From dc2a219057166a41841b3330ae5c0e9416d0d710 Mon Sep 17 00:00:00 2001 From: juntongni Date: Sun, 28 Jul 2024 17:18:46 +0800 Subject: [PATCH] Update doc --- docs/_build/doctrees/environment.pickle | Bin 24689 -> 42861 bytes docs/_build/doctrees/index.doctree | Bin 3215 -> 3631 bytes docs/_build/doctrees/installation.doctree | Bin 3841 -> 3813 bytes docs/_build/doctrees/quickstart.doctree | Bin 5395 -> 5383 bytes docs/_build/html/.buildinfo | 2 +- docs/_build/html/_sources/index.rst.txt | 18 +- docs/_build/html/_sources/installation.md.txt | 2 +- docs/_build/html/_static/basic.css | 6 +- docs/_build/html/_static/doctools.js | 2 +- .../html/_static/documentation_options.js | 3 +- docs/_build/html/_static/language_data.js | 4 +- docs/_build/html/_static/searchtools.js | 190 +++++++----------- docs/_build/html/_static/sphinx_highlight.js | 16 +- docs/_build/html/genindex.html | 22 +- docs/_build/html/index.html | 54 +++-- docs/_build/html/installation.html | 41 ++-- 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y^GowebaONFN=s6Ur)15a+$5yLvH_-JkB}ncyvg^3Or_=mg|O;azgbuK79#+k*-Uo; diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo index 6914967..a0d505d 100644 --- a/docs/_build/html/.buildinfo +++ b/docs/_build/html/.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: 9fc46237014b323953bec2db0824f101 +config: 4ec3bd3c41e66b7a2e925c66e399cf70 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_build/html/_sources/index.rst.txt b/docs/_build/html/_sources/index.rst.txt index 1d5df6f..eea0344 100644 --- a/docs/_build/html/_sources/index.rst.txt +++ b/docs/_build/html/_sources/index.rst.txt @@ -4,8 +4,22 @@ Welcome to GraphSlim's documentation! A comprehensive package for graph sparsification, coarsening and condensation based on PyG. .. toctree:: - :maxdepth: 2 + :maxdepth: 1 + :caption: Installation installation + +.. toctree:: + :maxdepth: 1 + :caption: Usage + quickstart - packageref/index + +.. toctree:: + :maxdepth: 1 + :caption: Package API + + API/dataset + API/evaluation + API/method + diff --git a/docs/_build/html/_sources/installation.md.txt b/docs/_build/html/_sources/installation.md.txt index b68092e..5f22e88 100644 --- a/docs/_build/html/_sources/installation.md.txt +++ b/docs/_build/html/_sources/installation.md.txt @@ -8,6 +8,6 @@ pip install graphslim ```shell git clone https://github.com/Emory-Melody/GraphSlim.git cd GraphSlim/graphslim -pip install -r requirements_torch2+.txt +pip install -r requirements.txt python setup.py ``` \ No newline at end of file diff --git a/docs/_build/html/_static/basic.css b/docs/_build/html/_static/basic.css index f316efc..cfc60b8 100644 --- a/docs/_build/html/_static/basic.css +++ b/docs/_build/html/_static/basic.css @@ -4,7 +4,7 @@ * * Sphinx stylesheet -- basic theme. * - * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -237,10 +237,6 @@ a.headerlink { visibility: hidden; } -a:visited { - color: #551A8B; -} - h1:hover > a.headerlink, h2:hover > a.headerlink, h3:hover > a.headerlink, diff --git a/docs/_build/html/_static/doctools.js b/docs/_build/html/_static/doctools.js index 4d67807..d06a71d 100644 --- a/docs/_build/html/_static/doctools.js +++ b/docs/_build/html/_static/doctools.js @@ -4,7 +4,7 @@ * * Base JavaScript utilities for all Sphinx HTML documentation. * - * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/docs/_build/html/_static/documentation_options.js b/docs/_build/html/_static/documentation_options.js index 7e4c114..b57ae3b 100644 --- a/docs/_build/html/_static/documentation_options.js +++ b/docs/_build/html/_static/documentation_options.js @@ -1,4 +1,5 @@ -const DOCUMENTATION_OPTIONS = { +var DOCUMENTATION_OPTIONS = { + URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), VERSION: '', LANGUAGE: 'en', COLLAPSE_INDEX: false, diff --git a/docs/_build/html/_static/language_data.js b/docs/_build/html/_static/language_data.js index 367b8ed..250f566 100644 --- a/docs/_build/html/_static/language_data.js +++ b/docs/_build/html/_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 2007-2024 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2023 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, if available */ +/* Non-minified version is copied as a separate JS file, is available */ /** * Porter Stemmer diff --git a/docs/_build/html/_static/searchtools.js b/docs/_build/html/_static/searchtools.js index b08d58c..184a177 100644 --- a/docs/_build/html/_static/searchtools.js +++ b/docs/_build/html/_static/searchtools.js @@ -4,7 +4,7 @@ * * Sphinx JavaScript utilities for the full-text search. * - * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -57,12 +57,12 @@ const _removeChildren = (element) => { const _escapeRegExp = (string) => string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string -const _displayItem = (item, searchTerms, highlightTerms) => { +const _displayItem = (item, searchTerms) => { const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT; const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; const [docName, title, anchor, descr, score, _filename] = item; @@ -75,35 +75,28 @@ const _displayItem = (item, searchTerms, highlightTerms) => { if (dirname.match(/\/index\/$/)) dirname = dirname.substring(0, dirname.length - 6); else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; + requestUrl = docUrlRoot + dirname; linkUrl = requestUrl; } else { // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; + requestUrl = docUrlRoot + docName + docFileSuffix; linkUrl = docName + docLinkSuffix; } let linkEl = listItem.appendChild(document.createElement("a")); linkEl.href = linkUrl + anchor; linkEl.dataset.score = score; linkEl.innerHTML = title; - if (descr) { + if (descr) listItem.appendChild(document.createElement("span")).innerHTML = " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } else if (showSearchSummary) fetch(requestUrl) .then((responseData) => responseData.text()) .then((data) => { if (data) listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) + Search.makeSearchSummary(data, searchTerms) ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); }); Search.output.appendChild(listItem); }; @@ -116,43 +109,26 @@ const _finishSearch = (resultCount) => { ); else Search.status.innerText = _( - "Search finished, found ${resultCount} page(s) matching the search query." - ).replace('${resultCount}', resultCount); + `Search finished, found ${resultCount} page(s) matching the search query.` + ); }; const _displayNextItem = ( results, resultCount, - searchTerms, - highlightTerms, + searchTerms ) => { // results left, load the summary and display it // this is intended to be dynamic (don't sub resultsCount) if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); + _displayItem(results.pop(), searchTerms); setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + () => _displayNextItem(results, resultCount, searchTerms), 5 ); } // 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 @@ -176,26 +152,15 @@ const Search = { _queued_query: null, _pulse_status: -1, - htmlToText: (htmlString, anchor) => { + htmlToText: (htmlString) => { const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "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 + htmlElement.querySelectorAll(".headerlink").forEach((el) => { + el.remove() + }); const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - + if (docContent !== undefined) return docContent.textContent; console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." ); return ""; }, @@ -268,7 +233,16 @@ const Search = { else Search.deferQuery(query); }, - _parseQuery: (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; + // stem the search terms and add them to the correct list const stemmer = new Stemmer(); const searchTerms = new Set(); @@ -304,38 +278,21 @@ const Search = { // console.info("required: ", [...searchTerms]); // console.info("excluded: ", [...excludedTerms]); - 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 = []; - + // array of [docname, title, anchor, descr, score, filename] + let results = []; _removeChildren(document.getElementById("search-progress")); - const queryLower = query.toLowerCase().trim(); + const queryLower = query.toLowerCase(); for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length / 2)) { for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ + let score = Math.round(100 * queryLower.length / title.length) + results.push([ docNames[file], titles[file] !== title ? `${titles[file]} > ${title}` : title, id !== null ? "#" + id : "", null, - score + boost, + score, filenames[file], ]); } @@ -345,47 +302,46 @@ 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, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ 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) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) + results.push(...Search.performObjectSearch(term, objectTerms)) ); // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); // let the scorer override scores with a custom scoring function - 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]; + 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; + }); // remove duplicate search results // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept @@ -399,19 +355,14 @@ const Search = { return acc; }, []); - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + results = results.reverse(); // for debugging //Search.lastresults = results.slice(); // a copy // console.info("search results:", Search.lastresults); // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); + _displayNextItem(results, results.length, searchTerms); }, /** @@ -509,18 +460,14 @@ const Search = { // add support for partial matches if (word.length > 2) { const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); + if (term.match(escapedWord) && !terms[word]) + 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 }); + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({files: titleTerms[word], score: Scorer.partialTitle}); }); - } } // no match but word was a required one @@ -543,8 +490,9 @@ const Search = { // create the mapping files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); }); }); @@ -595,8 +543,8 @@ const Search = { * search summary for a given text. keywords is a list * of stemmed words. */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); if (text === "") return null; const textLower = text.toLowerCase(); diff --git a/docs/_build/html/_static/sphinx_highlight.js b/docs/_build/html/_static/sphinx_highlight.js index 8a96c69..0f5fb86 100644 --- a/docs/_build/html/_static/sphinx_highlight.js +++ b/docs/_build/html/_static/sphinx_highlight.js @@ -29,19 +29,14 @@ const _highlight = (node, addItems, text, className) => { } span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); parent.insertBefore( span, parent.insertBefore( - rest, + document.createTextNode(val.substr(pos + text.length)), node.nextSibling ) ); node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); if (isInSVG) { const rect = document.createElementNS( @@ -145,10 +140,5 @@ const SphinxHighlight = { }, }; -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); +_ready(SphinxHighlight.highlightSearchWords); +_ready(SphinxHighlight.initEscapeListener); diff --git a/docs/_build/html/genindex.html b/docs/_build/html/genindex.html index 948997d..b58e0af 100644 --- a/docs/_build/html/genindex.html +++ b/docs/_build/html/genindex.html @@ -1,5 +1,5 @@ - + @@ -14,9 +14,9 @@ - - - + + + @@ -41,10 +41,20 @@ diff --git a/docs/_build/html/index.html b/docs/_build/html/index.html index e49ae9a..f046199 100644 --- a/docs/_build/html/index.html +++ b/docs/_build/html/index.html @@ -1,5 +1,5 @@ - + @@ -15,9 +15,9 @@ - - - + + + @@ -43,10 +43,20 @@ @@ -74,26 +84,28 @@
-

Welcome to GraphSlim’s documentation!

+

Welcome to GraphSlim’s documentation!

A comprehensive package for graph sparsification, coarsening and condensation based on PyG.

+

Installation

+
+

Usage

+ - +
+
+

Package API

+
diff --git a/docs/_build/html/installation.html b/docs/_build/html/installation.html index 61f8604..7b678b5 100644 --- a/docs/_build/html/installation.html +++ b/docs/_build/html/installation.html @@ -1,5 +1,5 @@ - + @@ -15,14 +15,12 @@ - - - + + + - - - + @@ -44,16 +42,17 @@
@@ -79,18 +78,19 @@
-

Installation

+

Installation

-

Install from pip

+

Install from pip

pip install graphslim
-

Install source code

+

Install source code + 

git clone https://github.com/Emory-Melody/GraphSlim.git
 cd GraphSlim/graphslim
-pip install -r requirements_torch2+.txt
+pip install -r requirements.txt
 python setup.py
@@ -100,10 +100,7 @@

Install source code - - -

+