Skip to content

Commit

Permalink
Updated documentation for new release
Browse files Browse the repository at this point in the history
  • Loading branch information
lindonroberts committed Apr 11, 2024
1 parent 889bc7b commit 3a3bd50
Show file tree
Hide file tree
Showing 92 changed files with 12,804 additions and 5,568 deletions.
Binary file modified docs/build/doctrees/advanced.doctree
Binary file not shown.
Binary file modified docs/build/doctrees/diagnostic.doctree
Binary file not shown.
Binary file modified docs/build/doctrees/environment.pickle
Binary file not shown.
Binary file modified docs/build/doctrees/history.doctree
Binary file not shown.
Binary file modified docs/build/doctrees/index.doctree
Binary file not shown.
Binary file modified docs/build/doctrees/info.doctree
Binary file not shown.
Binary file modified docs/build/doctrees/install.doctree
Binary file not shown.
Binary file modified docs/build/doctrees/userguide.doctree
Binary file not shown.
2 changes: 1 addition & 1 deletion docs/build/html/.buildinfo
Original file line number Diff line number Diff line change
@@ -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
5 changes: 5 additions & 0 deletions docs/build/html/_sources/history.rst.txt
Original file line number Diff line number Diff line change
Expand Up @@ -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
4 changes: 2 additions & 2 deletions docs/build/html/_sources/index.rst.txt
Original file line number Diff line number Diff line change
Expand Up @@ -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.

Expand Down
13 changes: 7 additions & 6 deletions docs/build/html/_sources/install.rst.txt
Original file line number Diff line number Diff line change
Expand Up @@ -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.

Expand Down Expand Up @@ -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
--------------
Expand Down
8 changes: 4 additions & 4 deletions docs/build/html/_sources/userguide.rst.txt
Original file line number Diff line number Diff line change
Expand Up @@ -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
--------------------
Expand Down Expand Up @@ -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>`_]
123 changes: 123 additions & 0 deletions docs/build/html/_static/_sphinx_javascript_frameworks_compat.js
Original file line number Diff line number Diff line change
@@ -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;
}
Loading

0 comments on commit 3a3bd50

Please sign in to comment.