update docs

docs/manual/build/html/_sources/docs/tutorials.rst.txt

@@ -206,6 +206,10 @@ The strength of the Gaussian noise is specified by ``g_sigma`` or the pair of ``
 The coefficient of the Pade weight, :math:`eta`, is specified by the ``PadeEta`` parameter.
 If ``PadeEta = 0``, the original SpM method will be used.
 
+``param_spm.in`` and ``param_spmpade.in`` are input files for the SpM (:math:`\eta=0`) and SpM-Pade (:math:`\eta=1`) method, respectively.
+Note that optimal :math:`\lambda` for the SpM and SpM-Pade differ, and hence users may need to change the range of :math:`lambda` (``lambdalogbegin`` and ``lambdalogend``).
+The following figure shows the result:
+
 .. image:: figs/spectrum_spmpade.png
 
 The blue curve and red curve show the spectrum reconstructed by the SpM method (:math:`\eta=0`) and the SpM-Pade method (:math:`\eta=1`), respectively.

docs/manual/build/html/_static/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -130,7 +130,7 @@ ul.search li a {
     font-weight: bold;
 }
 
-ul.search li p.context {
+ul.search li div.context {
     color: #888;
     margin: 2px 0 0 30px;
     text-align: left;
@@ -277,25 +277,25 @@ p.rubric {
     font-weight: bold;
 }
 
-img.align-left, figure.align-left, .figure.align-left, object.align-left {
+img.align-left, .figure.align-left, object.align-left {
     clear: left;
     float: left;
     margin-right: 1em;
 }
 
-img.align-right, figure.align-right, .figure.align-right, object.align-right {
+img.align-right, .figure.align-right, object.align-right {
     clear: right;
     float: right;
     margin-left: 1em;
 }
 
-img.align-center, figure.align-center, .figure.align-center, object.align-center {
+img.align-center, .figure.align-center, object.align-center {
   display: block;
   margin-left: auto;
   margin-right: auto;
 }
 
-img.align-default, figure.align-default, .figure.align-default {
+img.align-default, .figure.align-default {
   display: block;
   margin-left: auto;
   margin-right: auto;
@@ -319,8 +319,7 @@ img.align-default, figure.align-default, .figure.align-default {
 
 /* -- sidebars -------------------------------------------------------------- */
 
-div.sidebar,
-aside.sidebar {
+div.sidebar {
     margin: 0 0 0.5em 1em;
     border: 1px solid #ddb;
     padding: 7px;
@@ -378,14 +377,12 @@ div.body p.centered {
 /* -- content of sidebars/topics/admonitions -------------------------------- */
 
 div.sidebar > :last-child,
-aside.sidebar > :last-child,
 div.topic > :last-child,
 div.admonition > :last-child {
     margin-bottom: 0;
 }
 
 div.sidebar::after,
-aside.sidebar::after,
 div.topic::after,
 div.admonition::after,
 blockquote::after {
@@ -458,22 +455,20 @@ td > :last-child {
 
 /* -- figures --------------------------------------------------------------- */
 
-div.figure, figure {
+div.figure {
     margin: 0.5em;
     padding: 0.5em;
 }
 
-div.figure p.caption, figcaption {
+div.figure p.caption {
     padding: 0.3em;
 }
 
-div.figure p.caption span.caption-number,
-figcaption span.caption-number {
+div.figure p.caption span.caption-number {
     font-style: italic;
 }
 
-div.figure p.caption span.caption-text,
-figcaption span.caption-text {
+div.figure p.caption span.caption-text {
 }
 
 /* -- field list styles ----------------------------------------------------- */
@@ -508,63 +503,6 @@ table.hlist td {
     vertical-align: top;
 }
 
-/* -- object description styles --------------------------------------------- */
-
-.sig {
-	font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
-}
-
-.sig-name, code.descname {
-    background-color: transparent;
-    font-weight: bold;
-}
-
-.sig-name {
-	font-size: 1.1em;
-}
-
-code.descname {
-    font-size: 1.2em;
-}
-
-.sig-prename, code.descclassname {
-    background-color: transparent;
-}
-
-.optional {
-    font-size: 1.3em;
-}
-
-.sig-paren {
-    font-size: larger;
-}
-
-.sig-param.n {
-	font-style: italic;
-}
-
-/* C++ specific styling */
-
-.sig-inline.c-texpr,
-.sig-inline.cpp-texpr {
-	font-family: unset;
-}
-
-.sig.c   .k, .sig.c   .kt,
-.sig.cpp .k, .sig.cpp .kt {
-	color: #0033B3;
-}
-
-.sig.c   .m,
-.sig.cpp .m {
-	color: #1750EB;
-}
-
-.sig.c   .s, .sig.c   .sc,
-.sig.cpp .s, .sig.cpp .sc {
-	color: #067D17;
-}
-
 
 /* -- other body styles ----------------------------------------------------- */
 
@@ -691,6 +629,14 @@ dl.glossary dt {
     font-size: 1.1em;
 }
 
+.optional {
+    font-size: 1.3em;
+}
+
+.sig-paren {
+    font-size: larger;
+}
+
 .versionmodified {
     font-style: italic;
 }
@@ -818,13 +764,8 @@ div.code-block-caption code {
 }
 
 table.highlighttable td.linenos,
-span.linenos,
 div.doctest > div.highlight span.gp {  /* gp: Generic.Prompt */
-  user-select: none;
-  -webkit-user-select: text; /* Safari fallback only */
-  -webkit-user-select: none; /* Chrome/Safari */
-  -moz-user-select: none; /* Firefox */
-  -ms-user-select: none; /* IE10+ */
+    user-select: none;
 }
 
 div.code-block-caption span.caption-number {
@@ -839,6 +780,16 @@ div.literal-block-wrapper {
     margin: 1em 0;
 }
 
+code.descname {
+    background-color: transparent;
+    font-weight: bold;
+    font-size: 1.2em;
+}
+
+code.descclassname {
+    background-color: transparent;
+}
+
 code.xref, a code {
     background-color: transparent;
     font-weight: bold;

docs/manual/build/html/_static/doctools.js

@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for all documentation.
  *
- * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -29,14 +29,9 @@ if (!window.console || !console.firebug) {
 
 /**
  * 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, ' '));
+  return decodeURIComponent(x).replace(/\+/g, ' ');
 };
 
 /**
@@ -290,10 +285,9 @@ var Documentation = {
   initOnKeyListeners: function() {
     $(document).keydown(function(event) {
       var activeElementType = document.activeElement.tagName;
-      // don't navigate when in search box, textarea, dropdown or button
+      // don't navigate when in search box or textarea
       if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT'
-          && activeElementType !== 'BUTTON' && !event.altKey && !event.ctrlKey && !event.metaKey
-          && !event.shiftKey) {
+          && !event.altKey && !event.ctrlKey && !event.metaKey && !event.shiftKey) {
         switch (event.keyCode) {
           case 37: // left
             var prevHref = $('link[rel="prev"]').prop('href');

docs/manual/build/html/_static/pygments.css

@@ -1,7 +1,7 @@
 pre { line-height: 125%; }
-td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
-span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
-td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
+td.linenos pre { color: #000000; background-color: #f0f0f0; padding-left: 5px; padding-right: 5px; }
+span.linenos { color: #000000; background-color: #f0f0f0; padding-left: 5px; padding-right: 5px; }
+td.linenos pre.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
 span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
 .highlight .hll { background-color: #ffffcc }
 .highlight { background: #eeffcc; }

docs/manual/build/html/_static/searchtools.js

@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for the full-text search.
  *
- * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -59,10 +59,10 @@ var Search = {
   _pulse_status : -1,
 
   htmlToText : function(htmlString) {
-      var virtualDocument = document.implementation.createHTMLDocument('virtual');
-      var htmlElement = $(htmlString, virtualDocument);
-      htmlElement.find('.headerlink').remove();
-      docContent = htmlElement.find('[role=main]')[0];
+      var htmlElement = document.createElement('span');
+      htmlElement.innerHTML = htmlString;
+      $(htmlElement).find('.headerlink').remove();
+      docContent = $(htmlElement).find('[role=main]')[0];
       if(docContent === undefined) {
           console.warn("Content block not found. Sphinx search tries to obtain it " +
                        "via '[role=main]'. Could you check your theme or template.");
@@ -248,7 +248,7 @@ var Search = {
       // results left, load the summary and display it
       if (results.length) {
         var item = results.pop();
-        var listItem = $('<li></li>');
+        var listItem = $('<li style="display:none"></li>');
         var requestUrl = "";
         var linkUrl = "";
         if (DOCUMENTATION_OPTIONS.BUILDER === 'dirhtml') {
@@ -273,9 +273,9 @@ var Search = {
         if (item[3]) {
           listItem.append($('<span> (' + item[3] + ')</span>'));
           Search.output.append(listItem);
-          setTimeout(function() {
+          listItem.slideDown(5, function() {
             displayNextItem();
-          }, 5);
+          });
         } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
           $.ajax({url: requestUrl,
                   dataType: "text",
@@ -285,16 +285,16 @@ var Search = {
                       listItem.append(Search.makeSearchSummary(data, searchterms, hlterms));
                     }
                     Search.output.append(listItem);
-                    setTimeout(function() {
+                    listItem.slideDown(5, function() {
                       displayNextItem();
-                    }, 5);
+                    });
                   }});
         } else {
           // no source available, just display title
           Search.output.append(listItem);
-          setTimeout(function() {
+          listItem.slideDown(5, function() {
             displayNextItem();
-          }, 5);
+          });
         }
       }
       // search finished, update title and status message
@@ -379,13 +379,6 @@ var Search = {
     return results;
   },
 
-  /**
-   * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions
-   */
-  escapeRegExp : function(string) {
-    return string.replace(/[.*+\-?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string
-  },
-
   /**
    * search for full-text terms in the index
    */
@@ -409,14 +402,13 @@ var Search = {
       ];
       // add support for partial matches
       if (word.length > 2) {
-        var word_regex = this.escapeRegExp(word);
         for (var w in terms) {
-          if (w.match(word_regex) && !terms[word]) {
+          if (w.match(word) && !terms[word]) {
             _o.push({files: terms[w], score: Scorer.partialTerm})
           }
         }
         for (var w in titleterms) {
-          if (w.match(word_regex) && !titleterms[word]) {
+          if (w.match(word) && !titleterms[word]) {
               _o.push({files: titleterms[w], score: Scorer.partialTitle})
           }
         }
@@ -509,7 +501,7 @@ var Search = {
     var excerpt = ((start > 0) ? '...' : '') +
       $.trim(text.substr(start, 240)) +
       ((start + 240 - text.length) ? '...' : '');
-    var rv = $('<p class="context"></p>').text(excerpt);
+    var rv = $('<div class="context"></div>').text(excerpt);
     $.each(hlwords, function() {
       rv = rv.highlightText(this, 'highlighted');
     });