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update docs
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materialsproject committed Oct 6, 2024
1 parent cc3573b commit bec28b6
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8 changes: 8 additions & 0 deletions docs/_sources/matminer.utils.rst.txt
Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,14 @@ matminer.utils.utils module
:undoc-members:
:show-inheritance:

matminer.utils.warnings module
------------------------------

.. automodule:: matminer.utils.warnings
:members:
:undoc-members:
:show-inheritance:

Module contents
---------------

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8 changes: 8 additions & 0 deletions docs/_sources/matminer.utils.tests.rst.txt
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Expand Up @@ -36,6 +36,14 @@ matminer.utils.tests.test\_io module
:undoc-members:
:show-inheritance:

matminer.utils.tests.test\_utils module
---------------------------------------

.. automodule:: matminer.utils.tests.test_utils
:members:
:undoc-members:
:show-inheritance:

Module contents
---------------

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2 changes: 1 addition & 1 deletion docs/_static/basic.css
Original file line number Diff line number Diff line change
Expand Up @@ -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.
*
*/
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2 changes: 1 addition & 1 deletion docs/_static/doctools.js
Original file line number Diff line number Diff line change
Expand Up @@ -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.
*
*/
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2 changes: 1 addition & 1 deletion docs/_static/documentation_options.js
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
const DOCUMENTATION_OPTIONS = {
VERSION: '0.9.2',
VERSION: '0.9.3',
LANGUAGE: 'en',
COLLAPSE_INDEX: false,
BUILDER: 'html',
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4 changes: 2 additions & 2 deletions docs/_static/language_data.js
Original file line number Diff line number Diff line change
Expand Up @@ -5,15 +5,15 @@
* 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.
*
*/

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
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170 changes: 108 additions & 62 deletions docs/_static/searchtools.js
Original file line number Diff line number Diff line change
Expand Up @@ -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.
*
*/
Expand Down Expand Up @@ -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
Expand All @@ -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,
Expand All @@ -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
Expand All @@ -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 [".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
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 "";
},
Expand Down Expand Up @@ -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();
Expand Down Expand Up @@ -284,21 +304,38 @@ 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([
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([
docNames[file],
titles[file] !== title ? `${titles[file]} > ${title}` : title,
id !== null ? "#" + id : "",
null,
score,
score + boost,
filenames[file],
]);
}
Expand All @@ -308,46 +345,47 @@ 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
Expand All @@ -361,7 +399,12 @@ 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
Expand Down Expand Up @@ -466,14 +509,18 @@ 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
Expand All @@ -496,9 +543,8 @@ 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);
});
});

Expand Down Expand Up @@ -549,8 +595,8 @@ 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();
Expand Down
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