diff --git a/.buildinfo b/.buildinfo index 90c174952..5c146ee36 100644 --- a/.buildinfo +++ b/.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: 4684e9491dfaabdf6499532dce6b96f6 +config: da87502f4bec4ed891bdd1e665b8301a tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip b/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip index 865cd80d2..d2d6af79b 100644 Binary files a/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip and b/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip differ diff --git a/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip b/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip index 052a2275e..9ae28bd43 100644 Binary files a/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip and b/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip differ diff --git a/_images/sphx_glr_simple_arctan_fit_001.png b/_images/sphx_glr_simple_arctan_fit_001.png index 0466b8116..5704ebb61 100644 Binary files a/_images/sphx_glr_simple_arctan_fit_001.png and b/_images/sphx_glr_simple_arctan_fit_001.png differ diff --git a/_images/sphx_glr_simple_arctan_fit_thumb.png b/_images/sphx_glr_simple_arctan_fit_thumb.png index 8d5886926..ebc6b634a 100644 Binary files a/_images/sphx_glr_simple_arctan_fit_thumb.png and b/_images/sphx_glr_simple_arctan_fit_thumb.png differ diff --git a/_sources/auto_examples/index.rst.txt b/_sources/auto_examples/index.rst.txt index e90cb8158..2f7ccf74b 100644 --- a/_sources/auto_examples/index.rst.txt +++ b/_sources/auto_examples/index.rst.txt @@ -13,6 +13,9 @@ Below is a gallery of examples.
+.. thumbnail-parent-div-open + +.. thumbnail-parent-div-close .. raw:: html @@ -29,6 +32,7 @@ Below is a gallery of examples on model fitting.
+.. thumbnail-parent-div-open .. raw:: html @@ -81,6 +85,8 @@ Below is a gallery of examples on model fitting.
+.. thumbnail-parent-div-close + .. raw:: html
diff --git a/_sources/auto_examples/model_fitting/EELS_curve_fitting.rst.txt b/_sources/auto_examples/model_fitting/EELS_curve_fitting.rst.txt index df68af256..117c107b8 100644 --- a/_sources/auto_examples/model_fitting/EELS_curve_fitting.rst.txt +++ b/_sources/auto_examples/model_fitting/EELS_curve_fitting.rst.txt @@ -11,7 +11,7 @@ :class: sphx-glr-download-link-note :ref:`Go to the end ` - to download the full example code + to download the full example code. .. rst-class:: sphx-glr-example-title @@ -38,7 +38,7 @@ png file. .. code-block:: none - 0%| | 0.00/42.3M [00:00 +.. thumbnail-parent-div-open .. raw:: html @@ -65,6 +66,8 @@ Below is a gallery of examples on model fitting. +.. thumbnail-parent-div-close + .. raw:: html diff --git a/_sources/auto_examples/model_fitting/plot_residual.rst.txt b/_sources/auto_examples/model_fitting/plot_residual.rst.txt index b8a5cd3a3..02f9f6fe4 100644 --- a/_sources/auto_examples/model_fitting/plot_residual.rst.txt +++ b/_sources/auto_examples/model_fitting/plot_residual.rst.txt @@ -11,7 +11,7 @@ :class: sphx-glr-download-link-note :ref:`Go to the end ` - to download the full example code + to download the full example code. .. rst-class:: sphx-glr-example-title @@ -110,7 +110,7 @@ Fit for all navigation positions: .. code-block:: none - Exception ignored in: + Exception ignored in: Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/tqdm/std.py", line 1148, in __del__ self.close() @@ -118,7 +118,7 @@ Fit for all navigation positions: self.disp(bar_style='danger', check_delay=False) ^^^^^^^^^ AttributeError: 'tqdm_notebook' object has no attribute 'disp' - 0%| | 0/10 [00:00` - to download the full example code + to download the full example code. .. rst-class:: sphx-glr-example-title @@ -42,9 +42,9 @@ Fit an arctan function. Active: True Parameter Name | Free | Value | Std | Min | Max | Linear ============== | ======= | ========== | ========== | ========== | ========== | ====== - A | True | 0.99682161 | 0.00219186 | None | None | True - k | True | 1.01951706 | 0.09004865 | None | None | False - x0 | True | -0.0084718 | 0.08091178 | None | None | False + A | True | 0.99976981 | 0.00211443 | None | None | True + k | True | 1.04261145 | 0.08938656 | None | None | False + x0 | True | -0.1259175 | 0.07728784 | None | None | False @@ -91,7 +91,7 @@ Fit an arctan function. .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 0.362 seconds) + **Total running time of the script:** (0 minutes 0.361 seconds) .. _sphx_glr_download_auto_examples_model_fitting_simple_arctan_fit.py: diff --git a/_sources/sg_execution_times.rst.txt b/_sources/sg_execution_times.rst.txt index d4f4bcf9e..b274238a5 100644 --- a/_sources/sg_execution_times.rst.txt +++ b/_sources/sg_execution_times.rst.txt @@ -6,7 +6,7 @@ Computation times ================= -**00:08.435** total execution time for 3 files **from all galleries**: +**00:10.273** total execution time for 3 files **from all galleries**: .. container:: @@ -33,11 +33,11 @@ Computation times - Time - Mem (MB) * - :ref:`sphx_glr_auto_examples_model_fitting_EELS_curve_fitting.py` (``../examples/model_fitting/EELS_curve_fitting.py``) - - 00:07.511 + - 00:09.313 - 0.0 * - :ref:`sphx_glr_auto_examples_model_fitting_plot_residual.py` (``../examples/model_fitting/plot_residual.py``) - - 00:00.562 + - 00:00.599 - 0.0 * - :ref:`sphx_glr_auto_examples_model_fitting_simple_arctan_fit.py` (``../examples/model_fitting/simple_arctan_fit.py``) - - 00:00.362 + - 00:00.361 - 0.0 diff --git a/_static/basic.css b/_static/basic.css index e760386bd..2af6139e6 100644 --- a/_static/basic.css +++ b/_static/basic.css @@ -4,7 +4,7 @@ * * Sphinx stylesheet -- basic theme. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/_static/doctools.js b/_static/doctools.js index d06a71d75..4d67807d1 100644 --- a/_static/doctools.js +++ b/_static/doctools.js @@ -4,7 +4,7 @@ * * Base JavaScript utilities for all Sphinx HTML documentation. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/_static/language_data.js b/_static/language_data.js index 250f5665f..367b8ed81 100644 --- a/_static/language_data.js +++ b/_static/language_data.js @@ -5,7 +5,7 @@ * This script contains the language-specific data used by searchtools.js, * namely the list of stopwords, stemmer, scorer and splitter. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -13,7 +13,7 @@ var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; -/* Non-minified version is copied as a separate JS file, is available */ +/* Non-minified version is copied as a separate JS file, if available */ /** * Porter Stemmer diff --git a/_static/searchtools.js b/_static/searchtools.js index 7918c3fab..92da3f8b2 100644 --- a/_static/searchtools.js +++ b/_static/searchtools.js @@ -4,7 +4,7 @@ * * Sphinx JavaScript utilities for the full-text search. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -99,7 +99,7 @@ const _displayItem = (item, searchTerms, highlightTerms) => { .then((data) => { if (data) listItem.appendChild( - Search.makeSearchSummary(data, searchTerms) + Search.makeSearchSummary(data, searchTerms, anchor) ); // highlight search terms in the summary if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js @@ -116,8 +116,8 @@ const _finishSearch = (resultCount) => { ); else Search.status.innerText = _( - `Search finished, found ${resultCount} page(s) matching the search query.` - ); + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); }; const _displayNextItem = ( results, @@ -137,6 +137,22 @@ const _displayNextItem = ( // search finished, update title and status message else _finishSearch(resultCount); }; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; /** * Default splitQuery function. Can be overridden in ``sphinx.search`` with a @@ -160,13 +176,26 @@ const Search = { _queued_query: null, _pulse_status: -1, - htmlToText: (htmlString) => { + htmlToText: (htmlString, anchor) => { const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + for (const removalQuery of [".headerlinks", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent !== undefined) return docContent.textContent; + if (docContent) return docContent.textContent; + console.warn( - "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." ); return ""; }, @@ -239,16 +268,7 @@ const Search = { else Search.deferQuery(query); }, - /** - * execute search (requires search index to be loaded) - */ - query: (query) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - + _parseQuery: (query) => { // stem the search terms and add them to the correct list const stemmer = new Stemmer(); const searchTerms = new Set(); @@ -284,16 +304,32 @@ const Search = { // console.info("required: ", [...searchTerms]); // console.info("excluded: ", [...excludedTerms]); - // array of [docname, title, anchor, descr, score, filename] - let results = []; + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + _removeChildren(document.getElementById("search-progress")); - const queryLower = query.toLowerCase(); + const queryLower = query.toLowerCase().trim(); for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { for (const [file, id] of foundTitles) { let score = Math.round(100 * queryLower.length / title.length) - results.push([ + normalResults.push([ docNames[file], titles[file] !== title ? `${titles[file]} > ${title}` : title, id !== null ? "#" + id : "", @@ -308,46 +344,47 @@ const Search = { // search for explicit entries in index directives for (const [entry, foundEntries] of Object.entries(indexEntries)) { if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id] of foundEntries) { - let score = Math.round(100 * queryLower.length / entry.length) - results.push([ + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ docNames[file], titles[file], id ? "#" + id : "", null, score, filenames[file], - ]); + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } } } } // lookup as object objectTerms.forEach((term) => - results.push(...Search.performObjectSearch(term, objectTerms)) + normalResults.push(...Search.performObjectSearch(term, objectTerms)) ); // lookup as search terms in fulltext - results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); // let the scorer override scores with a custom scoring function - if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); - - // now sort the results by score (in opposite order of appearance, since the - // display function below uses pop() to retrieve items) and then - // alphabetically - results.sort((a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; - }); + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; // remove duplicate search results // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept @@ -361,7 +398,12 @@ const Search = { return acc; }, []); - results = results.reverse(); + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); // for debugging //Search.lastresults = results.slice(); // a copy @@ -466,14 +508,18 @@ const Search = { // add support for partial matches if (word.length > 2) { const escapedWord = _escapeRegExp(word); - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord) && !terms[word]) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord) && !titleTerms[word]) - arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); - }); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } } // no match but word was a required one @@ -496,9 +542,8 @@ const Search = { // create the mapping files.forEach((file) => { - if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) - fileMap.get(file).push(word); - else fileMap.set(file, [word]); + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); }); }); @@ -549,8 +594,8 @@ const Search = { * search summary for a given text. keywords is a list * of stemmed words. */ - makeSearchSummary: (htmlText, keywords) => { - const text = Search.htmlToText(htmlText); + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); if (text === "") return null; const textLower = text.toLowerCase(); diff --git a/auto_examples/index.html b/auto_examples/index.html index 231dbc9b5..fb372595a 100644 --- a/auto_examples/index.html +++ b/auto_examples/index.html @@ -42,7 +42,7 @@ - + @@ -565,7 +565,7 @@

Model fitting

- Created using Sphinx 7.2.6. + Created using Sphinx 7.3.7.

diff --git a/auto_examples/model_fitting/EELS_curve_fitting.html b/auto_examples/model_fitting/EELS_curve_fitting.html index 8a9659928..eec726fa0 100644 --- a/auto_examples/model_fitting/EELS_curve_fitting.html +++ b/auto_examples/model_fitting/EELS_curve_fitting.html @@ -42,7 +42,7 @@ - + @@ -450,37 +450,36 @@

Note

Go to the end -to download the full example code

+to download the full example code.

EELS curve fitting#

Performs curve fitting to an EELS spectrum, plots the result and saves it as png file.

coreloss_spectrum Signal
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@@ -502,7 +501,7 @@ m.plot()
-

Total running time of the script: (0 minutes 7.511 seconds)

+

Total running time of the script: (0 minutes 9.313 seconds)