Updated documentation for new release

Author: lindonroberts

docs/build/doctrees/advanced.doctree

@@ -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: 6a2288786364dcb1761dcd61fd935f30
+config: 71b7b5e9dd47a27f370b73edfaf0d9fa
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/doctrees/diagnostic.doctree

@@ -46,3 +46,8 @@ Version 1.4 (16 May 2023)
 * Handle Nan/Inf values in model gradient and Hessian by gracefully exiting trust-region subproblem
 * Bugfix: automatically make model Hessian symmetric before trust-region subproblem with warning, instead of returning an error
 * Bugfix: reset slow iteration counter when doing soft restarts
+
+Version 1.4.1 (11 Apr 2024)
+-------------------------
+* Migrate package setup to pyproject.toml (required for Python version 3.12)
+* Drop support for Python 2.7 and <=3.7 due to new setup process

docs/build/doctrees/environment.pickle

@@ -26,9 +26,9 @@ The upper and lower bounds on the variables are non-relaxable (i.e. Py-BOBYQA wi
 Full details of the Py-BOBYQA algorithm are given in our papers: 
 
 1. Coralia Cartis, Jan Fiala, Benjamin Marteau and Lindon Roberts, `Improving the Flexibility and Robustness of Model-Based Derivative-Free Optimization Solvers <https://doi.org/10.1145/3338517>`_, *ACM Transactions on Mathematical Software*, 45:3 (2019), pp. 32:1-32:41 [`preprint <https://arxiv.org/abs/1804.00154>`_] 
-2. Coralia Cartis, Lindon Roberts and Oliver Sheridan-Methven, `Escaping local minima with derivative-free methods: a numerical investigation <https://doi.org/10.1080/02331934.2021.1883015>`_, *Optimization* (2021). [`preprint <https://arxiv.org/abs/1812.11343>`_] 
+2. Coralia Cartis, Lindon Roberts and Oliver Sheridan-Methven, `Escaping local minima with derivative-free methods: a numerical investigation <https://doi.org/10.1080/02331934.2021.1883015>`_, *Optimization*, 71:8 (2022), pp. 2343-2373. [`arXiv preprint: 1812.11343 <https://arxiv.org/abs/1812.11343>`_] 
 
-Please cite [1] when using Py-BOBYQA for local optimization, and [1,2] when using Py-BOBYQA's global optimization heuristic functionality **(new in v1.1!)**.
+Please cite [1] when using Py-BOBYQA for local optimization, and [1,2] when using Py-BOBYQA's global optimization heuristic functionality.
 
 If you are interested in solving least-squares minimization problems, you may wish to try `DFO-LS <https://github.com/numericalalgorithmsgroup/dfols>`_, which has the same features as Py-BOBYQA (plus some more), and exploits the least-squares problem structure, so performs better on such problems.
 

docs/build/doctrees/history.doctree

@@ -5,13 +5,13 @@ Requirements
 ------------
 Py-BOBYQA requires the following software to be installed:
 
-* `Python 2.7 or Python 3 <http://www.python.org/>`_
+* Python 3.8 or higher (http://www.python.org/)
 
 Additionally, the following python packages should be installed (these will be installed automatically if using `pip <http://www.pip-installer.org/>`_, see `Installation using pip`_):
 
-* `NumPy 1.11 or higher <http://www.numpy.org/>`_ 
-* `SciPy 0.18 or higher <http://www.scipy.org/>`_
-* Optionally, `Pandas 0.17 or higher <https://pandas.pydata.org/>`_, to return the diagnostic information as a DataFrame
+* NumPy (http://www.numpy.org/)
+* SciPy (http://www.scipy.org/)
+* Pandas (http://pandas.pydata.org/)
 
 **Optional package:** Py-BOBYQA versions 1.2 and higher also support the `trustregion <https://github.com/lindonroberts/trust-region>`_ package for fast trust-region subproblem solutions. To install this, make sure you have a Fortran compiler (e.g. `gfortran <https://gcc.gnu.org/wiki/GFortran>`_) and NumPy installed, then run :code:`pip install trustregion`. You do not have to have trustregion installed for Py-BOBYQA to work, and it is not installed by default.
 
@@ -71,11 +71,12 @@ To upgrade Py-BOBYQA to the latest version, navigate to the top-level directory
 
 Testing
 -------
-If you installed Py-BOBYQA manually, you can test your installation by running:
+If you installed Py-BOBYQA manually, you can test your installation using the pytest package:
 
  .. code-block:: bash
 
-    $ python setup.py test
+    $ pip install pytest
+    $ python -m pytest --pyargs pybobyqa
 
 Uninstallation
 --------------

docs/build/doctrees/index.doctree

@@ -14,7 +14,7 @@ Py-BOBYQA is designed to solve the local optimization problem
 where the bound constraints :math:`a \leq x \leq b` are optional. The upper and lower bounds on the variables are non-relaxable (i.e. Py-BOBYQA will never ask to evaluate a point outside the bounds). The objective function :math:`f(x)` is usually nonlinear and nonquadratic. If you know your objective is linear or quadratic, you should consider a solver designed for such functions (see `here <https://neos-guide.org/Optimization-Guide>`_ for details).
 
 Py-BOBYQA iteratively constructs an interpolation-based model for the objective, and determines a step using a trust-region framework.
-For an in-depth technical description of the algorithm see the paper [CFMR2018]_, and for the global optimization heuristic, see [CRO2018]_.
+For an in-depth technical description of the algorithm see the paper [CFMR2018]_, and for the global optimization heuristic, see [CRO2022]_.
 
 How to use Py-BOBYQA
 --------------------
@@ -402,12 +402,12 @@ The output of this is:
       Warning (max evals): Objective has been called MAXFUN times
       ******************************
 
-As we can see, the :code:`seek_global_minimum` flag helped Py-BOBYQA escape the local minimum from the first run, and find the global minimum. More details are given in [CRO2018]_.
+As we can see, the :code:`seek_global_minimum` flag helped Py-BOBYQA escape the local minimum from the first run, and find the global minimum. More details are given in [CRO2022]_.
 
 References
 ----------
 
 .. [CFMR2018]   
    Coralia Cartis, Jan Fiala, Benjamin Marteau and Lindon Roberts, `Improving the Flexibility and Robustness of Model-Based Derivative-Free Optimization Solvers <https://doi.org/10.1145/3338517>`_, *ACM Transactions on Mathematical Software*, 45:3 (2019), pp. 32:1-32:41 [`preprint <https://arxiv.org/abs/1804.00154>`_] 
-.. [CRO2018]   
-   Coralia Cartis, Lindon Roberts and Oliver Sheridan-Methven, `Escaping local minima with derivative-free methods: a numerical investigation <https://doi.org/10.1080/02331934.2021.1883015>`_, *Optimization* (2021). [`preprint <https://arxiv.org/abs/1812.11343>`_] 
+.. [CRO2022]   
+   Coralia Cartis, Lindon Roberts and Oliver Sheridan-Methven, `Escaping local minima with derivative-free methods: a numerical investigation <https://doi.org/10.1080/02331934.2021.1883015>`_, *Optimization*, 71:8 (2022), pp. 2343-2373. [`arXiv preprint: 1812.11343 <https://arxiv.org/abs/1812.11343>`_] 

docs/build/doctrees/info.doctree

@@ -0,0 +1,123 @@
+/* Compatability shim for jQuery and underscores.js.
+ *
+ * Copyright Sphinx contributors
+ * Released under the two clause BSD licence
+ */
+
+/**
+ * small helper function to urldecode strings
+ *
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
+ */
+jQuery.urldecode = function(x) {
+    if (!x) {
+        return x
+    }
+    return decodeURIComponent(x.replace(/\+/g, ' '));
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+    if (typeof s === 'undefined')
+        s = document.location.search;
+    var parts = s.substr(s.indexOf('?') + 1).split('&');
+    var result = {};
+    for (var i = 0; i < parts.length; i++) {
+        var tmp = parts[i].split('=', 2);
+        var key = jQuery.urldecode(tmp[0]);
+        var value = jQuery.urldecode(tmp[1]);
+        if (key in result)
+            result[key].push(value);
+        else
+            result[key] = [value];
+    }
+    return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+    function highlight(node, addItems) {
+        if (node.nodeType === 3) {
+            var val = node.nodeValue;
+            var pos = val.toLowerCase().indexOf(text);
+            if (pos >= 0 &&
+                !jQuery(node.parentNode).hasClass(className) &&
+                !jQuery(node.parentNode).hasClass("nohighlight")) {
+                var span;
+                var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
+                if (isInSVG) {
+                    span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+                } else {
+                    span = document.createElement("span");
+                    span.className = className;
+                }
+                span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+                node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+                    document.createTextNode(val.substr(pos + text.length)),
+                    node.nextSibling));
+                node.nodeValue = val.substr(0, pos);
+                if (isInSVG) {
+                    var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+                    var bbox = node.parentElement.getBBox();
+                    rect.x.baseVal.value = bbox.x;
+                    rect.y.baseVal.value = bbox.y;
+                    rect.width.baseVal.value = bbox.width;
+                    rect.height.baseVal.value = bbox.height;
+                    rect.setAttribute('class', className);
+                    addItems.push({
+                        "parent": node.parentNode,
+                        "target": rect});
+                }
+            }
+        }
+        else if (!jQuery(node).is("button, select, textarea")) {
+            jQuery.each(node.childNodes, function() {
+                highlight(this, addItems);
+            });
+        }
+    }
+    var addItems = [];
+    var result = this.each(function() {
+        highlight(this, addItems);
+    });
+    for (var i = 0; i < addItems.length; ++i) {
+        jQuery(addItems[i].parent).before(addItems[i].target);
+    }
+    return result;
+};
+
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+    jQuery.uaMatch = function(ua) {
+        ua = ua.toLowerCase();
+
+        var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+            /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+            /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+            /(msie) ([\w.]+)/.exec(ua) ||
+            ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+            [];
+
+        return {
+            browser: match[ 1 ] || "",
+            version: match[ 2 ] || "0"
+        };
+    };
+    jQuery.browser = {};
+    jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}