[docs] head

lastralab · Sep 19, 2024 · ae1db0c · ae1db0c
1 parent a305b67
commit ae1db0c
Show file tree

Hide file tree

Showing 10 changed files with 44 additions and 44 deletions.
diff --git a/docs/about.md b/docs/about.md
@@ -8,10 +8,6 @@ For full documentation visit our [wiki](https://github.com/lastralab/ABISSMAL/wi
 
 ABISSMAL is a hardware and software platform for automated behavioral tracking with built-in system monitoring and error logging. ABISSMAL also provides the capacity to make behavioral inferences by integrating data across multiple types of movement sensors. We tested the tracking system by tracking parental care behaviors with captive zebra finches that raised young birds over 50 days. The system operates different modules written in python and managed by Linux Screen sessions scheduled by cron. See the accompanying methods manuscript for more detailed information about ABISSMAL. Our Wiki page has detailed information about how to set up and build hardware, as well as software installation and troubleshooting.
 
-## Github Collaborators
-- Tania Molina (Lead Developer/Project Manager): tanismo[at]lastralab.com
-- Grace Smith-Vidaurre, PhD (Developer): gsvidaurre[at]gmail.com
-
 ## Manuscript in preparation
 Smith-Vidaurre, G., Molina, T., Jarvis, E.D., and Hobson, E.A. (2023). Automated tracking of
 avian parental care behavior. In prep. EcoEvoRxiv preprint: [https://doi.org/10.32942/X2Z60C](https://doi.org/10.32942/X2Z60C)

diff --git a/docs/opensource.md b/docs/opensource.md
@@ -6,7 +6,11 @@ For full documentation visit our [wiki](https://github.com/lastralab/ABISSMAL/wi
 ## Gitflow
 ![abissmal gitflow](https://user-images.githubusercontent.com/22894897/150058257-d3c12516-95c2-45c8-b1d3-2591c44f5616.png)
 
-## Collaborators
+## Current Roles
+- Tania Molina (Lead Developer/Project Manager): [@lastralab](https://github.com/lastralab)
+- Grace Smith-Vidaurre, PhD (PI, Developer, R Lead): [@gsvidaurre](https://github.com/gsvidaurre)
+
+## New collaborators
 
 * Set up a local replicate of the tracking system that is separate from the code owner
 * Make sure that issues that require modifying the same file are merged to avoid conflicts downstream (copy and paste into a single issue, close the other). Alternatively, work on these issues one at a time (after one issue was merged to main)

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -4,13 +4,13 @@ site_url: https://lastralab.github.io/ABISSMAL/site/
 repo_url: https://github.com/lastralab/ABISSMAL
 repo_name: ABISSMAL
 site_author: tanismo
-copyright: 'tanismo, the smith-vidaurre lab'
+copyright: '© tanismo'
 edit_uri: blob/docs/docs
 nav:
-  - Home: index.md
+  - Getting Started: index.md
   - Usage: abissmal.md
   - About: about.md
-  - Open Source: opensource.md
+  - Github Collaboration: opensource.md
 theme: readthedocs
 extra_css:
   - css/extra.css

diff --git a/site/404.html b/site/404.html
@@ -34,7 +34,7 @@
 
       <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
-                <li class="toctree-l1"><a class="reference internal" href="/ABISSMAL/site/.">Home</a>
+                <li class="toctree-l1"><a class="reference internal" href="/ABISSMAL/site/.">Getting Started</a>
                 </li>
               </ul>
               <ul>
@@ -46,7 +46,7 @@
                 </li>
               </ul>
               <ul>
-                <li class="toctree-l1"><a class="reference internal" href="/ABISSMAL/site/opensource/">Open Source</a>
+                <li class="toctree-l1"><a class="reference internal" href="/ABISSMAL/site/opensource/">Github Collaboration</a>
                 </li>
               </ul>
       </div>
@@ -84,7 +84,7 @@ <h1 id="404-page-not-found">404</h1>
 
   <div role="contentinfo">
     <!-- Copyright etc -->
-      <p>tanismo, the smith-vidaurre lab</p>
+      <p>© tanismo</p>
   </div>
 
   Built with <a href="https://www.mkdocs.org/">MkDocs</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>.

diff --git a/site/abissmal/index.html b/site/abissmal/index.html
@@ -41,7 +41,7 @@
 
       <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
-                <li class="toctree-l1"><a class="reference internal" href="..">Home</a>
+                <li class="toctree-l1"><a class="reference internal" href="..">Getting Started</a>
                 </li>
               </ul>
               <ul class="current">
@@ -83,7 +83,7 @@
                 </li>
               </ul>
               <ul>
-                <li class="toctree-l1"><a class="reference internal" href="../opensource/">Open Source</a>
+                <li class="toctree-l1"><a class="reference internal" href="../opensource/">Github Collaboration</a>
                 </li>
               </ul>
       </div>
@@ -215,15 +215,15 @@ <h3 id="blank-display-with-tracking-system-running">Blank display with tracking
             </div>
           </div><footer>
     <div class="rst-footer-buttons" role="navigation" aria-label="Footer Navigation">
-        <a href=".." class="btn btn-neutral float-left" title="Home"><span class="icon icon-circle-arrow-left"></span> Previous</a>
+        <a href=".." class="btn btn-neutral float-left" title="Getting Started"><span class="icon icon-circle-arrow-left"></span> Previous</a>
         <a href="../about/" class="btn btn-neutral float-right" title="About">Next <span class="icon icon-circle-arrow-right"></span></a>
     </div>
 
   <hr/>
 
   <div role="contentinfo">
     <!-- Copyright etc -->
-      <p>tanismo, the smith-vidaurre lab</p>
+      <p>© tanismo</p>
   </div>
 
   Built with <a href="https://www.mkdocs.org/">MkDocs</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>.

diff --git a/site/about/index.html b/site/about/index.html
@@ -41,7 +41,7 @@
 
       <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
-                <li class="toctree-l1"><a class="reference internal" href="..">Home</a>
+                <li class="toctree-l1"><a class="reference internal" href="..">Getting Started</a>
                 </li>
               </ul>
               <ul>
@@ -53,8 +53,6 @@
     <ul class="current">
     <li class="toctree-l2"><a class="reference internal" href="#about">About</a>
     </li>
-    <li class="toctree-l2"><a class="reference internal" href="#github-collaborators">Github Collaborators</a>
-    </li>
     <li class="toctree-l2"><a class="reference internal" href="#manuscript-in-preparation">Manuscript in preparation</a>
         <ul>
     <li class="toctree-l3"><a class="reference internal" href="#ethics-statement">Ethics Statement</a>
@@ -65,7 +63,7 @@
                 </li>
               </ul>
               <ul>
-                <li class="toctree-l1"><a class="reference internal" href="../opensource/">Open Source</a>
+                <li class="toctree-l1"><a class="reference internal" href="../opensource/">Github Collaboration</a>
                 </li>
               </ul>
       </div>
@@ -97,11 +95,6 @@ <h1 id="abissmal">ABISSMAL</h1>
 <p>For full documentation visit our <a href="https://github.com/lastralab/ABISSMAL/wiki">wiki</a></p>
 <h2 id="about">About</h2>
 <p>ABISSMAL is a hardware and software platform for automated behavioral tracking with built-in system monitoring and error logging. ABISSMAL also provides the capacity to make behavioral inferences by integrating data across multiple types of movement sensors. We tested the tracking system by tracking parental care behaviors with captive zebra finches that raised young birds over 50 days. The system operates different modules written in python and managed by Linux Screen sessions scheduled by cron. See the accompanying methods manuscript for more detailed information about ABISSMAL. Our Wiki page has detailed information about how to set up and build hardware, as well as software installation and troubleshooting.</p>
-<h2 id="github-collaborators">Github Collaborators</h2>
-<ul>
-<li>Tania Molina (Lead Developer/Project Manager): tanismo[at]lastralab.com</li>
-<li>Grace Smith-Vidaurre, PhD (Developer): gsvidaurre[at]gmail.com</li>
-</ul>
 <h2 id="manuscript-in-preparation">Manuscript in preparation</h2>
 <p>Smith-Vidaurre, G., Molina, T., Jarvis, E.D., and Hobson, E.A. (2023). Automated tracking of
 avian parental care behavior. In prep. EcoEvoRxiv preprint: <a href="https://doi.org/10.32942/X2Z60C">https://doi.org/10.32942/X2Z60C</a></p>
@@ -112,14 +105,14 @@ <h3 id="ethics-statement">Ethics Statement</h3>
           </div><footer>
     <div class="rst-footer-buttons" role="navigation" aria-label="Footer Navigation">
         <a href="../abissmal/" class="btn btn-neutral float-left" title="Usage"><span class="icon icon-circle-arrow-left"></span> Previous</a>
-        <a href="../opensource/" class="btn btn-neutral float-right" title="Open Source">Next <span class="icon icon-circle-arrow-right"></span></a>
+        <a href="../opensource/" class="btn btn-neutral float-right" title="Github Collaboration">Next <span class="icon icon-circle-arrow-right"></span></a>
     </div>
 
   <hr/>
 
   <div role="contentinfo">
     <!-- Copyright etc -->
-      <p>tanismo, the smith-vidaurre lab</p>
+      <p>© tanismo</p>
   </div>
 
   Built with <a href="https://www.mkdocs.org/">MkDocs</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>.

diff --git a/site/index.html b/site/index.html
@@ -13,7 +13,7 @@
 
       <script>
         // Current page data
-        var mkdocs_page_name = "Home";
+        var mkdocs_page_name = "Getting Started";
         var mkdocs_page_input_path = "index.md";
         var mkdocs_page_url = "/ABISSMAL/site/";
       </script>
@@ -41,7 +41,7 @@
 
       <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
-                <li class="toctree-l1 current"><a class="reference internal current" href="#">Home</a>
+                <li class="toctree-l1 current"><a class="reference internal current" href="#">Getting Started</a>
     <ul class="current">
     <li class="toctree-l2"><a class="reference internal" href="#pre-requisites">Pre-requisites</a>
     </li>
@@ -61,7 +61,7 @@
                 </li>
               </ul>
               <ul>
-                <li class="toctree-l1"><a class="reference internal" href="opensource/">Open Source</a>
+                <li class="toctree-l1"><a class="reference internal" href="opensource/">Github Collaboration</a>
                 </li>
               </ul>
       </div>
@@ -78,7 +78,7 @@
         <div class="rst-content"><div role="navigation" aria-label="breadcrumbs navigation">
   <ul class="wy-breadcrumbs">
     <li><a href="." class="icon icon-home" aria-label="Docs"></a></li>
-      <li class="breadcrumb-item active">Home</li>
+      <li class="breadcrumb-item active">Getting Started</li>
     <li class="wy-breadcrumbs-aside">
           <a href="https://github.com/lastralab/ABISSMAL/blob/docs/docs/index.md">Edit on ABISSMAL</a>
     </li>
@@ -156,7 +156,7 @@ <h2 id="directory-structure">Directory Structure</h2>
 
   <div role="contentinfo">
     <!-- Copyright etc -->
-      <p>tanismo, the smith-vidaurre lab</p>
+      <p>© tanismo</p>
   </div>
 
   Built with <a href="https://www.mkdocs.org/">MkDocs</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>.
@@ -198,5 +198,5 @@ <h2 id="directory-structure">Directory Structure</h2>
 
 <!--
 MkDocs version : 1.6.1
-Build Date UTC : 2024-09-19 19:48:49.505998+00:00
+Build Date UTC : 2024-09-19 20:01:57.268723+00:00
 -->
diff --git a/site/opensource/index.html b/site/opensource/index.html
@@ -5,15 +5,15 @@
     <meta http-equiv="X-UA-Compatible" content="IE=edge" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="author" content="tanismo" /><link rel="canonical" href="https://lastralab.github.io/ABISSMAL/site/opensource/" />
       <link rel="shortcut icon" href="../img/favicon.ico" />
-    <title>Open Source - ABISSMAL Docs</title>
+    <title>Github Collaboration - ABISSMAL Docs</title>
     <link rel="stylesheet" href="../css/theme.css" />
     <link rel="stylesheet" href="../css/theme_extra.css" />
         <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.8.0/styles/github.min.css" />
         <link href="../css/extra.css" rel="stylesheet" />
 
       <script>
         // Current page data
-        var mkdocs_page_name = "Open Source";
+        var mkdocs_page_name = "Github Collaboration";
         var mkdocs_page_input_path = "opensource.md";
         var mkdocs_page_url = "/ABISSMAL/site/opensource/";
       </script>
@@ -41,7 +41,7 @@
 
       <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
-                <li class="toctree-l1"><a class="reference internal" href="..">Home</a>
+                <li class="toctree-l1"><a class="reference internal" href="..">Getting Started</a>
                 </li>
               </ul>
               <ul>
@@ -53,11 +53,13 @@
                 </li>
               </ul>
               <ul class="current">
-                <li class="toctree-l1 current"><a class="reference internal current" href="#">Open Source</a>
+                <li class="toctree-l1 current"><a class="reference internal current" href="#">Github Collaboration</a>
     <ul class="current">
     <li class="toctree-l2"><a class="reference internal" href="#gitflow">Gitflow</a>
     </li>
-    <li class="toctree-l2"><a class="reference internal" href="#collaborators">Collaborators</a>
+    <li class="toctree-l2"><a class="reference internal" href="#current-roles">Current Roles</a>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#new-collaborators">New collaborators</a>
     </li>
     </ul>
                 </li>
@@ -76,7 +78,7 @@
         <div class="rst-content"><div role="navigation" aria-label="breadcrumbs navigation">
   <ul class="wy-breadcrumbs">
     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
-      <li class="breadcrumb-item active">Open Source</li>
+      <li class="breadcrumb-item active">Github Collaboration</li>
     <li class="wy-breadcrumbs-aside">
           <a href="https://github.com/lastralab/ABISSMAL/blob/docs/docs/opensource.md">Edit on ABISSMAL</a>
     </li>
@@ -90,7 +92,12 @@ <h1 id="github-collaboration">Github Collaboration</h1>
 <p>For full documentation visit our <a href="https://github.com/lastralab/ABISSMAL/wiki">wiki</a></p>
 <h2 id="gitflow">Gitflow</h2>
 <p><img alt="abissmal gitflow" src="https://user-images.githubusercontent.com/22894897/150058257-d3c12516-95c2-45c8-b1d3-2591c44f5616.png" /></p>
-<h2 id="collaborators">Collaborators</h2>
+<h2 id="current-roles">Current Roles</h2>
+<ul>
+<li>Tania Molina (Lead Developer/Project Manager): <a href="https://github.com/lastralab">@lastralab</a></li>
+<li>Grace Smith-Vidaurre, PhD (PI, Developer, R Lead): <a href="https://github.com/gsvidaurre">@gsvidaurre</a></li>
+</ul>
+<h2 id="new-collaborators">New collaborators</h2>
 <ul>
 <li>Set up a local replicate of the tracking system that is separate from the code owner</li>
 <li>Make sure that issues that require modifying the same file are merged to avoid conflicts downstream (copy and paste into a single issue, close the other). Alternatively, work on these issues one at a time (after one issue was merged to main)</li>
@@ -138,7 +145,7 @@ <h2>Setup Git credentials before cloning</h2>
 
   <div role="contentinfo">
     <!-- Copyright etc -->
-      <p>tanismo, the smith-vidaurre lab</p>
+      <p>© tanismo</p>
   </div>
 
   Built with <a href="https://www.mkdocs.org/">MkDocs</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>.

diff --git a/site/search.html b/site/search.html
@@ -34,7 +34,7 @@
 
       <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
-                <li class="toctree-l1"><a class="reference internal" href="./.">Home</a>
+                <li class="toctree-l1"><a class="reference internal" href="./.">Getting Started</a>
                 </li>
               </ul>
               <ul>
@@ -46,7 +46,7 @@
                 </li>
               </ul>
               <ul>
-                <li class="toctree-l1"><a class="reference internal" href="./opensource/">Open Source</a>
+                <li class="toctree-l1"><a class="reference internal" href="./opensource/">Github Collaboration</a>
                 </li>
               </ul>
       </div>
@@ -91,7 +91,7 @@ <h1 id="search">Search Results</h1>
 
   <div role="contentinfo">
     <!-- Copyright etc -->
-      <p>tanismo, the smith-vidaurre lab</p>
+      <p>© tanismo</p>
   </div>
 
   Built with <a href="https://www.mkdocs.org/">MkDocs</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>.

diff --git a/site/search/search_index.json b/site/search/search_index.json