Update docs

docs/_sources/cg-updating-docs.rst

@@ -3,7 +3,7 @@ Updating the Documentation
 
 About the `cfr` documentation
 """""""""""""""""""""""""""""""""
-`cfr`'s documentation is built automatically from the function and class docstrings, via `Sphinx The Docs <https://www.sphinx-doc.org>`_.
+`cfr`'s documentation is built automatically from the function and class docstrings, via `Sphinx <https://www.sphinx-doc.org>`_.
 It is therefore especially important for your code to include a docstring, and to modify the docstrings of the functions/classes you modified to make sure the documentation is current.
 
 Updating docstrings

docs/_sources/ug-api.rst

@@ -46,11 +46,6 @@ DA
 .. autoclass:: cfr.da.EnKF
     :members:
 
-GraphEM
--------
-
-.. autoclass:: cfr.graphem.solver.GraphEM
-    :members:
 
 ReconJob
 --------

docs/_sources/ug-proxy.rst

@@ -12,5 +12,4 @@ In this section, we will cover the below topics:
     notebooks/proxy-ops
     notebooks/proxy-analysis
     notebooks/proxy-composites
-    .. notebooks/proxy-viz
-    .. notebooks/proxy-get-nearest-climate
+    notebooks/proxy-dups

docs/_static/_sphinx_javascript_frameworks_compat.js

@@ -0,0 +1,134 @@
+/*
+ * _sphinx_javascript_frameworks_compat.js
+ * ~~~~~~~~~~
+ *
+ * Compatability shim for jQuery and underscores.js.
+ *
+ * WILL BE REMOVED IN Sphinx 6.0
+ * xref RemovedInSphinx60Warning
+ *
+ */
+
+/**
+ * select a different prefix for underscore
+ */
+$u = _.noConflict();
+
+
+/**
+ * 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;
+}

docs/_static/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -324,17 +324,17 @@ 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;
@@ -375,6 +375,7 @@ 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;
@@ -384,6 +385,7 @@ div.sidebar::after,
 aside.sidebar::after,
 nav.contents::after,
 aside.topic::after,
+
 div.topic::after,
 div.admonition::after,
 blockquote::after {
@@ -609,6 +611,25 @@ ul.simple p {
     margin-bottom: 0;
 }
 
+/* Docutils 0.17 and older (footnotes & citations) */
+dl.footnote > dt,
+dl.citation > dt {
+    float: left;
+    margin-right: 0.5em;
+}
+
+dl.footnote > dd,
+dl.citation > dd {
+    margin-bottom: 0em;
+}
+
+dl.footnote > dd:after,
+dl.citation > dd:after {
+    content: "";
+    clear: both;
+}
+
+/* Docutils 0.18+ (footnotes & citations) */
 aside.footnote > span,
 div.citation > span {
     float: left;
@@ -633,6 +654,8 @@ div.citation > p:last-of-type:after {
     clear: both;
 }
 
+/* Footnotes & citations ends */
+
 dl.field-list {
     display: grid;
     grid-template-columns: fit-content(30%) auto;
@@ -645,6 +668,10 @@ dl.field-list > dt {
     padding-right: 5px;
 }
 
+dl.field-list > dt:after {
+    content: ":";
+}
+
 dl.field-list > dd {
     padding-left: 0.5em;
     margin-top: 0em;