Rebuild documentation

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: 61941cefe668ad71aa6328c3f0514bbc
+config: 97c996ba62da576f30398b69a6c53a93
 tags: 645f666f9bcd5a90fca523b33c5a78b7

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

@@ -2,6 +2,11 @@ Version History
 ===============
 This section lists the different versions of PyCUTEst and the updates between them.
 
+Version 1.6.0 (24 Jan 2024)
+---------------------------
+* New grad function to evaluate the gradient only
+* New lag function to evaluate the Lagrangian
+
 Version 1.5.1 (8 Aug 2023)
 --------------------------
 * Fix invalid sparse dimensions while dropping fixed variables

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

@@ -8,12 +8,9 @@ PyCUTEst
 Python interface to the CUTEst optimization test environment
 ------------------------------------------------------------
 
-.. warning::
-    PyCUTEst v1.5.0 broke existing cached problems, when upgrading to v1.5.0 please clear out your cache by deleting the $PYCUTEST_CACHE/pycutest_cache_holder directory.
-
 **Release:** |version|
 
-**Date:** 8 August 2023
+**Date:** 24 January 2024
 
 **Author:** `Jaroslav Fowkes <jaroslav.fowkes@maths.ox.ac.uk>`_ and `Lindon Roberts <https://lindonroberts.github.io/>`_
 

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

@@ -9,9 +9,11 @@ Problem Methods
 
 The methods available for each :code:`CUTEstProblem` instance are:
 
-* `objcons(x) <methods/pycutest.CUTEstProblem.objcons.html>`_: evaluate objective and constraints
 * `obj(x[, gradient]) <methods/pycutest.CUTEstProblem.obj.html>`_: evaluate objective (and optionally its gradient)
+* `grad(x[, index]) <methods/pycutest.CUTEstProblem.grad.html>`_: evaluate objective gradient or specific constraint gradient
+* `objcons(x) <methods/pycutest.CUTEstProblem.objcons.html>`_: evaluate objective and constraints
 * `cons(x[, index, gradient]) <methods/pycutest.CUTEstProblem.cons.html>`_: evaluate constraint(s) and optionally their Jacobian/its gradient
+* `lag(x, v[, gradient]) <methods/pycutest.CUTEstProblem.lag.html>`_: evaluate Lagrangian function value and optionally its gradient
 * `lagjac(x[, v]) <methods/pycutest.CUTEstProblem.lagjac.html>`_: evaluate gradient of objective/Lagrangian and Jacobian of constraints
 * `jprod(p[, transpose, x]) <methods/pycutest.CUTEstProblem.jprod.html>`_: evaluate constraint Jacobian-vector product
 * `hess(x[, v]) <methods/pycutest.CUTEstProblem.hess.html>`_: evaluate Hessian of objective or Lagrangian
@@ -72,9 +74,11 @@ Please click on a :code:`CUTEstProblem` method below for full documentation:
    :toctree: methods
    :template: method.rst
 
-   objcons 
    obj 
+   grad 
+   objcons 
    cons 
+   lag 
    lagjac 
    jprod 
    hess 

docs/_build/html/_sources/methods/pycutest.CUTEstProblem.grad.rst.txt

@@ -0,0 +1,6 @@
+CUTEstProblem.grad
+==================
+
+.. currentmodule:: pycutest
+
+.. automethod:: CUTEstProblem.grad

docs/_build/html/_sources/methods/pycutest.CUTEstProblem.lag.rst.txt

@@ -0,0 +1,6 @@
+CUTEstProblem.lag
+=================
+
+.. currentmodule:: pycutest
+
+.. automethod:: CUTEstProblem.lag

docs/_build/html/_static/basic.css

@@ -237,6 +237,10 @@ a.headerlink {
     visibility: hidden;
 }
 
+a:visited {
+    color: #551A8B;
+}
+
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -670,6 +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;
@@ -738,6 +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/documentation_options.js

@@ -1,6 +1,5 @@
-var DOCUMENTATION_OPTIONS = {
-    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '1.5.1',
+const DOCUMENTATION_OPTIONS = {
+    VERSION: '1.6.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

docs/_build/html/_static/pygments.css

@@ -17,6 +17,7 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
 .highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
 .highlight .gd { color: #A00000 } /* Generic.Deleted */
 .highlight .ge { font-style: italic } /* Generic.Emph */
+.highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */
 .highlight .gr { color: #FF0000 } /* Generic.Error */
 .highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
 .highlight .gi { color: #00A000 } /* Generic.Inserted */

docs/_build/html/_static/searchtools.js

@@ -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();
+});

docs/_build/html/building.html

@@ -1,21 +1,23 @@
 <!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" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Building Test Problems &mdash; PyCUTEst v1.5.1 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+  <title>Building Test Problems &mdash; PyCUTEst v1.6.0 documentation</title>
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
+
+
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script src="_static/jquery.js"></script>
-        <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
-        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
-        <script src="_static/doctools.js"></script>
-        <script src="_static/sphinx_highlight.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=72d88caf"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -35,7 +37,7 @@
             PyCUTEst
           </a>
               <div class="version">
-                1.5.1
+                1.6.0
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
@@ -95,10 +97,10 @@
            <div itemprop="articleBody">
 
   <section id="building-test-problems">
-<h1>Building Test Problems<a class="headerlink" href="#building-test-problems" title="Permalink to this heading"></a></h1>
+<h1>Building Test Problems<a class="headerlink" href="#building-test-problems" title="Link to this heading"></a></h1>
 <p>In this section, we describe the interface for finding and compiling CUTEst problems.</p>
 <section id="finding-problems">
-<h2>Finding Problems<a class="headerlink" href="#finding-problems" title="Permalink to this heading"></a></h2>
+<h2>Finding Problems<a class="headerlink" href="#finding-problems" title="Link to this heading"></a></h2>
 <p>CUTEst has a scheme for classifying problems (see <a class="reference external" href="http://www.cuter.rl.ac.uk/Problems/classification.shtml">here</a>).
 Based on these properties, we can search for test problems using the <a class="reference external" href="functions/pycutest.find_problems.html">find_problems()</a> function.
 We can check the properties of a specific problem with <a class="reference external" href="functions/pycutest.problem_properties.html">problem_properties()</a>.</p>
@@ -127,7 +129,7 @@ <h2>Finding Problems<a class="headerlink" href="#finding-problems" title="Permal
 <p>Full documentation for these functions is given below.</p>
 </section>
 <section id="building-problems">
-<h2>Building Problems<a class="headerlink" href="#building-problems" title="Permalink to this heading"></a></h2>
+<h2>Building Problems<a class="headerlink" href="#building-problems" title="Link to this heading"></a></h2>
 <p>Many CUTEst problems have optional input parameters. The <a class="reference external" href="functions/pycutest.print_available_sif_params.html">print_available_sif_params()</a> function prints a list of valid parameters for a given problem.
 Then, we can build a problem, including optional parameters, with <a class="reference external" href="functions/pycutest.import_problem.html">import_problem()</a>.
 This returns an instance of the <code class="code docutils literal notranslate"><span class="pre">CUTEstProblem</span></code> class (see next section).</p>
@@ -165,13 +167,13 @@ <h2>Building Problems<a class="headerlink" href="#building-problems" title="Perm
 <p>Full documentation for these functions is given below.</p>
 </section>
 <section id="cache-management">
-<h2>Cache Management<a class="headerlink" href="#cache-management" title="Permalink to this heading"></a></h2>
+<h2>Cache Management<a class="headerlink" href="#cache-management" title="Link to this heading"></a></h2>
 <p>PyCUTEst works by compiling each problem in its own folder inside its cache (given by the <code class="code docutils literal notranslate"><span class="pre">PYCUTEST_CACHE</span></code> environment variable if specified, or the current working directory if not).
 A problem can be cleared from the cache using <a class="reference external" href="functions/pycutest.clear_cache.html">clear_cache()</a>, and a list of all problems currently installed can be displayed with <a class="reference external" href="functions/pycutest.all_cached_problems.html">all_cached_problems()</a>.
 Documentation for these functions is given below.</p>
 </section>
 <section id="full-function-documentation">
-<h2>Full function documentation<a class="headerlink" href="#full-function-documentation" title="Permalink to this heading"></a></h2>
+<h2>Full function documentation<a class="headerlink" href="#full-function-documentation" title="Link to this heading"></a></h2>
 <p>Please click on a <code class="code docutils literal notranslate"><span class="pre">pycutest</span></code> function below for full documentation:</p>
 <table class="autosummary longtable docutils align-default">
 <tbody>