From 7b702d7e447c62a6a31e2ead232bb7f98514ddd3 Mon Sep 17 00:00:00 2001
From: Sanjay C Nagi <sanjay.c.nagi@gmail.com>
Date: Tue, 14 May 2024 09:38:58 +0100
Subject: [PATCH] Update documentation

---
 _sources/notebooks/data_access.ipynb        |  46 ++
 genindex.html                               |   1 +
 landing-page.html                           |   2 +
 notebooks/api.html                          |   1 +
 notebooks/data_access.html                  | 534 ++++++++++++++++++++
 notebooks/notebooks.html                    |   7 +-
 notebooks/troubleshooting_contributing.html |   7 +-
 objects.inv                                 | Bin 404 -> 426 bytes
 search.html                                 |   1 +
 searchindex.js                              |   2 +-
 10 files changed, 594 insertions(+), 7 deletions(-)
 create mode 100644 _sources/notebooks/data_access.ipynb
 create mode 100644 notebooks/data_access.html

diff --git a/_sources/notebooks/data_access.ipynb b/_sources/notebooks/data_access.ipynb
new file mode 100644
index 0000000..57fc969
--- /dev/null
+++ b/_sources/notebooks/data_access.ipynb
@@ -0,0 +1,46 @@
+{
+ "cells": [
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "id": "cce4eedb",
+   "metadata": {},
+   "source": [
+    "# Data Access\n",
+    "\n",
+    "## Accessing MalariaGEN Vector Observatory Data\n",
+    "\n",
+    "AnoPrimer relies on the malariagen_data package to access genetic variation data from wild whole-genome sequenced specimens of *An. gambiae* and *An. funestus*. Recently, the access process for the MalariaGEN Vector Observatory data has been updated. \n",
+    "\n",
+    "If using AnoPrimer within Google Colab, you will be asked to sign-in with your malariagen_data associated credentials. If using AnoPrimer elsewhere, you will need to set up your credentials as described in the [malariagen_data documentation](https://malariagen.github.io/vector-data/vobs/vobs-data-access.html).\n",
+    "\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.9 (default, Nov 25 2022, 14:10:45) \n[GCC 8.4.0]"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "31f2aee4e71d21fbe5cf8b01ff0e069b9275f58929596ceb00d14d90e3e16cd6"
+   }
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/genindex.html b/genindex.html
index 04f0bf8..b8908fe 100644
--- a/genindex.html
+++ b/genindex.html
@@ -190,6 +190,7 @@
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="notebooks/api.html">AnoPrimer API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/notebooks.html">Notebooks</a></li>
+<li class="toctree-l1"><a class="reference internal" href="notebooks/data_access.html">Data Access</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/troubleshooting_contributing.html">Troubleshooting</a></li>
 
 </ul>
diff --git a/landing-page.html b/landing-page.html
index 24bdb8e..594fa30 100644
--- a/landing-page.html
+++ b/landing-page.html
@@ -192,6 +192,7 @@
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="notebooks/api.html">AnoPrimer API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/notebooks.html">Notebooks</a></li>
+<li class="toctree-l1"><a class="reference internal" href="notebooks/data_access.html">Data Access</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/troubleshooting_contributing.html">Troubleshooting</a></li>
 
 </ul>
@@ -398,6 +399,7 @@ <h1>AnoPrimer<a class="headerlink" href="#anoprimer" title="Permalink to this he
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/api.html">AnoPrimer API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/notebooks.html">Notebooks</a></li>
+<li class="toctree-l1"><a class="reference internal" href="notebooks/data_access.html">Data Access</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/troubleshooting_contributing.html">Troubleshooting</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/troubleshooting_contributing.html#contributing">Contributing</a></li>
 </ul>
diff --git a/notebooks/api.html b/notebooks/api.html
index 0cc1ecf..37983b6 100644
--- a/notebooks/api.html
+++ b/notebooks/api.html
@@ -193,6 +193,7 @@
 <ul class="current nav bd-sidenav">
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">AnoPrimer API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks.html">Notebooks</a></li>
+<li class="toctree-l1"><a class="reference internal" href="data_access.html">Data Access</a></li>
 <li class="toctree-l1"><a class="reference internal" href="troubleshooting_contributing.html">Troubleshooting</a></li>
 
 </ul>
diff --git a/notebooks/data_access.html b/notebooks/data_access.html
new file mode 100644
index 0000000..bc69a6b
--- /dev/null
+++ b/notebooks/data_access.html
@@ -0,0 +1,534 @@
+
+
+<!DOCTYPE html>
+
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+<html >
+
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+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
+
+    <title>Data Access</title>
+  
+  
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+  <script data-cfasync="false">
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+    <script>var togglebuttonSelector = '.toggle, .admonition.dropdown';</script>
+    <script src="../_static/design-tabs.js"></script>
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+              
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+<div id="jb-print-docs-body" class="onlyprint">
+    <h1>Data Access</h1>
+    <!-- Table of contents -->
+    <div id="print-main-content">
+        <div id="jb-print-toc">
+            
+            <div>
+                <h2> Contents </h2>
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+            <nav aria-label="Page">
+                <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#accessing-malariagen-vector-observatory-data">Accessing MalariaGEN Vector Observatory Data</a></li>
+</ul>
+            </nav>
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+<div id="searchbox"></div>
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+                  
+  <section class="tex2jax_ignore mathjax_ignore" id="data-access">
+<h1>Data Access<a class="headerlink" href="#data-access" title="Permalink to this headline">#</a></h1>
+<section id="accessing-malariagen-vector-observatory-data">
+<h2>Accessing MalariaGEN Vector Observatory Data<a class="headerlink" href="#accessing-malariagen-vector-observatory-data" title="Permalink to this headline">#</a></h2>
+<p>AnoPrimer relies on the malariagen_data package to access genetic variation data from wild whole-genome sequenced specimens of <em>An. gambiae</em> and <em>An. funestus</em>. Recently, the access process for the MalariaGEN Vector Observatory data has been updated.</p>
+<p>If using AnoPrimer within Google Colab, you will be asked to sign-in with your malariagen_data associated credentials. If using AnoPrimer elsewhere, you will need to set up your credentials as described in the <a class="reference external" href="https://malariagen.github.io/vector-data/vobs/vobs-data-access.html">malariagen_data documentation</a>.</p>
+</section>
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+  <div class="sidebar-secondary-item">
+  <div class="page-toc tocsection onthispage">
+    <i class="fa-solid fa-list"></i> Contents
+  </div>
+  <nav class="bd-toc-nav page-toc">
+    <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#accessing-malariagen-vector-observatory-data">Accessing MalariaGEN Vector Observatory Data</a></li>
+</ul>
+  </nav></div>
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+          <footer class="bd-footer-content">
+            
+<div class="bd-footer-content__inner container">
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+    
+<p class="component-author">
+By Sanjay Curtis Nagi
+</p>
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+  <div class="footer-item">
+    
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+    
+      © Copyright 2023.
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diff --git a/notebooks/notebooks.html b/notebooks/notebooks.html
index 041d399..6f597ca 100644
--- a/notebooks/notebooks.html
+++ b/notebooks/notebooks.html
@@ -97,7 +97,7 @@
     <script>DOCUMENTATION_OPTIONS.pagename = 'notebooks/notebooks';</script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="Troubleshooting" href="troubleshooting_contributing.html" />
+    <link rel="next" title="Data Access" href="data_access.html" />
     <link rel="prev" title="AnoPrimer API" href="api.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="None"/>
@@ -193,6 +193,7 @@
 <ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="api.html">AnoPrimer API</a></li>
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">Notebooks</a></li>
+<li class="toctree-l1"><a class="reference internal" href="data_access.html">Data Access</a></li>
 <li class="toctree-l1"><a class="reference internal" href="troubleshooting_contributing.html">Troubleshooting</a></li>
 
 </ul>
@@ -442,11 +443,11 @@ <h1>Notebooks<a class="headerlink" href="#notebooks" title="Permalink to this he
       </div>
     </a>
     <a class="right-next"
-       href="troubleshooting_contributing.html"
+       href="data_access.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">Troubleshooting</p>
+        <p class="prev-next-title">Data Access</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
     </a>
diff --git a/notebooks/troubleshooting_contributing.html b/notebooks/troubleshooting_contributing.html
index e9481de..3e59604 100644
--- a/notebooks/troubleshooting_contributing.html
+++ b/notebooks/troubleshooting_contributing.html
@@ -97,7 +97,7 @@
     <script>DOCUMENTATION_OPTIONS.pagename = 'notebooks/troubleshooting_contributing';</script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="prev" title="Notebooks" href="notebooks.html" />
+    <link rel="prev" title="Data Access" href="data_access.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="None"/>
   </head>
@@ -192,6 +192,7 @@
 <ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="api.html">AnoPrimer API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks.html">Notebooks</a></li>
+<li class="toctree-l1"><a class="reference internal" href="data_access.html">Data Access</a></li>
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">Troubleshooting</a></li>
 
 </ul>
@@ -444,12 +445,12 @@ <h1>Contributing<a class="headerlink" href="#contributing" title="Permalink to t
     <div class="footer-article-item"><!-- Previous / next buttons -->
 <div class="prev-next-area">
     <a class="left-prev"
-       href="notebooks.html"
+       href="data_access.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">Notebooks</p>
+        <p class="prev-next-title">Data Access</p>
       </div>
     </a>
 </div></div>
diff --git a/objects.inv b/objects.inv
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diff --git a/search.html b/search.html
index 55dd79e..51d51cf 100644
--- a/search.html
+++ b/search.html
@@ -192,6 +192,7 @@
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="notebooks/api.html">AnoPrimer API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/notebooks.html">Notebooks</a></li>
+<li class="toctree-l1"><a class="reference internal" href="notebooks/data_access.html">Data Access</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/troubleshooting_contributing.html">Troubleshooting</a></li>
 
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diff --git a/searchindex.js b/searchindex.js
index 3378717..d40c952 100644
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