.

README.rst

@@ -99,10 +99,10 @@ Examples
 
 Notebooks on how to use ``thefittest``:
 
-- `Solving binary and real-valued optimization problems with a genetic algorithm; <https://github.com/sherstpasha/thefittest-notebooks/blob/main/genetic_algorithm_binary_rastrigin_custom_problems.ipynb>`_
-- `Solving real-valued optimization problems with a differential evolution; <https://github.com/sherstpasha/thefittest-notebooks/blob/main/differential_evolution_griewank_custom_problems.ipynb>`_
-- `Symbolic regression problems solving using genetic programming algorithm; <https://github.com/sherstpasha/thefittest-notebooks/blob/main/genetic_programming_symbolic_regression_problem.ipynb>`_
-- `Neural network training using evolutionary algorithms for regression and classification problems; <https://github.com/sherstpasha/thefittest-notebooks/blob/main/mlpea_regression_classification_problem.ipynb>`_
-- `Optimization of neural network structure using genetic programming; <https://github.com/sherstpasha/thefittest-notebooks/blob/main/gpnn_regression_classification_problems.ipynb>`_
+- `Solving Binary and Real-Valued Optimization Problems with Genetic Algorithms;; <https://github.com/sherstpasha/thefittest-notebooks/blob/main/genetic_algorithm_binary_rastrigin_custom_problems.ipynb>`_
+- `Solving Real-Valued Optimization Problems with Differential Evolution; <https://github.com/sherstpasha/thefittest-notebooks/blob/main/differential_evolution_griewank_custom_problems.ipynb>`_
+- `Solving Symbolic Regression Problems Using Genetic Programming Algorithms; <https://github.com/sherstpasha/thefittest-notebooks/blob/main/genetic_programming_symbolic_regression_problem.ipynb>`_
+- `Training Neural Networks Using Evolutionary Algorithms for Regression and Classification Problems; <https://github.com/sherstpasha/thefittest-notebooks/blob/main/mlpea_regression_classification_problem.ipynb>`_
+- `Optimizing Neural Network Structure Using Genetic Programming; <https://github.com/sherstpasha/thefittest-notebooks/blob/main/gpnn_regression_classification_problems.ipynb>`_
 
 If some notebooks are too big to display, you can use `NBviewer <https://nbviewer.org/>`_.

docs/.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: 50dd6d3cf8f380de8a3d2fc45324b704
+config: 2900ab9c12defc5c2690b8ac62d414df
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_sources/index.rst.txt

@@ -37,15 +37,15 @@ Installation
 Dependencies
 ------------
 
-thefittest requires:
+``thefittest`` requires:
 
-- python (>=3.7,<3.12);
-- numpy;
-- numba;
-- scipy.
+- `Python (>=3.7,<3.12) <https://www.python.org/>`_,
+- `NumPy <https://numpy.org/>`_, 
+- `Numba <https://numba.pydata.org/>`_;
+- `Scipy <https://scipy.org/>`_.
 
-The package contains methods
-----------------------------
+``thefittest`` contains methods
+-------------------------------
 
 - **Genetic algorithm** (Holland, J. H. (1992). Genetic algorithms. Scientific American, 267(1), 66-72):
 
@@ -79,13 +79,13 @@ Benchmarks
 Examples
 --------
 
-Notebooks on how to use thefittest:
+Notebooks on how to use ``thefittest``:
 
-- `Solving binary and real-valued optimization problems with a genetic algorithm; <https://github.com/sherstpasha/thefittest-notebooks/blob/main/genetic_algorithm_binary_rastrigin_custom_problems.ipynb>`_
-- `Solving real-valued optimization problems with a differential evolution; <https://github.com/sherstpasha/thefittest-notebooks/blob/main/differential_evolution_griewank_custom_problems.ipynb>`_
-- `Symbolic regression problems solving using genetic programming algorithm; <https://github.com/sherstpasha/thefittest-notebooks/blob/main/genetic_programming_symbolic_regression_problem.ipynb>`_
-- `Neural network training using evolutionary algorithms for regression and classification problems; <https://github.com/sherstpasha/thefittest-notebooks/blob/main/mlpea_regression_classification_problem.ipynb>`_
-- `Optimization of neural network structure using genetic programming; <https://github.com/sherstpasha/thefittest-notebooks/blob/main/gpnn_regression_classification_problems.ipynb>`_
+- `Solving Binary and Real-Valued Optimization Problems with Genetic Algorithms; <https://github.com/sherstpasha/thefittest-notebooks/blob/main/genetic_algorithm_binary_rastrigin_custom_problems.ipynb>`_
+- `Solving Real-Valued Optimization Problems with Differential Evolution; <https://github.com/sherstpasha/thefittest-notebooks/blob/main/differential_evolution_griewank_custom_problems.ipynb>`_
+- `Solving Symbolic Regression Problems Using Genetic Programming Algorithms; <https://github.com/sherstpasha/thefittest-notebooks/blob/main/genetic_programming_symbolic_regression_problem.ipynb>`_
+- `Training Neural Networks Using Evolutionary Algorithms for Regression and Classification Problems; <https://github.com/sherstpasha/thefittest-notebooks/blob/main/mlpea_regression_classification_problem.ipynb>`_
+- `Optimizing Neural Network Structure Using Genetic Programming; <https://github.com/sherstpasha/thefittest-notebooks/blob/main/gpnn_regression_classification_problems.ipynb>`_
 
 If some notebooks are too big to display, you can use `NBviewer <https://nbviewer.org/>`_.
 

docs/_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.
  *
  */

docs/_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.
  *
  */

docs/_static/language_data.js

@@ -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 2007-2024 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 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, if available */
+/* Non-minified version is copied as a separate JS file, is available */
 
 /**
  * Porter Stemmer

docs/_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.
  *
  */
@@ -99,7 +99,7 @@ const _displayItem = (item, searchTerms, highlightTerms) => {
       .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
@@ -116,8 +116,8 @@ 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,
@@ -137,22 +137,6 @@ 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
@@ -176,26 +160,13 @@ 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 [".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
+    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 +239,16 @@ 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();
@@ -304,32 +284,16 @@ 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) {
           let score = Math.round(100 * queryLower.length / title.length)
-          normalResults.push([
+          results.push([
             docNames[file],
             titles[file] !== title ? `${titles[file]} > ${title}` : title,
             id !== null ? "#" + id : "",
@@ -344,47 +308,46 @@ 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
@@ -398,12 +361,7 @@ 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
@@ -508,18 +466,14 @@ 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 (!titleTerms.hasOwnProperty(word)) {
-          Object.keys(titleTerms).forEach((term) => {
-            if (term.match(escapedWord))
-              arr.push({ files: titleTerms[term], score: Scorer.partialTitle });
-          });
-        }
+        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 });
+        });
       }
 
       // no match but word was a required one
@@ -542,8 +496,9 @@ 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]);
       });
     });
 
@@ -594,8 +549,8 @@ 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();

docs/genindex.html

@@ -15,7 +15,7 @@
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="_static/documentation_options.js?v=a47416a6"></script>
-        <script src="_static/doctools.js?v=9a2dae69"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="#" />