Update documentation

cc-ats · Dec 8, 2023 · 7c05f8a · 7c05f8a
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diff --git a/.buildinfo b/.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.
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+config: b0faa91d031557db9658431bb536ec40
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/ColabFold/AlphaFold2.html b/ColabFold/AlphaFold2.html
@@ -136,8 +136,14 @@
 
 
 
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+    <img src="../_static/schrodinger_cat_white_bbg.png" class="logo__image only-light" alt="Logo image"/>
+    <script>document.write(`<img src="../_static/schrodinger_cat_white_bbg.png" class="logo__image only-dark" alt="Logo image"/>`);</script>
 
-    <p class="title logo__title">Tutorials</p>
 
 </a></div>
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">
@@ -207,7 +213,7 @@
 
 
 
-      <li><a href="https://github.com/executablebooks/jupyter-book" target="_blank"
+      <li><a href="https://github.com/cc-ats/Tutorials" target="_blank"
    class="btn btn-sm btn-source-repository-button dropdown-item"
    title="Source repository"
    data-bs-placement="left" data-bs-toggle="tooltip"
@@ -224,7 +230,7 @@
 
 
 
-      <li><a href="https://github.com/executablebooks/jupyter-book/issues/new?title=Issue%20on%20page%20%2FColabFold/AlphaFold2.html&body=Your%20issue%20content%20here." target="_blank"
+      <li><a href="https://github.com/cc-ats/Tutorials/issues/new?title=Issue%20on%20page%20%2FColabFold/AlphaFold2.html&body=Your%20issue%20content%20here." target="_blank"
    class="btn btn-sm btn-source-issues-button dropdown-item"
    title="Open an issue"
    data-bs-placement="left" data-bs-toggle="tooltip"

diff --git a/ColabFold/Tutorial_Monomer.html b/ColabFold/Tutorial_Monomer.html
@@ -137,8 +137,14 @@
 
 
 
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+    <img src="../_static/schrodinger_cat_white_bbg.png" class="logo__image only-light" alt="Logo image"/>
+    <script>document.write(`<img src="../_static/schrodinger_cat_white_bbg.png" class="logo__image only-dark" alt="Logo image"/>`);</script>
 
-    <p class="title logo__title">Tutorials</p>
 
 </a></div>
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">
@@ -208,7 +214,7 @@
 
 
 
-      <li><a href="https://github.com/executablebooks/jupyter-book" target="_blank"
+      <li><a href="https://github.com/cc-ats/Tutorials" target="_blank"
    class="btn btn-sm btn-source-repository-button dropdown-item"
    title="Source repository"
    data-bs-placement="left" data-bs-toggle="tooltip"
@@ -225,7 +231,7 @@
 
 
 
-      <li><a href="https://github.com/executablebooks/jupyter-book/issues/new?title=Issue%20on%20page%20%2FColabFold/Tutorial_Monomer.html&body=Your%20issue%20content%20here." target="_blank"
+      <li><a href="https://github.com/cc-ats/Tutorials/issues/new?title=Issue%20on%20page%20%2FColabFold/Tutorial_Monomer.html&body=Your%20issue%20content%20here." target="_blank"
    class="btn btn-sm btn-source-issues-button dropdown-item"
    title="Open an issue"
    data-bs-placement="left" data-bs-toggle="tooltip"

diff --git a/ColabFold/Tutorial_Multimer.html b/ColabFold/Tutorial_Multimer.html
@@ -135,8 +135,14 @@
 
 
 
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+    <img src="../_static/schrodinger_cat_white_bbg.png" class="logo__image only-light" alt="Logo image"/>
+    <script>document.write(`<img src="../_static/schrodinger_cat_white_bbg.png" class="logo__image only-dark" alt="Logo image"/>`);</script>
 
-    <p class="title logo__title">Tutorials</p>
 
 </a></div>
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">
@@ -206,7 +212,7 @@
 
 
 
-      <li><a href="https://github.com/executablebooks/jupyter-book" target="_blank"
+      <li><a href="https://github.com/cc-ats/Tutorials" target="_blank"
    class="btn btn-sm btn-source-repository-button dropdown-item"
    title="Source repository"
    data-bs-placement="left" data-bs-toggle="tooltip"
@@ -223,7 +229,7 @@
 
 
 
-      <li><a href="https://github.com/executablebooks/jupyter-book/issues/new?title=Issue%20on%20page%20%2FColabFold/Tutorial_Multimer.html&body=Your%20issue%20content%20here." target="_blank"
+      <li><a href="https://github.com/cc-ats/Tutorials/issues/new?title=Issue%20on%20page%20%2FColabFold/Tutorial_Multimer.html&body=Your%20issue%20content%20here." target="_blank"
    class="btn btn-sm btn-source-issues-button dropdown-item"
    title="Open an issue"
    data-bs-placement="left" data-bs-toggle="tooltip"

diff --git a/ColabFold/old/ColabFold_AF2_mmseqs2.html b/ColabFold/old/ColabFold_AF2_mmseqs2.html
@@ -135,8 +135,14 @@
 
 
 
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+    <img src="../../_static/schrodinger_cat_white_bbg.png" class="logo__image only-light" alt="Logo image"/>
+    <script>document.write(`<img src="../../_static/schrodinger_cat_white_bbg.png" class="logo__image only-dark" alt="Logo image"/>`);</script>
 
-    <p class="title logo__title">Tutorials</p>
 
 </a></div>
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">
@@ -206,7 +212,7 @@
 
 
 
-      <li><a href="https://github.com/executablebooks/jupyter-book" target="_blank"
+      <li><a href="https://github.com/cc-ats/Tutorials" target="_blank"
    class="btn btn-sm btn-source-repository-button dropdown-item"
    title="Source repository"
    data-bs-placement="left" data-bs-toggle="tooltip"
@@ -223,7 +229,7 @@
 
 
 
-      <li><a href="https://github.com/executablebooks/jupyter-book/issues/new?title=Issue%20on%20page%20%2FColabFold/old/ColabFold_AF2_mmseqs2.html&body=Your%20issue%20content%20here." target="_blank"
+      <li><a href="https://github.com/cc-ats/Tutorials/issues/new?title=Issue%20on%20page%20%2FColabFold/old/ColabFold_AF2_mmseqs2.html&body=Your%20issue%20content%20here." target="_blank"
    class="btn btn-sm btn-source-issues-button dropdown-item"
    title="Open an issue"
    data-bs-placement="left" data-bs-toggle="tooltip"

diff --git a/_static/logo.png b/_static/logo.png
diff --git a/_static/schrodinger_cat_white_bbg.png b/_static/schrodinger_cat_white_bbg.png
diff --git a/genindex.html b/genindex.html
@@ -134,8 +134,14 @@
 
 
 
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+    <img src="_static/schrodinger_cat_white_bbg.png" class="logo__image only-light" alt="Logo image"/>
+    <script>document.write(`<img src="_static/schrodinger_cat_white_bbg.png" class="logo__image only-dark" alt="Logo image"/>`);</script>
 
-    <p class="title logo__title">Tutorials</p>
 
 </a></div>
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">
@@ -205,7 +211,7 @@
 
 
 
-      <li><a href="https://github.com/executablebooks/jupyter-book" target="_blank"
+      <li><a href="https://github.com/cc-ats/Tutorials" target="_blank"
    class="btn btn-sm btn-source-repository-button dropdown-item"
    title="Source repository"
    data-bs-placement="left" data-bs-toggle="tooltip"
@@ -222,7 +228,7 @@
 
 
 
-      <li><a href="https://github.com/executablebooks/jupyter-book/issues/new?title=Issue%20on%20page%20%2Fgenindex.html&body=Your%20issue%20content%20here." target="_blank"
+      <li><a href="https://github.com/cc-ats/Tutorials/issues/new?title=Issue%20on%20page%20%2Fgenindex.html&body=Your%20issue%20content%20here." target="_blank"
    class="btn btn-sm btn-source-issues-button dropdown-item"
    title="Open an issue"
    data-bs-placement="left" data-bs-toggle="tooltip"

diff --git a/index.html b/index.html
@@ -136,8 +136,14 @@
 
 
 
+
+
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+
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+    <img src="_static/schrodinger_cat_white_bbg.png" class="logo__image only-light" alt="Logo image"/>
+    <script>document.write(`<img src="_static/schrodinger_cat_white_bbg.png" class="logo__image only-dark" alt="Logo image"/>`);</script>
 
-    <p class="title logo__title">Tutorials</p>
 
 </a></div>
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">
@@ -207,7 +213,7 @@
 
 
 
-      <li><a href="https://github.com/executablebooks/jupyter-book" target="_blank"
+      <li><a href="https://github.com/cc-ats/Tutorials" target="_blank"
    class="btn btn-sm btn-source-repository-button dropdown-item"
    title="Source repository"
    data-bs-placement="left" data-bs-toggle="tooltip"
@@ -224,7 +230,7 @@
 
 
 
-      <li><a href="https://github.com/executablebooks/jupyter-book/issues/new?title=Issue%20on%20page%20%2Findex.html&body=Your%20issue%20content%20here." target="_blank"
+      <li><a href="https://github.com/cc-ats/Tutorials/issues/new?title=Issue%20on%20page%20%2Findex.html&body=Your%20issue%20content%20here." target="_blank"
    class="btn btn-sm btn-source-issues-button dropdown-item"
    title="Open an issue"
    data-bs-placement="left" data-bs-toggle="tooltip"

diff --git a/reports/ColabFold/AlphaFold2.err.log b/reports/ColabFold/AlphaFold2.err.log
diff --git a/search.html b/search.html
@@ -136,8 +136,14 @@
 
 
 
+
+
+
+
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+    <img src="_static/schrodinger_cat_white_bbg.png" class="logo__image only-light" alt="Logo image"/>
+    <script>document.write(`<img src="_static/schrodinger_cat_white_bbg.png" class="logo__image only-dark" alt="Logo image"/>`);</script>
 
-    <p class="title logo__title">Tutorials</p>
 
 </a></div>
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">
@@ -207,7 +213,7 @@
 
 
 
-      <li><a href="https://github.com/executablebooks/jupyter-book" target="_blank"
+      <li><a href="https://github.com/cc-ats/Tutorials" target="_blank"
    class="btn btn-sm btn-source-repository-button dropdown-item"
    title="Source repository"
    data-bs-placement="left" data-bs-toggle="tooltip"
@@ -224,7 +230,7 @@
 
 
 
-      <li><a href="https://github.com/executablebooks/jupyter-book/issues/new?title=Issue%20on%20page%20%2Fsearch.html&body=Your%20issue%20content%20here." target="_blank"
+      <li><a href="https://github.com/cc-ats/Tutorials/issues/new?title=Issue%20on%20page%20%2Fsearch.html&body=Your%20issue%20content%20here." target="_blank"
    class="btn btn-sm btn-source-issues-button dropdown-item"
    title="Open an issue"
    data-bs-placement="left" data-bs-toggle="tooltip"