chore(docs): render docs

graeter-group · Nov 5, 2024 · 98d1c36 · 98d1c36
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diff --git a/docs/_reference/analysis.html b/docs/_reference/analysis.html
@@ -66,6 +66,7 @@
 <meta name="quarto:offset" content="../">
 <link href="../_reference/utils.html" rel="next">
 <link href="../_reference/plugins.html" rel="prev">
+<link href=".././www/favicon.png" rel="icon" type="image/png">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -187,6 +188,11 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
+      <a href="../index.html" class="sidebar-logo-link">
+      <img src=".././www/kimmdy_logo.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
+      </a>
+      </div>
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">

diff --git a/docs/_reference/cmd.html b/docs/_reference/cmd.html
@@ -66,6 +66,7 @@
 <meta name="quarto:offset" content="../">
 <link href="../_reference/topology.topology.html" rel="next">
 <link href="../guide/references/cmd_ref.html" rel="prev">
+<link href=".././www/favicon.png" rel="icon" type="image/png">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -187,6 +188,11 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
+      <a href="../index.html" class="sidebar-logo-link">
+      <img src=".././www/kimmdy_logo.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
+      </a>
+      </div>
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">

diff --git a/docs/_reference/config.html b/docs/_reference/config.html
@@ -66,6 +66,7 @@
 <meta name="quarto:offset" content="../">
 <link href="../_reference/kmc.html" rel="next">
 <link href="../_reference/coordinates.html" rel="prev">
+<link href=".././www/favicon.png" rel="icon" type="image/png">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -187,6 +188,11 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
+      <a href="../index.html" class="sidebar-logo-link">
+      <img src=".././www/kimmdy_logo.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
+      </a>
+      </div>
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">

diff --git a/docs/_reference/constants.html b/docs/_reference/constants.html
@@ -32,6 +32,7 @@
 <meta name="quarto:offset" content="../">
 <link href="../_reference/coordinates.html" rel="next">
 <link href="../_reference/dummyreaction.reaction.DummyReaction.html" rel="prev">
+<link href=".././www/favicon.png" rel="icon" type="image/png">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -153,6 +154,11 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
+      <a href="../index.html" class="sidebar-logo-link">
+      <img src=".././www/kimmdy_logo.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
+      </a>
+      </div>
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">

diff --git a/docs/_reference/coordinates.html b/docs/_reference/coordinates.html
@@ -66,6 +66,7 @@
 <meta name="quarto:offset" content="../">
 <link href="../_reference/config.html" rel="next">
 <link href="../_reference/constants.html" rel="prev">
+<link href=".././www/favicon.png" rel="icon" type="image/png">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -187,6 +188,11 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
+      <a href="../index.html" class="sidebar-logo-link">
+      <img src=".././www/kimmdy_logo.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
+      </a>
+      </div>
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">

diff --git a/docs/_reference/dummyreaction.reaction.DummyReaction.html b/docs/_reference/dummyreaction.reaction.DummyReaction.html
@@ -66,6 +66,7 @@
 <meta name="quarto:offset" content="../">
 <link href="../_reference/constants.html" rel="next">
 <link href="../_reference/hat_naive.reaction.NaiveHAT.html" rel="prev">
+<link href=".././www/favicon.png" rel="icon" type="image/png">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -187,6 +188,11 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
+      <a href="../index.html" class="sidebar-logo-link">
+      <img src=".././www/kimmdy_logo.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
+      </a>
+      </div>
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">

diff --git a/docs/_reference/hat_naive.reaction.NaiveHAT.html b/docs/_reference/hat_naive.reaction.NaiveHAT.html
@@ -66,6 +66,7 @@
 <meta name="quarto:offset" content="../">
 <link href="../_reference/dummyreaction.reaction.DummyReaction.html" rel="next">
 <link href="../_reference/homolysis.reaction.Homolysis.html" rel="prev">
+<link href=".././www/favicon.png" rel="icon" type="image/png">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -187,6 +188,11 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
+      <a href="../index.html" class="sidebar-logo-link">
+      <img src=".././www/kimmdy_logo.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
+      </a>
+      </div>
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">

diff --git a/docs/_reference/homolysis.reaction.Homolysis.html b/docs/_reference/homolysis.reaction.Homolysis.html
@@ -66,6 +66,7 @@
 <meta name="quarto:offset" content="../">
 <link href="../_reference/hat_naive.reaction.NaiveHAT.html" rel="next">
 <link href="../_reference/parsing.TopologyDict.html" rel="prev">
+<link href=".././www/favicon.png" rel="icon" type="image/png">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -187,6 +188,11 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
+      <a href="../index.html" class="sidebar-logo-link">
+      <img src=".././www/kimmdy_logo.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
+      </a>
+      </div>
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">

diff --git a/docs/_reference/index.html b/docs/_reference/index.html
@@ -32,6 +32,7 @@
 <meta name="quarto:offset" content="../">
 <link href="../guide/references/input.html" rel="next">
 <link href="../guide/explanation/topology.html" rel="prev">
+<link href=".././www/favicon.png" rel="icon" type="image/png">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -153,6 +154,11 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
+      <a href="../index.html" class="sidebar-logo-link">
+      <img src=".././www/kimmdy_logo.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
+      </a>
+      </div>
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">

diff --git a/docs/_reference/kmc.html b/docs/_reference/kmc.html
@@ -66,6 +66,7 @@
 <meta name="quarto:offset" content="../">
 <link href="../_reference/parsing.html" rel="next">
 <link href="../_reference/config.html" rel="prev">
+<link href=".././www/favicon.png" rel="icon" type="image/png">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -187,6 +188,11 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
+      <a href="../index.html" class="sidebar-logo-link">
+      <img src=".././www/kimmdy_logo.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
+      </a>
+      </div>
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">

diff --git a/docs/_reference/parsing.TopologyDict.html b/docs/_reference/parsing.TopologyDict.html
@@ -32,6 +32,7 @@
 <meta name="quarto:offset" content="../">
 <link href="../_reference/homolysis.reaction.Homolysis.html" rel="next">
 <link href="../_reference/topology.atomic.html" rel="prev">
+<link href=".././www/favicon.png" rel="icon" type="image/png">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -153,6 +154,11 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
+      <a href="../index.html" class="sidebar-logo-link">
+      <img src=".././www/kimmdy_logo.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
+      </a>
+      </div>
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">

diff --git a/docs/_reference/parsing.html b/docs/_reference/parsing.html
@@ -66,6 +66,7 @@
 <meta name="quarto:offset" content="../">
 <link href="../_reference/runmanager.html" rel="next">
 <link href="../_reference/kmc.html" rel="prev">
+<link href=".././www/favicon.png" rel="icon" type="image/png">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -187,6 +188,11 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
+      <a href="../index.html" class="sidebar-logo-link">
+      <img src=".././www/kimmdy_logo.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
+      </a>
+      </div>
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">

diff --git a/docs/_reference/plugins.html b/docs/_reference/plugins.html
@@ -66,6 +66,7 @@
 <meta name="quarto:offset" content="../">
 <link href="../_reference/analysis.html" rel="next">
 <link href="../_reference/recipe.html" rel="prev">
+<link href=".././www/favicon.png" rel="icon" type="image/png">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -187,6 +188,11 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
+      <a href="../index.html" class="sidebar-logo-link">
+      <img src=".././www/kimmdy_logo.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
+      </a>
+      </div>
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">

diff --git a/docs/_reference/recipe.html b/docs/_reference/recipe.html
@@ -66,6 +66,7 @@
 <meta name="quarto:offset" content="../">
 <link href="../_reference/plugins.html" rel="next">
 <link href="../_reference/tasks.html" rel="prev">
+<link href=".././www/favicon.png" rel="icon" type="image/png">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -187,6 +188,11 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
+      <a href="../index.html" class="sidebar-logo-link">
+      <img src=".././www/kimmdy_logo.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
+      </a>
+      </div>
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">

diff --git a/docs/_reference/runmanager.html b/docs/_reference/runmanager.html
@@ -66,6 +66,7 @@
 <meta name="quarto:offset" content="../">
 <link href="../_reference/tasks.html" rel="next">
 <link href="../_reference/parsing.html" rel="prev">
+<link href=".././www/favicon.png" rel="icon" type="image/png">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -187,6 +188,11 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
+      <a href="../index.html" class="sidebar-logo-link">
+      <img src=".././www/kimmdy_logo.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
+      </a>
+      </div>
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">

diff --git a/docs/_reference/schema.html b/docs/_reference/schema.html
@@ -64,6 +64,7 @@
 <script src="../site_libs/quarto-search/fuse.min.js"></script>
 <script src="../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../">
+<link href=".././www/favicon.png" rel="icon" type="image/png">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -185,6 +186,11 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
+      <a href="../index.html" class="sidebar-logo-link">
+      <img src=".././www/kimmdy_logo.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
+      </a>
+      </div>
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">

diff --git a/docs/_reference/tasks.html b/docs/_reference/tasks.html
@@ -66,6 +66,7 @@
 <meta name="quarto:offset" content="../">
 <link href="../_reference/recipe.html" rel="next">
 <link href="../_reference/runmanager.html" rel="prev">
+<link href=".././www/favicon.png" rel="icon" type="image/png">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -187,6 +188,11 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
+      <a href="../index.html" class="sidebar-logo-link">
+      <img src=".././www/kimmdy_logo.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
+      </a>
+      </div>
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">

diff --git a/docs/_reference/tools.html b/docs/_reference/tools.html
@@ -65,6 +65,7 @@
 <script src="../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../">
 <link href="../_reference/utils.html" rel="prev">
+<link href=".././www/favicon.png" rel="icon" type="image/png">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -186,6 +187,11 @@
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
+    <div class="pt-lg-2 mt-2 text-left sidebar-header">
+      <a href="../index.html" class="sidebar-logo-link">
+      <img src=".././www/kimmdy_logo.png" alt="" class="sidebar-logo py-0 d-lg-inline d-none">
+      </a>
+      </div>
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">