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LewisResearchGroup · Jun 11, 2024 · 0870c39 · 0870c39
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diff --git a/404.html b/404.html
@@ -214,11 +214,11 @@
 
 
     <li class="md-nav__item">
-      <a href="/lewisresearchgroup/ms-mint-app/quickstart/" class="md-nav__link">
+      <a href="/lewisresearchgroup/ms-mint-app/install/" class="md-nav__link">
 
 
   <span class="md-ellipsis">
-    Quickstart
+    Installation
   </span>
 
 
@@ -234,11 +234,11 @@
 
 
     <li class="md-nav__item">
-      <a href="/lewisresearchgroup/ms-mint-app/install/" class="md-nav__link">
+      <a href="/lewisresearchgroup/ms-mint-app/quickstart/" class="md-nav__link">
 
 
   <span class="md-ellipsis">
-    Installation
+    Quickstart
   </span>
 
 

diff --git a/developer-notes/index.html b/developer-notes/index.html
@@ -225,11 +225,11 @@
 
 
     <li class="md-nav__item">
-      <a href="../quickstart/" class="md-nav__link">
+      <a href="../install/" class="md-nav__link">
 
 
   <span class="md-ellipsis">
-    Quickstart
+    Installation
   </span>
 
 
@@ -245,11 +245,11 @@
 
 
     <li class="md-nav__item">
-      <a href="../install/" class="md-nav__link">
+      <a href="../quickstart/" class="md-nav__link">
 
 
   <span class="md-ellipsis">
-    Installation
+    Quickstart
   </span>
 
 
@@ -350,10 +350,19 @@
     </label>
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
 
+        <li class="md-nav__item">
+  <a href="#building-and-uploading-the-package" class="md-nav__link">
+    <span class="md-ellipsis">
+      Building and Uploading the Package
+    </span>
+  </a>
+
+</li>
+
         <li class="md-nav__item">
   <a href="#windows-executables" class="md-nav__link">
     <span class="md-ellipsis">
-      Windows executables
+      Windows Executables
     </span>
   </a>
 
@@ -362,16 +371,16 @@
         <li class="md-nav__item">
   <a href="#documentation-deployment" class="md-nav__link">
     <span class="md-ellipsis">
-      Documentation deployment
+      Documentation Deployment
     </span>
   </a>
 
 </li>
 
         <li class="md-nav__item">
-  <a href="#example-nginx-config" class="md-nav__link">
+  <a href="#example-nginx-configuration" class="md-nav__link">
     <span class="md-ellipsis">
-      Example NGINX config
+      Example NGINX Configuration
     </span>
   </a>
 
@@ -431,10 +440,19 @@
     </label>
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
 
+        <li class="md-nav__item">
+  <a href="#building-and-uploading-the-package" class="md-nav__link">
+    <span class="md-ellipsis">
+      Building and Uploading the Package
+    </span>
+  </a>
+
+</li>
+
         <li class="md-nav__item">
   <a href="#windows-executables" class="md-nav__link">
     <span class="md-ellipsis">
-      Windows executables
+      Windows Executables
     </span>
   </a>
 
@@ -443,16 +461,16 @@
         <li class="md-nav__item">
   <a href="#documentation-deployment" class="md-nav__link">
     <span class="md-ellipsis">
-      Documentation deployment
+      Documentation Deployment
     </span>
   </a>
 
 </li>
 
         <li class="md-nav__item">
-  <a href="#example-nginx-config" class="md-nav__link">
+  <a href="#example-nginx-configuration" class="md-nav__link">
     <span class="md-ellipsis">
-      Example NGINX config
+      Example NGINX Configuration
     </span>
   </a>
 
@@ -474,27 +492,59 @@
 
 
 <h1 id="developer-notes">Developer Notes</h1>
-<pre><code>python3 setup.py sdist bdist_wheel
-python3 -m twine upload --repository ms-mint dist/ms*mint-*
+<h2 id="building-and-uploading-the-package">Building and Uploading the Package</h2>
+<p>To build the source distribution and wheel for <code>ms-mint-app</code>, follow these steps:</p>
+<ol>
+<li>Navigate to the root directory of the project.</li>
+<li>Run the following command to create the source distribution (<code>sdist</code>) and wheel (<code>bdist_wheel</code>):</li>
+</ol>
+<pre><code class="language-bash">python3 setup.py sdist bdist_wheel
+</code></pre>
+<p>This will generate distribution archives in the <code>dist</code> directory.</p>
+<ol>
+<li>To upload the built package to the <code>ms-mint</code> repository, use <code>twine</code>. Ensure you have <code>twine</code> installed (<code>pip install twine</code> if not). Then, run:</li>
+</ol>
+<pre><code class="language-bash">python3 -m twine upload --repository ms-mint dist/ms*mint-*
 </code></pre>
-<h2 id="windows-executables">Windows executables</h2>
-<pre><code>cd specfiles &amp;&amp; pyinstaller --noconfirm Mint.spec ..\scripts\Mint.py
+<p>This command will upload all matching distribution files to the specified repository.</p>
+<h2 id="windows-executables">Windows Executables</h2>
+<p>To create Windows executables for the <code>ms-mint</code> application, use <code>pyinstaller</code>. Follow these steps:</p>
+<ol>
+<li>Navigate to the <code>specfiles</code> directory.</li>
+<li>Run the <code>pyinstaller</code> command with the provided specification file:</li>
+</ol>
+<pre><code class="language-bash">cd specfiles &amp;&amp; pyinstaller --noconfirm Mint.spec ..\scripts\Mint.py
 </code></pre>
-<h2 id="documentation-deployment">Documentation deployment</h2>
-<pre><code>mkdocs build &amp;&amp; mkdocs gh-deploy
+<p>This will generate a standalone executable for Windows based on the <code>Mint.spec</code> file.</p>
+<h2 id="documentation-deployment">Documentation Deployment</h2>
+<p>To build and deploy the documentation using <code>mkdocs</code>, follow these steps:</p>
+<ol>
+<li>Ensure you have <code>mkdocs</code> installed (<code>pip install mkdocs</code> if not).</li>
+<li>Run the following commands to build the documentation and deploy it to GitHub Pages:</li>
+</ol>
+<pre><code class="language-bash">mkdocs build &amp;&amp; mkdocs gh-deploy
 </code></pre>
-<h2 id="example-nginx-config">Example NGINX config</h2>
-<p>To run Mint on a remote server you need to setup a remote proxy. </p>
+<p>The <code>mkdocs build</code> command generates the static site in the <code>site</code> directory, and <code>mkdocs gh-deploy</code> pushes it to the <code>gh-pages</code> branch of your GitHub repository.</p>
+<h2 id="example-nginx-configuration">Example NGINX Configuration</h2>
+<p>To run <code>ms-mint</code> on a remote server, you need to set up a reverse proxy using NGINX. Here is an example configuration:</p>
 <pre><code>server {
     ...
     location / {
-        proxy_pass              http://localhost:8080;
+        proxy_pass              http://localhost:8000;
         client_max_body_size    100G;
         proxy_set_header        X-Forwarded-Proto https;
         proxy_set_header        Host $host;
     }
 }
 </code></pre>
+<p>Explanation:</p>
+<ul>
+<li><code>proxy_pass http://localhost:8000;</code>: Forwards all requests to the <code>ms-mint</code> application running on port 8000.</li>
+<li><code>client_max_body_size 100G;</code>: Increases the maximum allowed size of client request bodies to 100GB.</li>
+<li><code>proxy_set_header X-Forwarded-Proto https;</code>: Sets the <code>X-Forwarded-Proto</code> header to <code>https</code>.</li>
+<li><code>proxy_set_header Host $host;</code>: Ensures the <code>Host</code> header from the original request is passed to the proxied server.</li>
+</ul>
+<p>Then start ms-mint via the <code>entrypoint.sh</code> script.</p>
 
 
 

diff --git a/gallery/index.html b/gallery/index.html
@@ -223,11 +223,11 @@
 
 
     <li class="md-nav__item">
-      <a href="../quickstart/" class="md-nav__link">
+      <a href="../install/" class="md-nav__link">
 
 
   <span class="md-ellipsis">
-    Quickstart
+    Installation
   </span>
 
 
@@ -243,11 +243,11 @@
 
 
     <li class="md-nav__item">
-      <a href="../install/" class="md-nav__link">
+      <a href="../quickstart/" class="md-nav__link">
 
 
   <span class="md-ellipsis">
-    Installation
+    Quickstart
   </span>
 
 

diff --git a/gui/index.html b/gui/index.html
@@ -13,7 +13,7 @@
         <link rel="canonical" href="https://github.com/lewisresearchgroup/ms-mint-app/gui/">
 
 
-        <link rel="prev" href="../install/">
+        <link rel="prev" href="../quickstart/">
 
 
         <link rel="next" href="../targets/">
@@ -225,11 +225,11 @@
 
 
     <li class="md-nav__item">
-      <a href="../quickstart/" class="md-nav__link">
+      <a href="../install/" class="md-nav__link">
 
 
   <span class="md-ellipsis">
-    Quickstart
+    Installation
   </span>
 
 
@@ -245,11 +245,11 @@
 
 
     <li class="md-nav__item">
-      <a href="../install/" class="md-nav__link">
+      <a href="../quickstart/" class="md-nav__link">
 
 
   <span class="md-ellipsis">
-    Installation
+    Quickstart
   </span>
 
 

diff --git a/index.html b/index.html
@@ -14,7 +14,7 @@
 
 
 
-        <link rel="next" href="quickstart/">
+        <link rel="next" href="install/">
 
 
       <link rel="icon" href="assets/images/favicon.png">
@@ -248,6 +248,15 @@
     </label>
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
 
+        <li class="md-nav__item">
+  <a href="#links" class="md-nav__link">
+    <span class="md-ellipsis">
+      Links
+    </span>
+  </a>
+
+</li>
+
         <li class="md-nav__item">
   <a href="#quickstart" class="md-nav__link">
     <span class="md-ellipsis">
@@ -308,11 +317,11 @@
 
 
     <li class="md-nav__item">
-      <a href="quickstart/" class="md-nav__link">
+      <a href="install/" class="md-nav__link">
 
 
   <span class="md-ellipsis">
-    Quickstart
+    Installation
   </span>
 
 
@@ -328,11 +337,11 @@
 
 
     <li class="md-nav__item">
-      <a href="install/" class="md-nav__link">
+      <a href="quickstart/" class="md-nav__link">
 
 
   <span class="md-ellipsis">
-    Installation
+    Quickstart
   </span>
 
 
@@ -447,6 +456,15 @@
     </label>
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
 
+        <li class="md-nav__item">
+  <a href="#links" class="md-nav__link">
+    <span class="md-ellipsis">
+      Links
+    </span>
+  </a>
+
+</li>
+
         <li class="md-nav__item">
   <a href="#quickstart" class="md-nav__link">
     <span class="md-ellipsis">
@@ -510,6 +528,12 @@
 <p><img alt="" src="image/MINT-logo.jpg" /></p>
 <h1 id="mint-metabolomics-integrator">MINT - Metabolomics Integrator</h1>
 <p>MINT is a sophisticated post-processing tool designed for <em>liquid chromatography-mass spectrometry</em> (LCMS) based <em>metabolomics</em>. Metabolomics, the comprehensive study of small molecule metabolites within biological samples, plays a pivotal role in biomedical research. These metabolites serve as crucial biomarkers for disease diagnostics, therapeutic interventions, and pathogen identification, including methicillin-resistant <em>Staphylococcus aureus</em> (MRSA).</p>
+<h2 id="links">Links</h2>
+<ul>
+<li><a href="https://github.com/LewisResearchGroup/ms-mint-app">GitHub repository of ms-mint-app (the browser based application)</a></li>
+<li><a href="https://github.com/LewisResearchGroup/ms-mint">GitHub repository of ms-mint (the Python package)</a></li>
+<li><a href="https://github.com/sorenwacker/ms-mint-plugin-template">GitHub repository of ms-mint-app plugin template</a></li>
+</ul>
 <h2 id="quickstart">Quickstart</h2>
 <p>Check out the <a href="quickstart/">Quickstart</a> to jump right into it.</p>
 <h2 id="what-is-lcms">What is LCMS?</h2>