created documentation based on sisl

.readthedocs.yaml

@@ -0,0 +1,37 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: macOS-15.0.1
+  tools:
+    python: "3.9"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  builder: html
+  configuration: docs/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+ formats:
+   - pdf
+#   - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+ python:
+   install:
+     - requirements: docs/requirements.txt
+     - requirements: requirements.txt

README.md

@@ -6,6 +6,7 @@ More on the theoretical background can be seen on [arXiv](https://arxiv.org/abs/
 - Run tests on different magnetic materials and compare it to Grogu Matlab --> ran on Jij_for_Marci_6p45ang, but I could not compare data
 
 ## Developing
+- Use ReadThe Docs [addons](https://docs.readthedocs.io/en/stable/addons.html)
 - Check the symmetrization of the Hamiltonian and overlap matrix to make them hermitian
 - Check if exchange field has scalar part
 - Add more tests!!

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: d8f86c3651bae6bbb2cfa348920c9196
+config: 320e5b6dc420902025e0d306c97e86be
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/html/_sources/bibliography.rst.txt

@@ -0,0 +1,4 @@
+Bibliography
+============
+
+.. bibliography:: bibliography.bib

docs/_build/html/_sources/changelog/index.rst.txt

@@ -0,0 +1,4 @@
+Changelog
+=========
+
+Coming soon...

docs/_build/html/_sources/cite.rst.txt

@@ -0,0 +1,4 @@
+Citing grogupy
+==============
+
+Coming soon...

docs/_build/html/_sources/dev/index.rst.txt

@@ -0,0 +1,4 @@
+Contributing to grogupy
+=======================
+
+Coming soon...

docs/_build/html/_sources/environment.rst.txt

@@ -0,0 +1,2 @@
+Environment variables
+=====================

docs/_build/html/_sources/implementation/index.rst.txt

@@ -0,0 +1,2 @@
+Implementation
+==============

docs/_build/html/_sources/index.rst.txt

@@ -0,0 +1,74 @@
+.. grogupy documentation master file, created by
+   sphinx-quickstart on Thu Oct 10 17:10:03 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+
+.. module:: grogupy
+
+.. title:: grogupy: Script for calculating magnetic interactions 
+.. meta::
+   :description: Relativistic magnetic interactions from non-orthogonal basis sets.
+   :keywords: DFT, physics, grogu, magnetic interactions, Siesta
+
+
+grogupy: Script for calculating magnetic interactions 
+=====================================================
+
+Groupy is a generalized python script based on the Grogu matlab implementation. 
+More on the theoretical background can be seen `here <https://arxiv.org/abs/2309.02558>`_.
+
+.. grid:: 1 1 2 2
+    :gutter: 2
+
+    .. grid-item-card:: -- Quick-start guides
+        :link: quickstart/index
+        :link-type: doc
+
+        Basic tutorial on how to use the `grogupy` script.
+
+    .. grid-item-card::  -- Implementation
+        :link: implementation/index
+        :link-type: doc
+
+        Detailed description of the implementation.
+
+
+.. toctree::
+   :hidden:
+   :maxdepth: 2
+   :caption: Getting started
+
+   introduction
+   quickstart/index
+   cite
+
+.. toctree::
+   :hidden:
+   :maxdepth: 2
+   :caption: User Guide
+
+   tutorials/index
+
+.. toctree::
+   :hidden:
+   :maxdepth: 2
+   :caption: Advanced usage
+
+   implementation/index
+   environment
+   
+.. toctree::
+   :hidden:
+   :maxdepth: 2
+   :caption: Development
+
+   dev/index
+
+.. toctree::
+   :hidden:
+   :maxdepth: 3
+   :caption: Extras
+
+   changelog/index
+   bibliography

docs/_build/html/_sources/introduction.rst.txt

@@ -0,0 +1,17 @@
+Introduction
+============
+
+The format of the documentation was based on and inspired by `sisl <https://sisl.readthedocs.io/en/latest/index.html>`_.
+1.
+
+2.
+
+Package
+-------
+
+Go to :ref:`installation <quickstart>`.
+
+Command line usage
+------------------
+
+Coming soon...

docs/_build/html/_sources/quickstart/index.rst.txt

@@ -0,0 +1,21 @@
+Quickstart
+==========
+
+installation
+------------
+
+.. grid:: 1 2 2 2
+    :gutter: 4
+
+    .. grid-item-card:: pip
+        :columns: 12 12 6 6
+
+        grogupy can be installed via pip from `Test PyPI <https://test.pypi.org>`_.
+
+        ++++
+
+        .. code-block:: bash
+
+            python3 -m pip install --index-url https://test.pypi.org/simple/ grogupy
+
+Coming soon...

docs/_build/html/_sources/tutorials/index.rst.txt

@@ -0,0 +1,4 @@
+Tutorials
+=========
+
+Coming soon...

docs/_build/html/_sphinx_design_static/design-tabs.js

@@ -0,0 +1,101 @@
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+
+// Extra JS capability for selected tabs to be synced
+// The selection is stored in local storage so that it persists across page loads.
+
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+const storageKeyPrefix = "sphinx-design-tab-id-";
+
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+ * @param {HTMLElement} el - The tab element.
+ * @returns {[string, string, string] | null} - The key.
+ *
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+  let syncGroup = el.getAttribute("data-sync-group");
+  if (!syncId || !syncGroup) return null;
+  return [syncGroup, syncId, syncGroup + "--" + syncId];
+}
+
+/**
+ * Initialize the tab selection.
+ *
+ */
+function ready() {
+  // Find all tabs with sync data
+
+  /** @type {string[]} */
+  let groups = [];
+
+  document.querySelectorAll(".sd-tab-label").forEach((label) => {
+    if (label instanceof HTMLElement) {
+      let data = create_key(label);
+      if (data) {
+        let [group, id, key] = data;
+
+        // add click event listener
+        // @ts-ignore
+        label.onclick = onSDLabelClick;
+
+        // store map of key to elements
+        if (!sd_id_to_elements[key]) {
+          sd_id_to_elements[key] = [];
+        }
+        sd_id_to_elements[key].push(label);
+
+        if (groups.indexOf(group) === -1) {
+          groups.push(group);
+          // Check if a specific tab has been selected via URL parameter
+          const tabParam = new URLSearchParams(window.location.search).get(
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+          if (tabParam) {
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+                tabParam
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+            window.sessionStorage.setItem(storageKeyPrefix + group, tabParam);
+          }
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+
+        // Check is a specific tab has been selected previously
+        let previousId = window.sessionStorage.getItem(
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+        );
+        if (previousId === id) {
+          // console.log(
+          //   "sphinx-design: Selecting tab from session storage: " + id
+          // );
+          // @ts-ignore
+          label.previousElementSibling.checked = true;
+        }
+      }
+    }
+  });
+}
+
+/**
+ *  Activate other tabs with the same sync id.
+ *
+ * @this {HTMLElement} - The element that was clicked.
+ */
+function onSDLabelClick() {
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+  let [group, id, key] = data;
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+    // @ts-ignore
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+  }
+  window.sessionStorage.setItem(storageKeyPrefix + group, id);
+}
+
+document.addEventListener("DOMContentLoaded", ready, false);

docs/_build/html/_static/design-tabs.js

@@ -0,0 +1,101 @@
+// @ts-check
+
+// Extra JS capability for selected tabs to be synced
+// The selection is stored in local storage so that it persists across page loads.
+
+/**
+ * @type {Record<string, HTMLElement[]>}
+ */
+let sd_id_to_elements = {};
+const storageKeyPrefix = "sphinx-design-tab-id-";
+
+/**
+ * Create a key for a tab element.
+ * @param {HTMLElement} el - The tab element.
+ * @returns {[string, string, string] | null} - The key.
+ *
+ */
+function create_key(el) {
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+  let syncGroup = el.getAttribute("data-sync-group");
+  if (!syncId || !syncGroup) return null;
+  return [syncGroup, syncId, syncGroup + "--" + syncId];
+}
+
+/**
+ * Initialize the tab selection.
+ *
+ */
+function ready() {
+  // Find all tabs with sync data
+
+  /** @type {string[]} */
+  let groups = [];
+
+  document.querySelectorAll(".sd-tab-label").forEach((label) => {
+    if (label instanceof HTMLElement) {
+      let data = create_key(label);
+      if (data) {
+        let [group, id, key] = data;
+
+        // add click event listener
+        // @ts-ignore
+        label.onclick = onSDLabelClick;
+
+        // store map of key to elements
+        if (!sd_id_to_elements[key]) {
+          sd_id_to_elements[key] = [];
+        }
+        sd_id_to_elements[key].push(label);
+
+        if (groups.indexOf(group) === -1) {
+          groups.push(group);
+          // Check if a specific tab has been selected via URL parameter
+          const tabParam = new URLSearchParams(window.location.search).get(
+            group
+          );
+          if (tabParam) {
+            console.log(
+              "sphinx-design: Selecting tab id for group '" +
+                group +
+                "' from URL parameter: " +
+                tabParam
+            );
+            window.sessionStorage.setItem(storageKeyPrefix + group, tabParam);
+          }
+        }
+
+        // Check is a specific tab has been selected previously
+        let previousId = window.sessionStorage.getItem(
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+        );
+        if (previousId === id) {
+          // console.log(
+          //   "sphinx-design: Selecting tab from session storage: " + id
+          // );
+          // @ts-ignore
+          label.previousElementSibling.checked = true;
+        }
+      }
+    }
+  });
+}
+
+/**
+ *  Activate other tabs with the same sync id.
+ *
+ * @this {HTMLElement} - The element that was clicked.
+ */
+function onSDLabelClick() {
+  let data = create_key(this);
+  if (!data) return;
+  let [group, id, key] = data;
+  for (const label of sd_id_to_elements[key]) {
+    if (label === this) continue;
+    // @ts-ignore
+    label.previousElementSibling.checked = true;
+  }
+  window.sessionStorage.setItem(storageKeyPrefix + group, id);
+}
+
+document.addEventListener("DOMContentLoaded", ready, false);

docs/_build/html/_static/documentation_options.js

@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.0.1',
+    VERSION: '1.0.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

docs/_build/html/_static/language_data.js

@@ -196,3 +196,4 @@ var Stemmer = function() {
     return w;
   }
 }
+

docs/_build/html/bibliography.html

@@ -6,20 +6,22 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>asd documentation &mdash; Grogu 0.0.1 documentation</title>
+  <title>Bibliography &mdash; grogupy 1.0.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="_static/sphinx-design.min.css?v=95c83b7e" />
 
   
       <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=d45e8c67"></script>
+      <script src="_static/documentation_options.js?v=8d563738"></script>
       <script src="_static/doctools.js?v=9a2dae69"></script>
       <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+      <script src="_static/design-tabs.js?v=f930bc37"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="src" href="modules.html" />
+    <link rel="prev" title="Changelog" href="changelog/index.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -30,8 +32,8 @@
 
           
           
-          <a href="#" class="icon icon-home">
-            Grogu
+          <a href="index.html" class="icon icon-home">
+            grogupy
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
@@ -41,9 +43,29 @@
   </form>
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
-              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+              <p class="caption" role="heading"><span class="caption-text">Getting started</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="modules.html">src</a></li>
+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="quickstart/index.html">Quickstart</a></li>
+<li class="toctree-l1"><a class="reference internal" href="cite.html">Citing grogupy</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="tutorials/index.html">Tutorials</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Advanced usage</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="implementation/index.html">Implementation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="environment.html">Environment variables</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Development</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="dev/index.html">Contributing to grogupy</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Extras</span></p>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="changelog/index.html">Changelog</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Bibliography</a></li>
 </ul>
 
         </div>
@@ -52,17 +74,17 @@
 
     <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
           <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-          <a href="#">Grogu</a>
+          <a href="index.html">grogupy</a>
       </nav>
 
       <div class="wy-nav-content">
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="#" class="icon icon-home" aria-label="Home"></a></li>
-      <li class="breadcrumb-item active">asd documentation</li>
+      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li class="breadcrumb-item active">Bibliography</li>
       <li class="wy-breadcrumbs-aside">
-            <a href="_sources/index.rst.txt" rel="nofollow"> View page source</a>
+            <a href="_sources/bibliography.rst.txt" rel="nofollow"> View page source</a>
       </li>
   </ul>
   <hr/>
@@ -70,41 +92,21 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
              
-  <section id="asd-documentation">
-<h1>asd documentation<a class="headerlink" href="#asd-documentation" title="Link to this heading"></a></h1>
-<p>Add your content using <code class="docutils literal notranslate"><span class="pre">reStructuredText</span></code> syntax. See the
-<a class="reference external" href="https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html">reStructuredText</a>
-documentation for details.</p>
-<div class="toctree-wrapper compound">
-<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="modules.html">src</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="grogu.html">grogu package</a></li>
-</ul>
-</li>
-</ul>
-</div>
-</section>
-<section id="indices-and-tables">
-<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Link to this heading"></a></h1>
-<ul class="simple">
-<li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li>
-<li><p><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></p></li>
-<li><p><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></p></li>
-</ul>
-</section>
+  <section id="bibliography">
+<h1>Bibliography<a class="headerlink" href="#bibliography" title="Link to this heading"></a></h1>
+<span class="target" id="id1"></span></section>
 
 
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="modules.html" class="btn btn-neutral float-right" title="src" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="changelog/index.html" class="btn btn-neutral float-left" title="Changelog" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
     </div>
 
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Grogu.</p>
+    <p>&#169; Copyright 2024, grogupy.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

docs/_build/html/changelog/index.html

@@ -0,0 +1,132 @@
+
+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../">
+<head>
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
+
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Changelog &mdash; grogupy 1.0.0 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="../_static/sphinx-design.min.css?v=95c83b7e" />
+
+  
+      <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=8d563738"></script>
+      <script src="../_static/doctools.js?v=9a2dae69"></script>
+      <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+      <script src="../_static/design-tabs.js?v=f930bc37"></script>
+    <script src="../_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" />
+    <link rel="next" title="Bibliography" href="../bibliography.html" />
+    <link rel="prev" title="Contributing to grogupy" href="../dev/index.html" /> 
+</head>
+
+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+
+          
+          
+          <a href="../index.html" class="icon icon-home">
+            grogupy
+          </a>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <p class="caption" role="heading"><span class="caption-text">Getting started</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../quickstart/index.html">Quickstart</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../cite.html">Citing grogupy</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../tutorials/index.html">Tutorials</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Advanced usage</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../implementation/index.html">Implementation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../environment.html">Environment variables</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Development</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../dev/index.html">Contributing to grogupy</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Extras</span></p>
+<ul class="current">
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Changelog</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../bibliography.html">Bibliography</a></li>
+</ul>
+
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+<h1>Changelog<a class="headerlink" href="#changelog" title="Link to this heading"></a></h1>
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docs/_build/html/cite.html

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+<html class="writer-html5" lang="en" data-content_root="./">
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+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Citing grogupy &mdash; grogupy 1.0.0 documentation</title>
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
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+              <p class="caption" role="heading"><span class="caption-text">Getting started</span></p>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="quickstart/index.html">Quickstart</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Citing grogupy</a></li>
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+<ul>
+<li class="toctree-l1"><a class="reference internal" href="tutorials/index.html">Tutorials</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Advanced usage</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="implementation/index.html">Implementation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="environment.html">Environment variables</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Development</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="dev/index.html">Contributing to grogupy</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Extras</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="changelog/index.html">Changelog</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bibliography.html">Bibliography</a></li>
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+
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+  <section id="citing-grogupy">
+<h1>Citing grogupy<a class="headerlink" href="#citing-grogupy" title="Link to this heading"></a></h1>
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+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2024, grogupy.</p>
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docs/_build/html/dev/index.html

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+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../">
+<head>
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
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+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Contributing to grogupy &mdash; grogupy 1.0.0 documentation</title>
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+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
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+<li class="toctree-l1"><a class="reference internal" href="../quickstart/index.html">Quickstart</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../cite.html">Citing grogupy</a></li>
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+<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../tutorials/index.html">Tutorials</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Advanced usage</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../implementation/index.html">Implementation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../environment.html">Environment variables</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Development</span></p>
+<ul class="current">
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Contributing to grogupy</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Extras</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../changelog/index.html">Changelog</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../bibliography.html">Bibliography</a></li>
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+
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+           <div itemprop="articleBody">
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+  <section id="contributing-to-grogupy">
+<h1>Contributing to grogupy<a class="headerlink" href="#contributing-to-grogupy" title="Link to this heading"></a></h1>
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docs/_build/html/environment.html

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+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="./">
+<head>
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
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+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+    <link rel="next" title="Contributing to grogupy" href="dev/index.html" />
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+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
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+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <p class="caption" role="heading"><span class="caption-text">Getting started</span></p>
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+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="quickstart/index.html">Quickstart</a></li>
+<li class="toctree-l1"><a class="reference internal" href="cite.html">Citing grogupy</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="tutorials/index.html">Tutorials</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Advanced usage</span></p>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="implementation/index.html">Implementation</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Environment variables</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Development</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="dev/index.html">Contributing to grogupy</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Extras</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="changelog/index.html">Changelog</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bibliography.html">Bibliography</a></li>
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+  <section id="environment-variables">
+<h1>Environment variables<a class="headerlink" href="#environment-variables" title="Link to this heading"></a></h1>
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docs/_build/html/genindex.html

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+  <section id="grogupy-script-for-calculating-magnetic-interactions">
+<span id="module-grogupy"></span><h1>grogupy: Script for calculating magnetic interactions<a class="headerlink" href="#grogupy-script-for-calculating-magnetic-interactions" title="Link to this heading"></a></h1>
+<p>Groupy is a generalized python script based on the Grogu matlab implementation.
+More on the theoretical background can be seen <a class="reference external" href="https://arxiv.org/abs/2309.02558">here</a>.</p>
+<div class="sd-container-fluid sd-sphinx-override sd-mb-4 docutils">
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+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="index.html">grogupy</a>
+      </nav>
+
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="Page navigation">
+  <ul class="wy-breadcrumbs">
+      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li class="breadcrumb-item active">Introduction</li>
+      <li class="wy-breadcrumbs-aside">
+            <a href="_sources/introduction.rst.txt" rel="nofollow"> View page source</a>
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+  <section id="introduction">
+<h1>Introduction<a class="headerlink" href="#introduction" title="Link to this heading"></a></h1>
+<p>The format of the documentation was based on and inspired by <a class="reference external" href="https://sisl.readthedocs.io/en/latest/index.html">sisl</a>.
+1.</p>
+<ol class="arabic simple" start="2">
+<li></li>
+</ol>
+<section id="package">
+<h2>Package<a class="headerlink" href="#package" title="Link to this heading"></a></h2>
+<p>Go to <a class="reference internal" href="quickstart/index.html#quickstart"><span class="std std-ref">installation</span></a>.</p>
+</section>
+<section id="command-line-usage">
+<h2>Command line usage<a class="headerlink" href="#command-line-usage" title="Link to this heading"></a></h2>
+<p>Coming soon…</p>
+</section>
+</section>
+
+
+           </div>
+          </div>
+          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
+        <a href="index.html" class="btn btn-neutral float-left" title="grogupy: Script for calculating magnetic interactions" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="quickstart/index.html" class="btn btn-neutral float-right" title="Quickstart" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+    </div>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2024, grogupy.</p>
+  </div>
+
+  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
+    provided by <a href="https://readthedocs.org">Read the Docs</a>.
+   
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+</footer>
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+  <script>
+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script> 
+
+</body>
+</html>

docs/_build/html/objects.inv

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docs/_build/html/py-modindex.html

@@ -5,21 +5,27 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Python Module Index &mdash; Grogu 0.0.1 documentation</title>
+  <title>Python Module Index &mdash; grogupy 1.0.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="_static/sphinx-design.min.css?v=95c83b7e" />
 
   
       <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=d45e8c67"></script>
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       <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+      <script src="_static/design-tabs.js?v=f930bc37"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
  
 
+    <script>
+      DOCUMENTATION_OPTIONS.COLLAPSE_INDEX = true;
+    </script>
+
 
 </head>
 
@@ -32,7 +38,7 @@
           
           
           <a href="index.html" class="icon icon-home">
-            Grogu
+            grogupy
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
@@ -42,9 +48,29 @@
   </form>
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
-              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+              <p class="caption" role="heading"><span class="caption-text">Getting started</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="quickstart/index.html">Quickstart</a></li>
+<li class="toctree-l1"><a class="reference internal" href="cite.html">Citing grogupy</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="tutorials/index.html">Tutorials</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Advanced usage</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="implementation/index.html">Implementation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="environment.html">Environment variables</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Development</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="dev/index.html">Contributing to grogupy</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Extras</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="modules.html">src</a></li>
+<li class="toctree-l1"><a class="reference internal" href="changelog/index.html">Changelog</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bibliography.html">Bibliography</a></li>
 </ul>
 
         </div>
@@ -53,7 +79,7 @@
 
     <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
           <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-          <a href="index.html">Grogu</a>
+          <a href="index.html">grogupy</a>
       </nav>
 
       <div class="wy-nav-content">
@@ -82,25 +108,9 @@
      <tr class="cap" id="cap-g"><td></td><td>
        <strong>g</strong></td><td></td></tr>
      <tr>
-       <td><img src="_static/minus.png" class="toggler"
-              id="toggle-1" style="display: none" alt="-" /></td>
-       <td>
-       <a href="grogu.html#module-grogu"><code class="xref">grogu</code></a></td><td>
-       <em></em></td></tr>
-     <tr class="cg-1">
-       <td></td>
-       <td>&#160;&#160;&#160;
-       <a href="grogu.html#module-grogu.example"><code class="xref">grogu.example</code></a></td><td>
-       <em></em></td></tr>
-     <tr class="cg-1">
-       <td></td>
-       <td>&#160;&#160;&#160;
-       <a href="grogu.html#module-grogu.jij"><code class="xref">grogu.jij</code></a></td><td>
-       <em></em></td></tr>
-     <tr class="cg-1">
        <td></td>
-       <td>&#160;&#160;&#160;
-       <a href="grogu.html#module-grogu.useful"><code class="xref">grogu.useful</code></a></td><td>
+       <td>
+       <a href="index.html#module-grogupy"><code class="xref">grogupy</code></a></td><td>
        <em></em></td></tr>
    </table>
 
@@ -112,7 +122,7 @@
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Grogu.</p>
+    <p>&#169; Copyright 2024, grogupy.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

docs/_build/html/quickstart/index.html

@@ -0,0 +1,156 @@
+
+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../">
+<head>
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
+
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Quickstart &mdash; grogupy 1.0.0 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="../_static/sphinx-design.min.css?v=95c83b7e" />
+
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+      <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=8d563738"></script>
+      <script src="../_static/doctools.js?v=9a2dae69"></script>
+      <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+      <script src="../_static/design-tabs.js?v=f930bc37"></script>
+    <script src="../_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" />
+    <link rel="next" title="Citing grogupy" href="../cite.html" />
+    <link rel="prev" title="Introduction" href="../introduction.html" /> 
+</head>
+
+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+
+          
+          
+          <a href="../index.html" class="icon icon-home">
+            grogupy
+          </a>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <p class="caption" role="heading"><span class="caption-text">Getting started</span></p>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="../introduction.html">Introduction</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Quickstart</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#installation">installation</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../cite.html">Citing grogupy</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../tutorials/index.html">Tutorials</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Advanced usage</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../implementation/index.html">Implementation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../environment.html">Environment variables</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Development</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../dev/index.html">Contributing to grogupy</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Extras</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../changelog/index.html">Changelog</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../bibliography.html">Bibliography</a></li>
+</ul>
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../index.html">grogupy</a>
+      </nav>
+
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="Page navigation">
+  <ul class="wy-breadcrumbs">
+      <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li class="breadcrumb-item active">Quickstart</li>
+      <li class="wy-breadcrumbs-aside">
+            <a href="../_sources/quickstart/index.rst.txt" rel="nofollow"> View page source</a>
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+  <section id="quickstart">
+<h1>Quickstart<a class="headerlink" href="#quickstart" title="Link to this heading"></a></h1>
+<section id="installation">
+<h2>installation<a class="headerlink" href="#installation" title="Link to this heading"></a></h2>
+<div class="sd-container-fluid sd-sphinx-override sd-mb-4 docutils">
+<div class="sd-row sd-row-cols-1 sd-row-cols-xs-1 sd-row-cols-sm-2 sd-row-cols-md-2 sd-row-cols-lg-2 sd-g-4 sd-g-xs-4 sd-g-sm-4 sd-g-md-4 sd-g-lg-4 docutils">
+<div class="sd-col sd-d-flex-row sd-col-12 sd-col-xs-12 sd-col-sm-12 sd-col-md-6 sd-col-lg-6 docutils">
+<div class="sd-card sd-sphinx-override sd-w-100 sd-shadow-sm docutils">
+<div class="sd-card-body docutils">
+<div class="sd-card-title sd-font-weight-bold docutils">
+pip</div>
+<p class="sd-card-text">grogupy can be installed via pip from <a class="reference external" href="https://test.pypi.org">Test PyPI</a>.</p>
+</div>
+<div class="sd-card-footer docutils">
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>python3<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>--index-url<span class="w"> </span>https://test.pypi.org/simple/<span class="w"> </span>grogupy
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+</div>
+</div>
+<p>Coming soon…</p>
+</section>
+</section>
+
+
+           </div>
+          </div>
+          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
+        <a href="../introduction.html" class="btn btn-neutral float-left" title="Introduction" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="../cite.html" class="btn btn-neutral float-right" title="Citing grogupy" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+    </div>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2024, grogupy.</p>
+  </div>
+
+  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
+    provided by <a href="https://readthedocs.org">Read the Docs</a>.
+   
+
+</footer>
+        </div>
+      </div>
+    </section>
+  </div>
+  <script>
+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script> 
+
+</body>
+</html>

docs/_build/html/search.html

@@ -5,17 +5,19 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Search &mdash; Grogu 0.0.1 documentation</title>
+  <title>Search &mdash; grogupy 1.0.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="_static/sphinx-design.min.css?v=95c83b7e" />
 
   
     
       <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=d45e8c67"></script>
+      <script src="_static/documentation_options.js?v=8d563738"></script>
       <script src="_static/doctools.js?v=9a2dae69"></script>
       <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+      <script src="_static/design-tabs.js?v=f930bc37"></script>
     <script src="_static/js/theme.js"></script>
     <script src="_static/searchtools.js"></script>
     <script src="_static/language_data.js"></script>
@@ -32,7 +34,7 @@
           
           
           <a href="index.html" class="icon icon-home">
-            Grogu
+            grogupy
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="#" method="get">
@@ -42,9 +44,29 @@
   </form>
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
-              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+              <p class="caption" role="heading"><span class="caption-text">Getting started</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="modules.html">src</a></li>
+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="quickstart/index.html">Quickstart</a></li>
+<li class="toctree-l1"><a class="reference internal" href="cite.html">Citing grogupy</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="tutorials/index.html">Tutorials</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Advanced usage</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="implementation/index.html">Implementation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="environment.html">Environment variables</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Development</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="dev/index.html">Contributing to grogupy</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Extras</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="changelog/index.html">Changelog</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bibliography.html">Bibliography</a></li>
 </ul>
 
         </div>
@@ -53,7 +75,7 @@
 
     <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
           <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-          <a href="index.html">Grogu</a>
+          <a href="index.html">grogupy</a>
       </nav>
 
       <div class="wy-nav-content">
@@ -90,7 +112,7 @@
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Grogu.</p>
+    <p>&#169; Copyright 2024, grogupy.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a