRoot + docName + docFileSuffix;
+    requestUrl = contentRoot + docName + docFileSuffix;
     linkUrl = docName + docLinkSuffix;
   }
   let linkEl = listItem.appendChild(document.createElement("a"));
   linkEl.href = linkUrl + anchor;
   linkEl.dataset.score = score;
   linkEl.innerHTML = title;
-  if (descr)
+  if (descr) {
     listItem.appendChild(document.createElement("span")).innerHTML =
       " (" + descr + ")";
+    // highlight search terms in the description
+    if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+      highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
+  }
   else if (showSearchSummary)
     fetch(requestUrl)
       .then((responseData) => responseData.text())
@@ -97,6 +101,9 @@ const _displayItem = (item, searchTerms) => {
           listItem.appendChild(
             Search.makeSearchSummary(data, searchTerms)
           );
+        // highlight search terms in the summary
+        if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+          highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
       });
   Search.output.appendChild(listItem);
 };
@@ -115,14 +122,15 @@ const _finishSearch = (resultCount) => {
 const _displayNextItem = (
   results,
   resultCount,
-  searchTerms
+  searchTerms,
+  highlightTerms,
 ) => {
   // results left, load the summary and display it
   // this is intended to be dynamic (don't sub resultsCount)
   if (results.length) {
-    _displayItem(results.pop(), searchTerms);
+    _displayItem(results.pop(), searchTerms, highlightTerms);
     setTimeout(
-      () => _displayNextItem(results, resultCount, searchTerms),
+      () => _displayNextItem(results, resultCount, searchTerms, highlightTerms),
       5
     );
   }
@@ -360,7 +368,7 @@ const Search = {
     // console.info("search results:", Search.lastresults);
 
     // print the results
-    _displayNextItem(results, results.length, searchTerms);
+    _displayNextItem(results, results.length, searchTerms, highlightTerms);
   },
 
   /**

docs/_build/html/_static/sphinx_highlight.js

@@ -29,14 +29,19 @@ const _highlight = (node, addItems, text, className) => {
       }
 
       span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+      const rest = document.createTextNode(val.substr(pos + text.length));
       parent.insertBefore(
         span,
         parent.insertBefore(
-          document.createTextNode(val.substr(pos + text.length)),
+          rest,
           node.nextSibling
         )
       );
       node.nodeValue = val.substr(0, pos);
+      /* There may be more occurrences of search term in this node. So call this
+       * function recursively on the remaining fragment.
+       */
+      _highlight(rest, addItems, text, className);
 
       if (isInSVG) {
         const rect = document.createElementNS(
@@ -140,5 +145,10 @@ const SphinxHighlight = {
   },
 };
 
-_ready(SphinxHighlight.highlightSearchWords);
-_ready(SphinxHighlight.initEscapeListener);
+_ready(() => {
+  /* Do not call highlightSearchWords() when we are on the search page.
+   * It will highlight words from the *previous* search query.
+   */
+  if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords();
+  SphinxHighlight.initEscapeListener();
+});