From b948b1ce62e511e8497eaf126a1a77fa29bf8bf4 Mon Sep 17 00:00:00 2001 From: PHYSBO Developers Date: Tue, 4 Jun 2024 00:52:45 +0000 Subject: [PATCH] Deploy docs to develop by GitHub Actions triggered by 842ef861b9be41abbe92d6980ad7b1ab2327cbfb --- manual/develop/en/.buildinfo | 2 +- manual/develop/en/_modules/index.html | 2 +- .../en/_modules/physbo/blm/basis/fourier.html | 2 +- .../en/_modules/physbo/blm/core/model.html | 2 +- .../en/_modules/physbo/blm/inf/exact.html | 2 +- .../en/_modules/physbo/blm/lik/gauss.html | 2 +- .../en/_modules/physbo/blm/lik/linear.html | 2 +- .../en/_modules/physbo/blm/predictor.html | 2 +- .../en/_modules/physbo/blm/prior/gauss.html | 2 +- .../en/_modules/physbo/gp/core/learning.html | 2 +- .../en/_modules/physbo/gp/core/model.html | 2 +- .../en/_modules/physbo/gp/core/prior.html | 2 +- .../en/_modules/physbo/gp/cov/gauss.html | 2 +- .../en/_modules/physbo/gp/inf/exact.html | 2 +- .../en/_modules/physbo/gp/lik/gauss.html | 2 +- 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+ diff --git a/manual/develop/en/_modules/physbo/search/pareto.html b/manual/develop/en/_modules/physbo/search/pareto.html index a8e7ce57..cdd6cf97 100644 --- a/manual/develop/en/_modules/physbo/search/pareto.html +++ b/manual/develop/en/_modules/physbo/search/pareto.html @@ -15,7 +15,7 @@ - + diff --git a/manual/develop/en/_modules/physbo/search/score.html b/manual/develop/en/_modules/physbo/search/score.html index 1d8c4282..c6c380f9 100644 --- a/manual/develop/en/_modules/physbo/search/score.html +++ b/manual/develop/en/_modules/physbo/search/score.html @@ -15,7 +15,7 @@ - + diff --git a/manual/develop/en/_modules/physbo/search/score_multi.html b/manual/develop/en/_modules/physbo/search/score_multi.html index 275ceb32..cf2ee642 100644 --- a/manual/develop/en/_modules/physbo/search/score_multi.html +++ b/manual/develop/en/_modules/physbo/search/score_multi.html @@ -15,7 +15,7 @@ - + diff --git a/manual/develop/en/_modules/physbo/search/utility.html b/manual/develop/en/_modules/physbo/search/utility.html index 1c66f472..5a9f3a9b 100644 --- a/manual/develop/en/_modules/physbo/search/utility.html +++ b/manual/develop/en/_modules/physbo/search/utility.html @@ -15,7 +15,7 @@ - + diff --git a/manual/develop/en/_modules/physbo/variable.html b/manual/develop/en/_modules/physbo/variable.html index 3bc14db9..f8472899 100644 --- a/manual/develop/en/_modules/physbo/variable.html +++ b/manual/develop/en/_modules/physbo/variable.html @@ -15,7 +15,7 @@ - + diff --git a/manual/develop/en/_static/basic.css b/manual/develop/en/_static/basic.css index 30fee9d0..f316efcb 100644 --- a/manual/develop/en/_static/basic.css +++ b/manual/develop/en/_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/manual/develop/en/_static/doctools.js b/manual/develop/en/_static/doctools.js index d06a71d7..4d67807d 100644 --- a/manual/develop/en/_static/doctools.js +++ b/manual/develop/en/_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/manual/develop/en/_static/language_data.js b/manual/develop/en/_static/language_data.js index 250f5665..367b8ed8 100644 --- a/manual/develop/en/_static/language_data.js +++ b/manual/develop/en/_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/manual/develop/en/_static/searchtools.js b/manual/develop/en/_static/searchtools.js index 7918c3fa..92da3f8b 100644 --- a/manual/develop/en/_static/searchtools.js +++ b/manual/develop/en/_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/manual/develop/en/acknowledgement.html b/manual/develop/en/acknowledgement.html index 6731ba65..1f281820 100644 --- a/manual/develop/en/acknowledgement.html +++ b/manual/develop/en/acknowledgement.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/algorithm.html b/manual/develop/en/algorithm.html index 1bac4b5d..e4372eda 100644 --- a/manual/develop/en/algorithm.html +++ b/manual/develop/en/algorithm.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/modules.html b/manual/develop/en/api/modules.html index 9c94128a..b5808c0a 100644 --- a/manual/develop/en/api/modules.html +++ b/manual/develop/en/api/modules.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.blm.basis.fourier.html b/manual/develop/en/api/physbo.blm.basis.fourier.html index 45c1abe8..50ef3211 100644 --- a/manual/develop/en/api/physbo.blm.basis.fourier.html +++ b/manual/develop/en/api/physbo.blm.basis.fourier.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.blm.basis.html b/manual/develop/en/api/physbo.blm.basis.html index 1569d5fc..0c8d727e 100644 --- a/manual/develop/en/api/physbo.blm.basis.html +++ b/manual/develop/en/api/physbo.blm.basis.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.blm.core.html b/manual/develop/en/api/physbo.blm.core.html index 2f0ef770..c2e1877a 100644 --- a/manual/develop/en/api/physbo.blm.core.html +++ b/manual/develop/en/api/physbo.blm.core.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.blm.core.model.html b/manual/develop/en/api/physbo.blm.core.model.html index ff3c8b7f..746d1cc7 100644 --- a/manual/develop/en/api/physbo.blm.core.model.html +++ b/manual/develop/en/api/physbo.blm.core.model.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.blm.html b/manual/develop/en/api/physbo.blm.html index bf2b3560..50c9d14b 100644 --- a/manual/develop/en/api/physbo.blm.html +++ b/manual/develop/en/api/physbo.blm.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.blm.inf.exact.html b/manual/develop/en/api/physbo.blm.inf.exact.html index 40c76dc7..d655be81 100644 --- a/manual/develop/en/api/physbo.blm.inf.exact.html +++ b/manual/develop/en/api/physbo.blm.inf.exact.html @@ -16,7 +16,7 @@ - + @@ -112,7 +112,7 @@
Parameters:
    -
  • blm (physbo.blm.core.model) –

  • +
  • blm (physbo.blm.core.model)

  • X (numpy.ndarray) – inputs

  • Psi (numpy.ndarray) – feature maps (default: blm.lik.linear.basis.get_basis(X))

  • @@ -133,7 +133,7 @@
    Parameters:
      -
    • blm (physbo.blm.core.model) –

    • +
    • blm (physbo.blm.core.model)

    • X (numpy.ndarray) – inputs

    • Psi (numpy.ndarray) – feature maps (default: blm.lik.linear.basis.get_basis(X))

    • @@ -153,7 +153,7 @@

      calculates mean of weight

      Parameters:
      -

      blm (physbo.blm.core.model) –

      +

      blm (physbo.blm.core.model)

      Return type:

      numpy.ndarray

      diff --git a/manual/develop/en/api/physbo.blm.inf.html b/manual/develop/en/api/physbo.blm.inf.html index 3648d408..d26ce245 100644 --- a/manual/develop/en/api/physbo.blm.inf.html +++ b/manual/develop/en/api/physbo.blm.inf.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.blm.lik.gauss.html b/manual/develop/en/api/physbo.blm.lik.gauss.html index b26a3315..c4a9593f 100644 --- a/manual/develop/en/api/physbo.blm.lik.gauss.html +++ b/manual/develop/en/api/physbo.blm.lik.gauss.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.blm.lik.html b/manual/develop/en/api/physbo.blm.lik.html index 6b3b3887..90960f86 100644 --- a/manual/develop/en/api/physbo.blm.lik.html +++ b/manual/develop/en/api/physbo.blm.lik.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.blm.lik.linear.html b/manual/develop/en/api/physbo.blm.lik.linear.html index 4d292747..e51cbc6e 100644 --- a/manual/develop/en/api/physbo.blm.lik.linear.html +++ b/manual/develop/en/api/physbo.blm.lik.linear.html @@ -16,7 +16,7 @@ - + @@ -172,7 +172,7 @@

      set bias

      Parameters:
      -

      bias (float) –

      +

      bias (float)

      @@ -183,7 +183,7 @@

      set parameters

      Parameters:
      -

      params (np.ndarray) –

      +

      params (np.ndarray)

    diff --git a/manual/develop/en/api/physbo.blm.predictor.html b/manual/develop/en/api/physbo.blm.predictor.html index dc8f27b7..f32f01c7 100644 --- a/manual/develop/en/api/physbo.blm.predictor.html +++ b/manual/develop/en/api/physbo.blm.predictor.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.blm.prior.gauss.html b/manual/develop/en/api/physbo.blm.prior.gauss.html index a033eae7..596eb79a 100644 --- a/manual/develop/en/api/physbo.blm.prior.gauss.html +++ b/manual/develop/en/api/physbo.blm.prior.gauss.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.blm.prior.html b/manual/develop/en/api/physbo.blm.prior.html index a722e659..ef6dcdfb 100644 --- a/manual/develop/en/api/physbo.blm.prior.html +++ b/manual/develop/en/api/physbo.blm.prior.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.gp.core.html b/manual/develop/en/api/physbo.gp.core.html index 74815378..956232cc 100644 --- a/manual/develop/en/api/physbo.gp.core.html +++ b/manual/develop/en/api/physbo.gp.core.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.gp.core.learning.html b/manual/develop/en/api/physbo.gp.core.learning.html index ba465719..952d510b 100644 --- a/manual/develop/en/api/physbo.gp.core.learning.html +++ b/manual/develop/en/api/physbo.gp.core.learning.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.gp.core.model.html b/manual/develop/en/api/physbo.gp.core.model.html index afc58b65..cb76d607 100644 --- a/manual/develop/en/api/physbo.gp.core.model.html +++ b/manual/develop/en/api/physbo.gp.core.model.html @@ -16,7 +16,7 @@ - + @@ -195,7 +195,7 @@
  • X (numpy.ndarray) – N x d dimensional matrix. Each row of X denotes the d-dimensional feature vector of search candidate.

  • t (numpy.ndarray) – N dimensional array. The negative energy of each search candidate (value of the objective function to be optimized).

  • -
  • config (physbo.misc.set_config object) –

  • +
  • config (physbo.misc.set_config object)

diff --git a/manual/develop/en/api/physbo.gp.core.prior.html b/manual/develop/en/api/physbo.gp.core.prior.html index 740b8832..eb0a61d5 100644 --- a/manual/develop/en/api/physbo.gp.core.prior.html +++ b/manual/develop/en/api/physbo.gp.core.prior.html @@ -16,7 +16,7 @@ - + @@ -222,7 +222,7 @@
Parameters:
Return type:
diff --git a/manual/develop/en/api/physbo.gp.cov.gauss.html b/manual/develop/en/api/physbo.gp.cov.gauss.html index a783a32d..934aadc0 100644 --- a/manual/develop/en/api/physbo.gp.cov.gauss.html +++ b/manual/develop/en/api/physbo.gp.cov.gauss.html @@ -16,7 +16,7 @@ - + @@ -118,8 +118,8 @@
Parameters:
    -
  • width (int) –

  • -
  • scale (int) –

  • +
  • width (int)

  • +
  • scale (int)

Returns:
@@ -201,7 +201,7 @@
Parameters:
  • X (numpy.ndarray) – N x d dimensional matrix. Each row of X denotes the d-dimensional feature vector of search candidate.

  • -
  • params (numpy.ndarray) –

  • +
  • params (numpy.ndarray)

Returns:
diff --git a/manual/develop/en/api/physbo.gp.cov.html b/manual/develop/en/api/physbo.gp.cov.html index c7e79127..b209851c 100644 --- a/manual/develop/en/api/physbo.gp.cov.html +++ b/manual/develop/en/api/physbo.gp.cov.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.gp.html b/manual/develop/en/api/physbo.gp.html index 8594feab..c48852bd 100644 --- a/manual/develop/en/api/physbo.gp.html +++ b/manual/develop/en/api/physbo.gp.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.gp.inf.exact.html b/manual/develop/en/api/physbo.gp.inf.exact.html index ac86f1ad..9f41a0eb 100644 --- a/manual/develop/en/api/physbo.gp.inf.exact.html +++ b/manual/develop/en/api/physbo.gp.inf.exact.html @@ -16,7 +16,7 @@ - + @@ -112,7 +112,7 @@
Parameters:
    -
  • gp (physbo.gp.core.model) –

  • +
  • gp (physbo.gp.core.model)

  • X (numpy.ndarray) – N x d dimensional matrix. Each row of X denotes the d-dimensional feature vector of search candidate.

  • t (numpy.ndarray) – N dimensional array. The negative energy of each search candidate (value of the objective function to be optimized).

  • @@ -135,7 +135,7 @@
    Parameters:
      -
    • gp (physbo.gp.core.model) –

    • +
    • gp (physbo.gp.core.model)

    • X (numpy.ndarray) – N x d dimensional matrix. Each row of X denotes the d-dimensional feature vector of search candidate.

    • t (numpy.ndarray) – N dimensional array. The negative energy of each search candidate (value of the objective function to be optimized).

    • @@ -158,7 +158,7 @@
      Parameters:
        -
      • gp (physbo.gp.core.model) –

      • +
      • gp (physbo.gp.core.model)

      • X (numpy.ndarray) – N x d dimensional matrix. Each row of X denotes the d-dimensional feature vector of search candidate.

      • Z (numpy.ndarray) – N x d dimensional matrix. Each row of Z denotes the d-dimensional feature vector of tests.

      • params (numpy.ndarray) – Parameters.

      • @@ -178,7 +178,7 @@
        Parameters:
          -
        • gp (physbo.gp.core.model) –

        • +
        • gp (physbo.gp.core.model)

        • X (numpy.ndarray) – N x d dimensional matrix. Each row of X denotes the d-dimensional feature vector of search candidate.

        • Z (numpy.ndarray) – N x d dimensional matrix. Each row of Z denotes the d-dimensional feature vector of tests.

        • params (numpy.ndarray) – Parameters.

        • @@ -196,7 +196,7 @@
          Parameters:
            -
          • gp (physbo.gp.core.model) –

          • +
          • gp (physbo.gp.core.model)

          • X (numpy.ndarray) – N x d dimensional matrix. Each row of X denotes the d-dimensional feature vector of search candidate.

          • t (numpy.ndarray) – N dimensional array. The negative energy of each search candidate (value of the objective function to be optimized).

          • diff --git a/manual/develop/en/api/physbo.gp.inf.html b/manual/develop/en/api/physbo.gp.inf.html index 67a7305c..259eaa41 100644 --- a/manual/develop/en/api/physbo.gp.inf.html +++ b/manual/develop/en/api/physbo.gp.inf.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.gp.lik.gauss.html b/manual/develop/en/api/physbo.gp.lik.gauss.html index 72f9758d..d70f0178 100644 --- a/manual/develop/en/api/physbo.gp.lik.gauss.html +++ b/manual/develop/en/api/physbo.gp.lik.gauss.html @@ -16,7 +16,7 @@ - + @@ -134,7 +134,7 @@
            Parameters:
              -
            • num_data (int) –

            • +
            • num_data (int)

            • params (numpy.ndarray) – Parameters for optimization. Array of real elements of size (n,), where ‘n’ is the number of independent variables.

            @@ -155,7 +155,7 @@
            Parameters:
              -
            • num_data (int) –

            • +
            • num_data (int)

            • params (numpy.ndarray) – Parameters for optimization. Array of real elements of size (n,), where ‘n’ is the number of independent variables.

            @@ -189,7 +189,7 @@

            Sampling by adding noise

            Parameters:
            -

            fmean (numpy.ndarray) –

            +

            fmean (numpy.ndarray)

            diff --git a/manual/develop/en/api/physbo.gp.lik.html b/manual/develop/en/api/physbo.gp.lik.html index 4dc07adb..1d450d49 100644 --- a/manual/develop/en/api/physbo.gp.lik.html +++ b/manual/develop/en/api/physbo.gp.lik.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.gp.mean.const.html b/manual/develop/en/api/physbo.gp.mean.const.html index c02b0d7e..d39b273c 100644 --- a/manual/develop/en/api/physbo.gp.mean.const.html +++ b/manual/develop/en/api/physbo.gp.mean.const.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.gp.mean.html b/manual/develop/en/api/physbo.gp.mean.html index 7b4f9a18..6c31b209 100644 --- a/manual/develop/en/api/physbo.gp.mean.html +++ b/manual/develop/en/api/physbo.gp.mean.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.gp.mean.zero.html b/manual/develop/en/api/physbo.gp.mean.zero.html index d9a44f08..53040fb8 100644 --- a/manual/develop/en/api/physbo.gp.mean.zero.html +++ b/manual/develop/en/api/physbo.gp.mean.zero.html @@ -16,7 +16,7 @@ - + @@ -149,7 +149,7 @@

            Not defined

            Parameters:
            -

            params

            +

            params

            diff --git a/manual/develop/en/api/physbo.gp.predictor.html b/manual/develop/en/api/physbo.gp.predictor.html index db141aeb..c16fa320 100644 --- a/manual/develop/en/api/physbo.gp.predictor.html +++ b/manual/develop/en/api/physbo.gp.predictor.html @@ -16,7 +16,7 @@ - + @@ -116,8 +116,8 @@
            Parameters:
              -
            • args

            • -
            • kwds

            • +
            • args

            • +
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            @@ -143,8 +143,8 @@
            Parameters:
              -
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            • -
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            • +
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            • +
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            @@ -191,8 +191,8 @@
            Parameters:
              -
            • args

            • -
            • kwds

            • +
            • args

            • +
            • kwds

            @@ -254,8 +254,8 @@
            Parameters:
              -
            • args

            • -
            • kwds

            • +
            • args

            • +
            • kwds

            diff --git a/manual/develop/en/api/physbo.html b/manual/develop/en/api/physbo.html index ce00f229..2f70df5f 100644 --- a/manual/develop/en/api/physbo.html +++ b/manual/develop/en/api/physbo.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.misc.centering.html b/manual/develop/en/api/physbo.misc.centering.html index 7a910234..4b57afbc 100644 --- a/manual/develop/en/api/physbo.misc.centering.html +++ b/manual/develop/en/api/physbo.misc.centering.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.misc.gauss_elim.html b/manual/develop/en/api/physbo.misc.gauss_elim.html index f3ea2de4..e7539639 100644 --- a/manual/develop/en/api/physbo.misc.gauss_elim.html +++ b/manual/develop/en/api/physbo.misc.gauss_elim.html @@ -16,7 +16,7 @@ - + @@ -111,9 +111,9 @@
            Parameters:
              -
            • U ((M, M) array_like) –

            • -
            • matrix (A triangular) –

            • -
            • t ((M,) or (M, N) array_like) –

            • +
            • U ((M, M) array_like)

            • +
            • matrix (A triangular)

            • +
            • t ((M,) or (M, N) array_like)

            Returns:
            diff --git a/manual/develop/en/api/physbo.misc.html b/manual/develop/en/api/physbo.misc.html index 996bd2aa..99838631 100644 --- a/manual/develop/en/api/physbo.misc.html +++ b/manual/develop/en/api/physbo.misc.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.misc.set_config.html b/manual/develop/en/api/physbo.misc.set_config.html index 4427afdf..302688d5 100644 --- a/manual/develop/en/api/physbo.misc.set_config.html +++ b/manual/develop/en/api/physbo.misc.set_config.html @@ -16,7 +16,7 @@ - + @@ -113,7 +113,7 @@

            Loading information of configuration from config._sectoins[‘adam’].

            Parameters:
            -

            config (physbo.misc.set_config object) –

            +

            config (physbo.misc.set_config object)

            @@ -136,7 +136,7 @@

            Loading information of configuration from config._sectoins[‘batch’].

            Parameters:
            -

            config (physbo.misc.set_config object) –

            +

            config (physbo.misc.set_config object)

          @@ -155,7 +155,7 @@

          Return boolean.

          Parameters:
          -

          str (str or boolean) –

          +

          str (str or boolean)

          Return type:

          True or False

          @@ -173,7 +173,7 @@

          Loading information of configuration from config._sectoins[‘learning’].

          Parameters:
          -

          config (physbo.misc.set_config object) –

          +

          config (physbo.misc.set_config object)

          @@ -196,7 +196,7 @@

          Loading information of configuration from config._sectoins[‘online’].

          Parameters:
          -

          config (physbo.misc.set_config object) –

          +

          config (physbo.misc.set_config object)

        @@ -219,7 +219,7 @@

        Loading information of configuration from config._sectoins[‘search’].

        Parameters:
        -

        config (physbo.misc.set_config object) –

        +

        config (physbo.misc.set_config object)

      @@ -243,8 +243,8 @@
      Parameters:
        -
      • file_name (str) –

      • -
      • configuration. (An input file name of) –

      • +
      • file_name (str)

      • +
      • configuration. (An input file name of)

      diff --git a/manual/develop/en/api/physbo.opt.adam.html b/manual/develop/en/api/physbo.opt.adam.html index 5388704d..f19d093e 100644 --- a/manual/develop/en/api/physbo.opt.adam.html +++ b/manual/develop/en/api/physbo.opt.adam.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.opt.html b/manual/develop/en/api/physbo.opt.html index 4d46db46..222c16e1 100644 --- a/manual/develop/en/api/physbo.opt.html +++ b/manual/develop/en/api/physbo.opt.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.predictor.html b/manual/develop/en/api/physbo.predictor.html index 52f04b99..dabd2a20 100644 --- a/manual/develop/en/api/physbo.predictor.html +++ b/manual/develop/en/api/physbo.predictor.html @@ -16,7 +16,7 @@ - + @@ -111,8 +111,8 @@
      Parameters:
        -
      • args

      • -
      • kwds

      • +
      • args

      • +
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      @@ -126,8 +126,8 @@
      Parameters:
        -
      • args

      • -
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      • +
      • args

      • +
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      @@ -141,8 +141,8 @@
      Parameters:
        -
      • args

      • -
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      • +
      • args

      • +
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      @@ -156,8 +156,8 @@
      Parameters:
        -
      • args

      • -
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      • +
      • args

      • +
      • kwds

      @@ -171,8 +171,8 @@
      Parameters:
        -
      • args

      • -
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      • +
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      • +
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      @@ -186,8 +186,8 @@
      Parameters:
        -
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      • -
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      • +
      • args

      • +
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      @@ -201,8 +201,8 @@
      Parameters:
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      • -
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      • +
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      @@ -216,8 +216,8 @@
      Parameters:
        -
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      • -
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      • +
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      • +
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      @@ -231,8 +231,8 @@
      Parameters:
        -
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      • -
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      • +
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      • +
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      @@ -258,8 +258,8 @@
      Parameters:
        -
      • args

      • -
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      • +
      • args

      • +
      • kwds

      @@ -285,8 +285,8 @@
      Parameters:
        -
      • args

      • -
      • kwds

      • +
      • args

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      • kwds

      diff --git a/manual/develop/en/api/physbo.search.discrete.html b/manual/develop/en/api/physbo.search.discrete.html index a8ef8b7c..86d20ece 100644 --- a/manual/develop/en/api/physbo.search.discrete.html +++ b/manual/develop/en/api/physbo.search.discrete.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.search.discrete.policy.html b/manual/develop/en/api/physbo.search.discrete.policy.html index 33566741..028acca1 100644 --- a/manual/develop/en/api/physbo.search.discrete.policy.html +++ b/manual/develop/en/api/physbo.search.discrete.policy.html @@ -16,7 +16,7 @@ - + @@ -268,7 +268,7 @@
      Parameters:
      • seed (int) – seed number

      • -
      • -------

      • +
      • -------

    diff --git a/manual/develop/en/api/physbo.search.discrete.results.html b/manual/develop/en/api/physbo.search.discrete.results.html index b10fc266..0b8a1701 100644 --- a/manual/develop/en/api/physbo.search.discrete.results.html +++ b/manual/develop/en/api/physbo.search.discrete.results.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.search.discrete_multi.html b/manual/develop/en/api/physbo.search.discrete_multi.html index bc2a0b1b..eb3441aa 100644 --- a/manual/develop/en/api/physbo.search.discrete_multi.html +++ b/manual/develop/en/api/physbo.search.discrete_multi.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.search.discrete_multi.policy.html b/manual/develop/en/api/physbo.search.discrete_multi.policy.html index 3de4b937..5c21c709 100644 --- a/manual/develop/en/api/physbo.search.discrete_multi.policy.html +++ b/manual/develop/en/api/physbo.search.discrete_multi.policy.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.search.discrete_multi.results.html b/manual/develop/en/api/physbo.search.discrete_multi.results.html index 5b517f06..3fddf2d0 100644 --- a/manual/develop/en/api/physbo.search.discrete_multi.results.html +++ b/manual/develop/en/api/physbo.search.discrete_multi.results.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.search.html b/manual/develop/en/api/physbo.search.html index 6d7b4b71..4ffb904d 100644 --- a/manual/develop/en/api/physbo.search.html +++ b/manual/develop/en/api/physbo.search.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.search.pareto.html b/manual/develop/en/api/physbo.search.pareto.html index c70dd02d..4e3bdeba 100644 --- a/manual/develop/en/api/physbo.search.pareto.html +++ b/manual/develop/en/api/physbo.search.pareto.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.search.score.html b/manual/develop/en/api/physbo.search.score.html index 4877b653..ed8a1271 100644 --- a/manual/develop/en/api/physbo.search.score.html +++ b/manual/develop/en/api/physbo.search.score.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.search.score_multi.html b/manual/develop/en/api/physbo.search.score_multi.html index 643b0d30..d8c6a58c 100644 --- a/manual/develop/en/api/physbo.search.score_multi.html +++ b/manual/develop/en/api/physbo.search.score_multi.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.search.utility.html b/manual/develop/en/api/physbo.search.utility.html index d8f80b12..72bc36f8 100644 --- a/manual/develop/en/api/physbo.search.utility.html +++ b/manual/develop/en/api/physbo.search.utility.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/api/physbo.variable.html b/manual/develop/en/api/physbo.variable.html index 7eb752b2..13f3d043 100644 --- a/manual/develop/en/api/physbo.variable.html +++ b/manual/develop/en/api/physbo.variable.html @@ -16,7 +16,7 @@ - + @@ -111,7 +111,7 @@
    • X (numpy array) – N x d dimensional matrix. Each row of X denotes the d-dimensional feature vector of each search candidate.

    • t (numpy array) – N dimensional array. The negative energy of each search candidate (value of the objective function to be optimized).

    • -
    • Z

    • +
    • Z

@@ -134,7 +134,7 @@

Adding variable Z. If self.Z is None, self.Z is set as Z.

Parameters:
-

Z

+

Z

diff --git a/manual/develop/en/contact.html b/manual/develop/en/contact.html index f935f714..6c9c5240 100644 --- a/manual/develop/en/contact.html +++ b/manual/develop/en/contact.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/genindex.html b/manual/develop/en/genindex.html index fa84fa9a..57666ba0 100644 --- a/manual/develop/en/genindex.html +++ b/manual/develop/en/genindex.html @@ -15,7 +15,7 @@ - + diff --git a/manual/develop/en/index.html b/manual/develop/en/index.html index 0d3c7bda..3344fcef 100644 --- a/manual/develop/en/index.html +++ b/manual/develop/en/index.html @@ -16,9 +16,11 @@ - + + + diff --git a/manual/develop/en/install.html b/manual/develop/en/install.html index fbfc7b0a..ae55d0ad 100644 --- a/manual/develop/en/install.html +++ b/manual/develop/en/install.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/introduction.html b/manual/develop/en/introduction.html index 41aa16bf..dd3b543d 100644 --- a/manual/develop/en/introduction.html +++ b/manual/develop/en/introduction.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/notebook/index.html b/manual/develop/en/notebook/index.html index b967a2fd..c8612482 100644 --- a/manual/develop/en/notebook/index.html +++ b/manual/develop/en/notebook/index.html @@ -16,9 +16,11 @@ - + + + diff --git a/manual/develop/en/notebook/tutorial_Gaussian_process.html b/manual/develop/en/notebook/tutorial_Gaussian_process.html index f273ae71..ccdd7a6f 100644 --- a/manual/develop/en/notebook/tutorial_Gaussian_process.html +++ b/manual/develop/en/notebook/tutorial_Gaussian_process.html @@ -17,7 +17,7 @@ - + diff --git a/manual/develop/en/notebook/tutorial_basic.html b/manual/develop/en/notebook/tutorial_basic.html index b875f0f2..396d115f 100644 --- a/manual/develop/en/notebook/tutorial_basic.html +++ b/manual/develop/en/notebook/tutorial_basic.html @@ -17,7 +17,7 @@ - + diff --git a/manual/develop/en/notebook/tutorial_basic_org.html b/manual/develop/en/notebook/tutorial_basic_org.html index f76781f2..0b06d9e0 100644 --- a/manual/develop/en/notebook/tutorial_basic_org.html +++ b/manual/develop/en/notebook/tutorial_basic_org.html @@ -17,7 +17,7 @@ - + diff --git a/manual/develop/en/notebook/tutorial_interactive_mode.html b/manual/develop/en/notebook/tutorial_interactive_mode.html index 1ea1ec95..0967c3f6 100644 --- a/manual/develop/en/notebook/tutorial_interactive_mode.html +++ b/manual/develop/en/notebook/tutorial_interactive_mode.html @@ -17,7 +17,7 @@ - + diff --git a/manual/develop/en/notebook/tutorial_multi_objective.html b/manual/develop/en/notebook/tutorial_multi_objective.html index ac743b15..6fa6d3d5 100644 --- a/manual/develop/en/notebook/tutorial_multi_objective.html +++ b/manual/develop/en/notebook/tutorial_multi_objective.html @@ -17,7 +17,7 @@ - + diff --git a/manual/develop/en/notebook/tutorial_multi_probe.html b/manual/develop/en/notebook/tutorial_multi_probe.html index ffe8b2eb..c12fcf2f 100644 --- a/manual/develop/en/notebook/tutorial_multi_probe.html +++ b/manual/develop/en/notebook/tutorial_multi_probe.html @@ -17,7 +17,7 @@ - + diff --git a/manual/develop/en/notebook/tutorial_once_mode.html b/manual/develop/en/notebook/tutorial_once_mode.html index 9749390e..a1122aa2 100644 --- a/manual/develop/en/notebook/tutorial_once_mode.html +++ b/manual/develop/en/notebook/tutorial_once_mode.html @@ -17,7 +17,7 @@ - + diff --git a/manual/develop/en/py-modindex.html b/manual/develop/en/py-modindex.html index 1c63f0c1..c14b970e 100644 --- a/manual/develop/en/py-modindex.html +++ b/manual/develop/en/py-modindex.html @@ -15,7 +15,7 @@ - + diff --git a/manual/develop/en/search.html b/manual/develop/en/search.html index adde1e3d..27de9602 100644 --- a/manual/develop/en/search.html +++ b/manual/develop/en/search.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/en/searchindex.js b/manual/develop/en/searchindex.js index e7b73865..8eda46f0 100644 --- a/manual/develop/en/searchindex.js +++ 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"physbo.blm.lik.linear module", "physbo.blm.predictor module", "physbo.blm.prior package", "physbo.blm.prior.gauss module", "physbo.gp package", "physbo.gp.core package", "physbo.gp.core.learning module", "physbo.gp.core.model module", "physbo.gp.core.prior module", "physbo.gp.cov package", "physbo.gp.cov.gauss module", "physbo.gp.inf package", "physbo.gp.inf.exact module", "physbo.gp.lik package", "physbo.gp.lik.gauss module", "physbo.gp.mean package", "physbo.gp.mean.const module", "physbo.gp.mean.zero module", "physbo.gp.predictor module", "physbo.misc package", "physbo.misc.centering module", "physbo.misc.gauss_elim module", "physbo.misc.set_config module", "physbo.opt package", "physbo.opt.adam module", "physbo.predictor module", "physbo.search package", "physbo.search.discrete package", "physbo.search.discrete.policy module", "physbo.search.discrete.results module", "physbo.search.discrete_multi package", "physbo.search.discrete_multi.policy module", 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method)": [[50, "physbo.variable.variable.delete_t"]], "get_subset() (physbo.variable.variable method)": [[50, "physbo.variable.variable.get_subset"]], "load() (physbo.variable.variable method)": [[50, "physbo.variable.variable.load"]], "physbo.variable": [[50, "module-physbo.variable"]], "save() (physbo.variable.variable method)": [[50, "physbo.variable.variable.save"]], "variable (class in physbo.variable)": [[50, "physbo.variable.variable"]]}}) \ No newline at end of file +Search.setIndex({"alltitles": {"About PHYSBO": [[54, "about-physbo"]], "Accelerating Bayesian Optimization with PHYSBO": [[1, "accelerating-bayesian-optimization-with-physbo"]], "Acknowledgement": [[0, "acknowledgement"]], "Acquisition function": [[57, "Acquisition-function"]], "Algorithm": [[1, "algorithm"]], "Appendix: Full search": [[60, "Appendix:-Full-search"]], "Basic structures": [[53, "basic-structures"]], "Basic usage": [[53, "basic-usage"]], "Basic usage of PHYSBO": [[57, "Basic-usage-of-PHYSBO"], [58, "Basic-usage-of-PHYSBO"]], "Bayesian Optimization": [[57, "Bayesian-Optimization"], [58, "Bayesian-Optimization"]], "Bayesian optimization": [[1, "bayesian-optimization"], [60, "Bayesian-optimization"]], "Calculate the volume of the dominated region": [[60, "Calculate-the-volume-of-the-dominated-region"]], "Calculation flow": [[53, "calculation-flow"]], "Checking results": [[60, "Checking-results"], [61, "Checking-results"]], "Checking the results": [[57, "Checking-the-results"], [58, "Checking-the-results"]], "Citation": [[54, "citation"]], "Contact": [[51, "contact"]], "Contents:": [[52, null], [55, null]], "Defining the search space": [[57, "Defining-the-search-space"]], "Defining the simulator class": [[57, "Defining-the-simulator-class"]], "Defining training data": [[56, "Defining-training-data"]], "Definition of simulator": [[58, "Definition-of-simulator"], [59, "Definition-of-simulator"], [60, "Definition-of-simulator"], [61, "Definition-of-simulator"]], "Download and Install": [[53, "download-and-install"]], "EHVI (Expected Hyper-Volume Improvement)": [[60, "EHVI-(Expected-Hyper-Volume-Improvement)"]], "Executing optimization": [[59, "Executing-optimization"]], "First objective function": [[60, "First-objective-function"]], "Gaussian process": [[56, "Gaussian-process"]], "Get the next parameter to be executed from PHYSBO": [[62, "Get-the-next-parameter-to-be-executed-from-PHYSBO"]], "HVPI (HyperVolume-based Probability of Improvement)": [[60, "HVPI-(HyperVolume-based-Probability-of-Improvement)"]], "Install": [[53, "install"]], "Introduction": [[54, "introduction"], [57, "Introduction"], [58, "Introduction"]], "Learning and Prediction of Gaussian Processes": [[56, "Learning-and-Prediction-of-Gaussian-Processes"]], "License": [[54, "license"]], "Main Developers": [[54, "main-developers"]], "Module contents": [[3, "module-physbo"], [4, "module-physbo.blm"], [5, "module-physbo.blm.basis"], [7, "module-physbo.blm.core"], [9, "module-physbo.blm.inf"], [11, "module-physbo.blm.lik"], [15, "module-physbo.blm.prior"], [17, "module-physbo.gp"], [18, "module-physbo.gp.core"], [22, "module-physbo.gp.cov"], [24, "module-physbo.gp.inf"], [26, "module-physbo.gp.lik"], [28, "module-physbo.gp.mean"], [32, "module-physbo.misc"], [36, "module-physbo.opt"], [39, "module-physbo.search"], [40, "module-physbo.search.discrete"], [43, "module-physbo.search.discrete_multi"]], "Multi-objective optimization": [[60, "Multi-objective-optimization"]], "Obtaining the Pareto solution": [[60, "Obtaining-the-Pareto-solution"]], "Parallelization": [[57, "Parallelization"]], "Performing optimization": [[57, "Performing-optimization"], [58, "Performing-optimization"]], "Performing optimizations": [[61, "Performing-optimizations"]], "Performing optimizations.": [[60, "Performing-optimizations."]], "Plotting the Pareto solution": [[60, "Plotting-the-Pareto-solution"], [60, "id1"], [60, "id3"]], "Plotting the functions": [[60, "Plotting-the-functions"]], "Plotting the solution (evaluated value)": [[60, "Plotting-the-solution-(evaluated-value)"]], "Prediction": [[57, "Prediction"]], "Prediction by trained models": [[56, "Prediction-by-trained-models"]], "Preparation of search candidate data": [[56, "Preparation-of-search-candidate-data"], [58, "Preparation-of-search-candidate-data"], [59, "Preparation-of-search-candidate-data"], [60, "Preparation-of-search-candidate-data"]], "Prepare the search candidate data": [[61, "Prepare-the-search-candidate-data"], [62, "Prepare-the-search-candidate-data"]], "Preparing the precomputed data": [[62, "Preparing-the-precomputed-data"]], "Random Search": [[57, "Random-Search"], [58, "Random-Search"]], "Random search": [[60, "Random-search"]], "Register action ID (parameter) and evaluation value to PHYSBO.": [[62, "Register-action-ID-(parameter)-and-evaluation-value-to-PHYSBO."]], "Required Packages": [[53, "required-packages"]], "Restart calculations by reading existing calculation results": [[62, 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+ diff --git a/manual/develop/ja/_modules/physbo/misc/set_config.html b/manual/develop/ja/_modules/physbo/misc/set_config.html index d9883a68..77a1b021 100644 --- a/manual/develop/ja/_modules/physbo/misc/set_config.html +++ b/manual/develop/ja/_modules/physbo/misc/set_config.html @@ -15,7 +15,7 @@ - + diff --git a/manual/develop/ja/_modules/physbo/opt/adam.html b/manual/develop/ja/_modules/physbo/opt/adam.html index c97d0512..73c85b14 100644 --- a/manual/develop/ja/_modules/physbo/opt/adam.html +++ b/manual/develop/ja/_modules/physbo/opt/adam.html @@ -15,7 +15,7 @@ - + diff --git a/manual/develop/ja/_modules/physbo/predictor.html b/manual/develop/ja/_modules/physbo/predictor.html index b2ac5c5a..80d97c5e 100644 --- a/manual/develop/ja/_modules/physbo/predictor.html +++ b/manual/develop/ja/_modules/physbo/predictor.html @@ -15,7 +15,7 @@ - + diff --git a/manual/develop/ja/_modules/physbo/search/discrete/policy.html b/manual/develop/ja/_modules/physbo/search/discrete/policy.html index f3287a8e..8683473b 100644 --- a/manual/develop/ja/_modules/physbo/search/discrete/policy.html +++ b/manual/develop/ja/_modules/physbo/search/discrete/policy.html @@ -15,7 +15,7 @@ - + diff --git a/manual/develop/ja/_modules/physbo/search/discrete/results.html b/manual/develop/ja/_modules/physbo/search/discrete/results.html index fdd2ca0c..16722c1e 100644 --- a/manual/develop/ja/_modules/physbo/search/discrete/results.html +++ b/manual/develop/ja/_modules/physbo/search/discrete/results.html @@ -15,7 +15,7 @@ - + diff --git a/manual/develop/ja/_modules/physbo/search/discrete_multi/policy.html b/manual/develop/ja/_modules/physbo/search/discrete_multi/policy.html index 730d3170..2a58616d 100644 --- a/manual/develop/ja/_modules/physbo/search/discrete_multi/policy.html +++ b/manual/develop/ja/_modules/physbo/search/discrete_multi/policy.html @@ -15,7 +15,7 @@ - + diff --git a/manual/develop/ja/_modules/physbo/search/discrete_multi/results.html b/manual/develop/ja/_modules/physbo/search/discrete_multi/results.html index ee50dd0e..9fd094bb 100644 --- a/manual/develop/ja/_modules/physbo/search/discrete_multi/results.html +++ b/manual/develop/ja/_modules/physbo/search/discrete_multi/results.html @@ -15,7 +15,7 @@ - + diff --git a/manual/develop/ja/_modules/physbo/search/pareto.html b/manual/develop/ja/_modules/physbo/search/pareto.html index 25a4b7df..644363e1 100644 --- a/manual/develop/ja/_modules/physbo/search/pareto.html +++ b/manual/develop/ja/_modules/physbo/search/pareto.html @@ -15,7 +15,7 @@ - + diff --git a/manual/develop/ja/_modules/physbo/search/score.html b/manual/develop/ja/_modules/physbo/search/score.html index caae9101..2f211db8 100644 --- a/manual/develop/ja/_modules/physbo/search/score.html +++ b/manual/develop/ja/_modules/physbo/search/score.html @@ -15,7 +15,7 @@ - + diff --git a/manual/develop/ja/_modules/physbo/search/score_multi.html b/manual/develop/ja/_modules/physbo/search/score_multi.html index c2b26566..bc077d6c 100644 --- a/manual/develop/ja/_modules/physbo/search/score_multi.html +++ b/manual/develop/ja/_modules/physbo/search/score_multi.html @@ -15,7 +15,7 @@ - + diff --git a/manual/develop/ja/_modules/physbo/search/utility.html b/manual/develop/ja/_modules/physbo/search/utility.html index 8eda89ee..a9569049 100644 --- a/manual/develop/ja/_modules/physbo/search/utility.html +++ b/manual/develop/ja/_modules/physbo/search/utility.html @@ -15,7 +15,7 @@ - + diff --git a/manual/develop/ja/_modules/physbo/variable.html b/manual/develop/ja/_modules/physbo/variable.html index a488dcf4..485b3835 100644 --- a/manual/develop/ja/_modules/physbo/variable.html +++ b/manual/develop/ja/_modules/physbo/variable.html @@ -15,7 +15,7 @@ - + diff --git a/manual/develop/ja/_static/basic.css b/manual/develop/ja/_static/basic.css index 30fee9d0..f316efcb 100644 --- a/manual/develop/ja/_static/basic.css +++ b/manual/develop/ja/_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/manual/develop/ja/_static/doctools.js b/manual/develop/ja/_static/doctools.js index d06a71d7..4d67807d 100644 --- a/manual/develop/ja/_static/doctools.js +++ b/manual/develop/ja/_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/manual/develop/ja/_static/language_data.js b/manual/develop/ja/_static/language_data.js index b3681270..89083d9e 100644 --- a/manual/develop/ja/_static/language_data.js +++ b/manual/develop/ja/_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 = []; -/* Non-minified version is copied as a separate JS file, is available */ +/* Non-minified version is copied as a separate JS file, if available */ /** * Dummy stemmer for languages without stemming rules. diff --git a/manual/develop/ja/_static/searchtools.js b/manual/develop/ja/_static/searchtools.js index 7918c3fa..92da3f8b 100644 --- a/manual/develop/ja/_static/searchtools.js +++ b/manual/develop/ja/_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/manual/develop/ja/acknowledgement.html b/manual/develop/ja/acknowledgement.html index e14a7dba..a872e8f4 100644 --- a/manual/develop/ja/acknowledgement.html +++ b/manual/develop/ja/acknowledgement.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/algorithm.html b/manual/develop/ja/algorithm.html index 59c8537d..ed532af1 100644 --- a/manual/develop/ja/algorithm.html +++ b/manual/develop/ja/algorithm.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/modules.html b/manual/develop/ja/api/modules.html index 599329b0..997d747a 100644 --- a/manual/develop/ja/api/modules.html +++ b/manual/develop/ja/api/modules.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.blm.basis.fourier.html b/manual/develop/ja/api/physbo.blm.basis.fourier.html index 6fc7804b..5adfb657 100644 --- a/manual/develop/ja/api/physbo.blm.basis.fourier.html +++ b/manual/develop/ja/api/physbo.blm.basis.fourier.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.blm.basis.html b/manual/develop/ja/api/physbo.blm.basis.html index e2443c57..b8296d56 100644 --- a/manual/develop/ja/api/physbo.blm.basis.html +++ b/manual/develop/ja/api/physbo.blm.basis.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.blm.core.html b/manual/develop/ja/api/physbo.blm.core.html index a0e2f69a..b1962b17 100644 --- a/manual/develop/ja/api/physbo.blm.core.html +++ b/manual/develop/ja/api/physbo.blm.core.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.blm.core.model.html b/manual/develop/ja/api/physbo.blm.core.model.html index 8e0fe355..681fcdd8 100644 --- a/manual/develop/ja/api/physbo.blm.core.model.html +++ b/manual/develop/ja/api/physbo.blm.core.model.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.blm.html b/manual/develop/ja/api/physbo.blm.html index 5f68a197..4dfeace4 100644 --- a/manual/develop/ja/api/physbo.blm.html +++ b/manual/develop/ja/api/physbo.blm.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.blm.inf.exact.html b/manual/develop/ja/api/physbo.blm.inf.exact.html index e54c131a..1c5575f9 100644 --- a/manual/develop/ja/api/physbo.blm.inf.exact.html +++ b/manual/develop/ja/api/physbo.blm.inf.exact.html @@ -16,7 +16,7 @@ - + @@ -113,7 +113,7 @@
パラメータ:
    -
  • blm (physbo.blm.core.model) --

  • +
  • blm (physbo.blm.core.model)

  • X (numpy.ndarray) -- inputs

  • Psi (numpy.ndarray) -- feature maps (default: blm.lik.linear.basis.get_basis(X))

  • @@ -134,7 +134,7 @@
    パラメータ:
      -
    • blm (physbo.blm.core.model) --

    • +
    • blm (physbo.blm.core.model)

    • X (numpy.ndarray) -- inputs

    • Psi (numpy.ndarray) -- feature maps (default: blm.lik.linear.basis.get_basis(X))

    • @@ -154,7 +154,7 @@

      calculates mean of weight

      パラメータ:
      -

      blm (physbo.blm.core.model) --

      +

      blm (physbo.blm.core.model)

      戻り値の型:

      numpy.ndarray

      diff --git a/manual/develop/ja/api/physbo.blm.inf.html b/manual/develop/ja/api/physbo.blm.inf.html index f125f33a..df009e9f 100644 --- a/manual/develop/ja/api/physbo.blm.inf.html +++ b/manual/develop/ja/api/physbo.blm.inf.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.blm.lik.gauss.html b/manual/develop/ja/api/physbo.blm.lik.gauss.html index b1770765..dc3f40aa 100644 --- a/manual/develop/ja/api/physbo.blm.lik.gauss.html +++ b/manual/develop/ja/api/physbo.blm.lik.gauss.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.blm.lik.html b/manual/develop/ja/api/physbo.blm.lik.html index b02c211f..70cdcb8b 100644 --- a/manual/develop/ja/api/physbo.blm.lik.html +++ b/manual/develop/ja/api/physbo.blm.lik.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.blm.lik.linear.html b/manual/develop/ja/api/physbo.blm.lik.linear.html index 32253fbe..2fdc60e9 100644 --- a/manual/develop/ja/api/physbo.blm.lik.linear.html +++ b/manual/develop/ja/api/physbo.blm.lik.linear.html @@ -16,7 +16,7 @@ - + @@ -173,7 +173,7 @@

      set bias

      パラメータ:
      -

      bias (float) --

      +

      bias (float)

      @@ -184,7 +184,7 @@

      set parameters

      パラメータ:
      -

      params (np.ndarray) --

      +

      params (np.ndarray)

    diff --git a/manual/develop/ja/api/physbo.blm.predictor.html b/manual/develop/ja/api/physbo.blm.predictor.html index d8bbc12b..68f77cb9 100644 --- a/manual/develop/ja/api/physbo.blm.predictor.html +++ b/manual/develop/ja/api/physbo.blm.predictor.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.blm.prior.gauss.html b/manual/develop/ja/api/physbo.blm.prior.gauss.html index 564605b7..f303a1aa 100644 --- a/manual/develop/ja/api/physbo.blm.prior.gauss.html +++ b/manual/develop/ja/api/physbo.blm.prior.gauss.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.blm.prior.html b/manual/develop/ja/api/physbo.blm.prior.html index ab113aba..612668ad 100644 --- a/manual/develop/ja/api/physbo.blm.prior.html +++ b/manual/develop/ja/api/physbo.blm.prior.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.gp.core.html b/manual/develop/ja/api/physbo.gp.core.html index 5b7ee855..42eab648 100644 --- a/manual/develop/ja/api/physbo.gp.core.html +++ b/manual/develop/ja/api/physbo.gp.core.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.gp.core.learning.html b/manual/develop/ja/api/physbo.gp.core.learning.html index d1a5179b..a0f9ff7c 100644 --- a/manual/develop/ja/api/physbo.gp.core.learning.html +++ b/manual/develop/ja/api/physbo.gp.core.learning.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.gp.core.model.html b/manual/develop/ja/api/physbo.gp.core.model.html index aeb35563..c7814661 100644 --- a/manual/develop/ja/api/physbo.gp.core.model.html +++ b/manual/develop/ja/api/physbo.gp.core.model.html @@ -16,7 +16,7 @@ - + @@ -196,7 +196,7 @@
  • X (numpy.ndarray) -- N x d dimensional matrix. Each row of X denotes the d-dimensional feature vector of search candidate.

  • t (numpy.ndarray) -- N dimensional array. The negative energy of each search candidate (value of the objective function to be optimized).

  • -
  • config (physbo.misc.set_config object) --

  • +
  • config (physbo.misc.set_config object)

diff --git a/manual/develop/ja/api/physbo.gp.core.prior.html b/manual/develop/ja/api/physbo.gp.core.prior.html index 8f33f6fa..92eecd4b 100644 --- a/manual/develop/ja/api/physbo.gp.core.prior.html +++ b/manual/develop/ja/api/physbo.gp.core.prior.html @@ -16,7 +16,7 @@ - + @@ -223,7 +223,7 @@
パラメータ:
戻り値の型:
diff --git a/manual/develop/ja/api/physbo.gp.cov.gauss.html b/manual/develop/ja/api/physbo.gp.cov.gauss.html index 10007d28..25e039b8 100644 --- a/manual/develop/ja/api/physbo.gp.cov.gauss.html +++ b/manual/develop/ja/api/physbo.gp.cov.gauss.html @@ -16,7 +16,7 @@ - + @@ -119,8 +119,8 @@
パラメータ:
    -
  • width (int) --

  • -
  • scale (int) --

  • +
  • width (int)

  • +
  • scale (int)

戻り値:
@@ -202,7 +202,7 @@
パラメータ:
  • X (numpy.ndarray) -- N x d dimensional matrix. Each row of X denotes the d-dimensional feature vector of search candidate.

  • -
  • params (numpy.ndarray) --

  • +
  • params (numpy.ndarray)

戻り値:
diff --git a/manual/develop/ja/api/physbo.gp.cov.html b/manual/develop/ja/api/physbo.gp.cov.html index e14c81fc..5cb4c823 100644 --- a/manual/develop/ja/api/physbo.gp.cov.html +++ b/manual/develop/ja/api/physbo.gp.cov.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.gp.html b/manual/develop/ja/api/physbo.gp.html index ce0e9f80..4ba3a941 100644 --- a/manual/develop/ja/api/physbo.gp.html +++ b/manual/develop/ja/api/physbo.gp.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.gp.inf.exact.html b/manual/develop/ja/api/physbo.gp.inf.exact.html index ec41c3b1..c5a90a88 100644 --- a/manual/develop/ja/api/physbo.gp.inf.exact.html +++ b/manual/develop/ja/api/physbo.gp.inf.exact.html @@ -16,7 +16,7 @@ - + @@ -113,7 +113,7 @@
パラメータ:
    -
  • gp (physbo.gp.core.model) --

  • +
  • gp (physbo.gp.core.model)

  • X (numpy.ndarray) -- N x d dimensional matrix. Each row of X denotes the d-dimensional feature vector of search candidate.

  • t (numpy.ndarray) -- N dimensional array. The negative energy of each search candidate (value of the objective function to be optimized).

  • @@ -136,7 +136,7 @@
    パラメータ:
      -
    • gp (physbo.gp.core.model) --

    • +
    • gp (physbo.gp.core.model)

    • X (numpy.ndarray) -- N x d dimensional matrix. Each row of X denotes the d-dimensional feature vector of search candidate.

    • t (numpy.ndarray) -- N dimensional array. The negative energy of each search candidate (value of the objective function to be optimized).

    • @@ -159,7 +159,7 @@
      パラメータ:
        -
      • gp (physbo.gp.core.model) --

      • +
      • gp (physbo.gp.core.model)

      • X (numpy.ndarray) -- N x d dimensional matrix. Each row of X denotes the d-dimensional feature vector of search candidate.

      • Z (numpy.ndarray) -- N x d dimensional matrix. Each row of Z denotes the d-dimensional feature vector of tests.

      • params (numpy.ndarray) -- Parameters.

      • @@ -179,7 +179,7 @@
        パラメータ:
          -
        • gp (physbo.gp.core.model) --

        • +
        • gp (physbo.gp.core.model)

        • X (numpy.ndarray) -- N x d dimensional matrix. Each row of X denotes the d-dimensional feature vector of search candidate.

        • Z (numpy.ndarray) -- N x d dimensional matrix. Each row of Z denotes the d-dimensional feature vector of tests.

        • params (numpy.ndarray) -- Parameters.

        • @@ -197,7 +197,7 @@
          パラメータ:
            -
          • gp (physbo.gp.core.model) --

          • +
          • gp (physbo.gp.core.model)

          • X (numpy.ndarray) -- N x d dimensional matrix. Each row of X denotes the d-dimensional feature vector of search candidate.

          • t (numpy.ndarray) -- N dimensional array. The negative energy of each search candidate (value of the objective function to be optimized).

          • diff --git a/manual/develop/ja/api/physbo.gp.inf.html b/manual/develop/ja/api/physbo.gp.inf.html index b5aa15c8..6a5f2b52 100644 --- a/manual/develop/ja/api/physbo.gp.inf.html +++ b/manual/develop/ja/api/physbo.gp.inf.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.gp.lik.gauss.html b/manual/develop/ja/api/physbo.gp.lik.gauss.html index 3dd56215..eac9f27c 100644 --- a/manual/develop/ja/api/physbo.gp.lik.gauss.html +++ b/manual/develop/ja/api/physbo.gp.lik.gauss.html @@ -16,7 +16,7 @@ - + @@ -135,7 +135,7 @@
            パラメータ:
              -
            • num_data (int) --

            • +
            • num_data (int)

            • params (numpy.ndarray) -- Parameters for optimization. Array of real elements of size (n,), where ‘n’ is the number of independent variables.

            @@ -156,7 +156,7 @@
            パラメータ:
              -
            • num_data (int) --

            • +
            • num_data (int)

            • params (numpy.ndarray) -- Parameters for optimization. Array of real elements of size (n,), where ‘n’ is the number of independent variables.

            @@ -190,7 +190,7 @@

            Sampling by adding noise

            パラメータ:
            -

            fmean (numpy.ndarray) --

            +

            fmean (numpy.ndarray)

            diff --git a/manual/develop/ja/api/physbo.gp.lik.html b/manual/develop/ja/api/physbo.gp.lik.html index 2b3292f4..d32dc1f0 100644 --- a/manual/develop/ja/api/physbo.gp.lik.html +++ b/manual/develop/ja/api/physbo.gp.lik.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.gp.mean.const.html b/manual/develop/ja/api/physbo.gp.mean.const.html index 995471d1..e14bf4e4 100644 --- a/manual/develop/ja/api/physbo.gp.mean.const.html +++ b/manual/develop/ja/api/physbo.gp.mean.const.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.gp.mean.html b/manual/develop/ja/api/physbo.gp.mean.html index 9625d4c0..b02e03a6 100644 --- a/manual/develop/ja/api/physbo.gp.mean.html +++ b/manual/develop/ja/api/physbo.gp.mean.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.gp.mean.zero.html b/manual/develop/ja/api/physbo.gp.mean.zero.html index 669bcf2e..5d2133c4 100644 --- a/manual/develop/ja/api/physbo.gp.mean.zero.html +++ b/manual/develop/ja/api/physbo.gp.mean.zero.html @@ -16,7 +16,7 @@ - + @@ -150,7 +150,7 @@

            Not defined

            パラメータ:
            -

            params --

            +

            params

            diff --git a/manual/develop/ja/api/physbo.gp.predictor.html b/manual/develop/ja/api/physbo.gp.predictor.html index 15efc0ae..5d83d266 100644 --- a/manual/develop/ja/api/physbo.gp.predictor.html +++ b/manual/develop/ja/api/physbo.gp.predictor.html @@ -16,7 +16,7 @@ - + @@ -117,8 +117,8 @@
            パラメータ:
              -
            • args --

            • -
            • kwds --

            • +
            • args

            • +
            • kwds

            @@ -144,8 +144,8 @@
            パラメータ:
              -
            • args --

            • -
            • kwds --

            • +
            • args

            • +
            • kwds

            @@ -192,8 +192,8 @@
            パラメータ:
              -
            • args --

            • -
            • kwds --

            • +
            • args

            • +
            • kwds

            @@ -255,8 +255,8 @@
            パラメータ:
              -
            • args --

            • -
            • kwds --

            • +
            • args

            • +
            • kwds

            diff --git a/manual/develop/ja/api/physbo.html b/manual/develop/ja/api/physbo.html index 5f7a9b23..2c29dff9 100644 --- a/manual/develop/ja/api/physbo.html +++ b/manual/develop/ja/api/physbo.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.misc.centering.html b/manual/develop/ja/api/physbo.misc.centering.html index d3135171..0c1d4d36 100644 --- a/manual/develop/ja/api/physbo.misc.centering.html +++ b/manual/develop/ja/api/physbo.misc.centering.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.misc.gauss_elim.html b/manual/develop/ja/api/physbo.misc.gauss_elim.html index ad1b928f..3ed7fb68 100644 --- a/manual/develop/ja/api/physbo.misc.gauss_elim.html +++ b/manual/develop/ja/api/physbo.misc.gauss_elim.html @@ -16,7 +16,7 @@ - + @@ -112,9 +112,9 @@
            パラメータ:
              -
            • U ((M, M) array_like) --

            • -
            • matrix (A triangular) --

            • -
            • t ((M,) or (M, N) array_like) --

            • +
            • U ((M, M) array_like)

            • +
            • matrix (A triangular)

            • +
            • t ((M,) or (M, N) array_like)

            戻り値:
            diff --git a/manual/develop/ja/api/physbo.misc.html b/manual/develop/ja/api/physbo.misc.html index 7b96e59a..8f813ff8 100644 --- a/manual/develop/ja/api/physbo.misc.html +++ b/manual/develop/ja/api/physbo.misc.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.misc.set_config.html b/manual/develop/ja/api/physbo.misc.set_config.html index 7dd31d3d..6be1f634 100644 --- a/manual/develop/ja/api/physbo.misc.set_config.html +++ b/manual/develop/ja/api/physbo.misc.set_config.html @@ -16,7 +16,7 @@ - + @@ -114,7 +114,7 @@

            Loading information of configuration from config._sectoins['adam'].

            パラメータ:
            -

            config (physbo.misc.set_config object) --

            +

            config (physbo.misc.set_config object)

            @@ -137,7 +137,7 @@

            Loading information of configuration from config._sectoins['batch'].

            パラメータ:
            -

            config (physbo.misc.set_config object) --

            +

            config (physbo.misc.set_config object)

          @@ -156,7 +156,7 @@

          Return boolean.

          パラメータ:
          -

          str (str or boolean) --

          +

          str (str or boolean)

          戻り値の型:

          True or False

          @@ -174,7 +174,7 @@

          Loading information of configuration from config._sectoins['learning'].

          パラメータ:
          -

          config (physbo.misc.set_config object) --

          +

          config (physbo.misc.set_config object)

          @@ -197,7 +197,7 @@

          Loading information of configuration from config._sectoins['online'].

          パラメータ:
          -

          config (physbo.misc.set_config object) --

          +

          config (physbo.misc.set_config object)

        @@ -220,7 +220,7 @@

        Loading information of configuration from config._sectoins['search'].

        パラメータ:
        -

        config (physbo.misc.set_config object) --

        +

        config (physbo.misc.set_config object)

      @@ -244,8 +244,8 @@
      パラメータ:
        -
      • file_name (str) --

      • -
      • configuration. (An input file name of) --

      • +
      • file_name (str)

      • +
      • configuration. (An input file name of)

      diff --git a/manual/develop/ja/api/physbo.opt.adam.html b/manual/develop/ja/api/physbo.opt.adam.html index aa745340..9065589d 100644 --- a/manual/develop/ja/api/physbo.opt.adam.html +++ b/manual/develop/ja/api/physbo.opt.adam.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.opt.html b/manual/develop/ja/api/physbo.opt.html index 45f9508c..89189744 100644 --- a/manual/develop/ja/api/physbo.opt.html +++ b/manual/develop/ja/api/physbo.opt.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.predictor.html b/manual/develop/ja/api/physbo.predictor.html index 1cbe4a5b..dd96b491 100644 --- a/manual/develop/ja/api/physbo.predictor.html +++ b/manual/develop/ja/api/physbo.predictor.html @@ -16,7 +16,7 @@ - + @@ -112,8 +112,8 @@
      パラメータ:
        -
      • args --

      • -
      • kwds --

      • +
      • args

      • +
      • kwds

      @@ -127,8 +127,8 @@
      パラメータ:
        -
      • args --

      • -
      • kwds --

      • +
      • args

      • +
      • kwds

      @@ -142,8 +142,8 @@
      パラメータ:
        -
      • args --

      • -
      • kwds --

      • +
      • args

      • +
      • kwds

      @@ -157,8 +157,8 @@
      パラメータ:
        -
      • args --

      • -
      • kwds --

      • +
      • args

      • +
      • kwds

      @@ -172,8 +172,8 @@
      パラメータ:
        -
      • args --

      • -
      • kwds --

      • +
      • args

      • +
      • kwds

      @@ -187,8 +187,8 @@
      パラメータ:
        -
      • args --

      • -
      • kwds --

      • +
      • args

      • +
      • kwds

      @@ -202,8 +202,8 @@
      パラメータ:
        -
      • args --

      • -
      • kwds --

      • +
      • args

      • +
      • kwds

      @@ -217,8 +217,8 @@
      パラメータ:
        -
      • args --

      • -
      • kwds --

      • +
      • args

      • +
      • kwds

      @@ -232,8 +232,8 @@
      パラメータ:
        -
      • args --

      • -
      • kwds --

      • +
      • args

      • +
      • kwds

      @@ -259,8 +259,8 @@
      パラメータ:
        -
      • args --

      • -
      • kwds --

      • +
      • args

      • +
      • kwds

      @@ -286,8 +286,8 @@
      パラメータ:
        -
      • args --

      • -
      • kwds --

      • +
      • args

      • +
      • kwds

      diff --git a/manual/develop/ja/api/physbo.search.discrete.html b/manual/develop/ja/api/physbo.search.discrete.html index f7a050a7..fdb6ca07 100644 --- a/manual/develop/ja/api/physbo.search.discrete.html +++ b/manual/develop/ja/api/physbo.search.discrete.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.search.discrete.policy.html b/manual/develop/ja/api/physbo.search.discrete.policy.html index 67e8e170..6480e0bd 100644 --- a/manual/develop/ja/api/physbo.search.discrete.policy.html +++ b/manual/develop/ja/api/physbo.search.discrete.policy.html @@ -16,7 +16,7 @@ - + @@ -269,7 +269,7 @@
      パラメータ:
      • seed (int) -- seed number

      • -
      • ------- --

      • +
      • -------

    diff --git a/manual/develop/ja/api/physbo.search.discrete.results.html b/manual/develop/ja/api/physbo.search.discrete.results.html index 2e74bac3..25e5e5ef 100644 --- a/manual/develop/ja/api/physbo.search.discrete.results.html +++ b/manual/develop/ja/api/physbo.search.discrete.results.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.search.discrete_multi.html b/manual/develop/ja/api/physbo.search.discrete_multi.html index d4bd423a..d10a0a3d 100644 --- a/manual/develop/ja/api/physbo.search.discrete_multi.html +++ b/manual/develop/ja/api/physbo.search.discrete_multi.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.search.discrete_multi.policy.html b/manual/develop/ja/api/physbo.search.discrete_multi.policy.html index e63434f6..64ebf4aa 100644 --- a/manual/develop/ja/api/physbo.search.discrete_multi.policy.html +++ b/manual/develop/ja/api/physbo.search.discrete_multi.policy.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.search.discrete_multi.results.html b/manual/develop/ja/api/physbo.search.discrete_multi.results.html index 3a5ffa0f..5a1ca16c 100644 --- a/manual/develop/ja/api/physbo.search.discrete_multi.results.html +++ b/manual/develop/ja/api/physbo.search.discrete_multi.results.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.search.html b/manual/develop/ja/api/physbo.search.html index 3e46c0d6..10a162b0 100644 --- a/manual/develop/ja/api/physbo.search.html +++ b/manual/develop/ja/api/physbo.search.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.search.pareto.html b/manual/develop/ja/api/physbo.search.pareto.html index f7f99808..ed65debc 100644 --- a/manual/develop/ja/api/physbo.search.pareto.html +++ b/manual/develop/ja/api/physbo.search.pareto.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.search.score.html b/manual/develop/ja/api/physbo.search.score.html index 529a04a6..58d0fe35 100644 --- a/manual/develop/ja/api/physbo.search.score.html +++ b/manual/develop/ja/api/physbo.search.score.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.search.score_multi.html b/manual/develop/ja/api/physbo.search.score_multi.html index 98918d46..0c766ed0 100644 --- a/manual/develop/ja/api/physbo.search.score_multi.html +++ b/manual/develop/ja/api/physbo.search.score_multi.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.search.utility.html b/manual/develop/ja/api/physbo.search.utility.html index 39005f8b..76558c87 100644 --- a/manual/develop/ja/api/physbo.search.utility.html +++ b/manual/develop/ja/api/physbo.search.utility.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/api/physbo.variable.html b/manual/develop/ja/api/physbo.variable.html index c0abb5de..df6d7300 100644 --- a/manual/develop/ja/api/physbo.variable.html +++ b/manual/develop/ja/api/physbo.variable.html @@ -16,7 +16,7 @@ - + @@ -112,7 +112,7 @@
    • X (numpy array) -- N x d dimensional matrix. Each row of X denotes the d-dimensional feature vector of each search candidate.

    • t (numpy array) -- N dimensional array. The negative energy of each search candidate (value of the objective function to be optimized).

    • -
    • Z --

    • +
    • Z

@@ -135,7 +135,7 @@

Adding variable Z. If self.Z is None, self.Z is set as Z.

パラメータ:
-

Z --

+

Z

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b/manual/develop/ja/introduction.html @@ -16,7 +16,7 @@ - + diff --git a/manual/develop/ja/notebook/index.html b/manual/develop/ja/notebook/index.html index c3838cd4..c300d57a 100644 --- a/manual/develop/ja/notebook/index.html +++ b/manual/develop/ja/notebook/index.html @@ -16,10 +16,12 @@ - + + + diff --git a/manual/develop/ja/notebook/tutorial_Gaussian_process.html b/manual/develop/ja/notebook/tutorial_Gaussian_process.html index 10f582c5..bbad23db 100644 --- a/manual/develop/ja/notebook/tutorial_Gaussian_process.html +++ b/manual/develop/ja/notebook/tutorial_Gaussian_process.html @@ -17,7 +17,7 @@ - + diff --git a/manual/develop/ja/notebook/tutorial_basic.html b/manual/develop/ja/notebook/tutorial_basic.html index 02dda0e4..244171aa 100644 --- a/manual/develop/ja/notebook/tutorial_basic.html +++ b/manual/develop/ja/notebook/tutorial_basic.html @@ -17,7 +17,7 @@ - + diff --git a/manual/develop/ja/notebook/tutorial_interactive_mode.html 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