chore(main): release 6.2.5 (#393)

* chore(main): release 6.2.5

* chore(docs): render docs

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>

Author: github-actions[bot]

CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+## [6.2.5](https://github.com/hits-mbm-dev/kimmdy/compare/v6.2.4...v6.2.5) (2024-02-27)
+
+
+### Bug Fixes
+
+* integration tests ([#390](https://github.com/hits-mbm-dev/kimmdy/issues/390)) ([526d888](https://github.com/hits-mbm-dev/kimmdy/commit/526d888d9198b450a654a5a9de03429a5c6f2e95))
+
 ## [6.2.4](https://github.com/hits-mbm-dev/kimmdy/compare/v6.2.3...v6.2.4) (2024-02-27)
 
 

docs/guide/explanation/index.html

@@ -537,7 +537,7 @@ <h1 class="title">Explanations</h1>
 </tr>
 </thead>
 <tbody class="list">
-<tr data-index="0" data-listing-file-modified-sort="1709047597697" data-listing-reading-time-sort="1" data-listing-title-sort="Visualize Topologies" data-listing-filename-sort="topology.qmd">
+<tr data-index="0" data-listing-file-modified-sort="1709062041706" data-listing-reading-time-sort="1" data-listing-title-sort="Visualize Topologies" data-listing-filename-sort="topology.qmd">
 <td>
 <a href="../../guide/explanation/topology.html" class="title listing-title">Visualize Topologies</a>
 </td>

docs/guide/how-to/index.html

@@ -537,39 +537,39 @@ <h1 class="title">How-To</h1>
 </tr>
 </thead>
 <tbody class="list">
-<tr data-index="0" data-listing-file-modified-sort="1709047597697" data-listing-reading-time-sort="2" data-listing-title-sort="Contribute" data-listing-filename-sort="contribute.qmd">
+<tr data-index="0" data-listing-file-modified-sort="1709062041706" data-listing-reading-time-sort="2" data-listing-title-sort="Contribute" data-listing-filename-sort="contribute.qmd">
 <td>
 <a href="../../guide/how-to/contribute.html" class="title listing-title">Contribute</a>
 </td>
 <td>
 <span class="listing-author">&nbsp;</span>
 </td>
 </tr>
-<tr data-index="1" data-listing-file-modified-sort="1709047597697" data-listing-reading-time-sort="1" data-listing-title-sort="Examples" data-listing-filename-sort="examples.qmd">
+<tr data-index="1" data-listing-file-modified-sort="1709062041706" data-listing-reading-time-sort="1" data-listing-title-sort="Examples" data-listing-filename-sort="examples.qmd">
 <td>
 <a href="../../guide/how-to/examples.html" class="title listing-title">Examples</a>
 </td>
 <td>
 <span class="listing-author">&nbsp;</span>
 </td>
 </tr>
-<tr data-index="2" data-listing-file-modified-sort="1709047597697" data-listing-reading-time-sort="1" data-listing-title-sort="High Performance Computing" data-listing-filename-sort="hcp.qmd">
+<tr data-index="2" data-listing-file-modified-sort="1709062041706" data-listing-reading-time-sort="1" data-listing-title-sort="High Performance Computing" data-listing-filename-sort="hcp.qmd">
 <td>
 <a href="../../guide/how-to/hcp.html" class="title listing-title">High Performance Computing</a>
 </td>
 <td>
 <span class="listing-author">&nbsp;</span>
 </td>
 </tr>
-<tr data-index="3" data-listing-file-modified-sort="1709047597697" data-listing-reading-time-sort="1" data-listing-title-sort="Install Machine Learning Plugins" data-listing-filename-sort="install-ml-plugins.qmd">
+<tr data-index="3" data-listing-file-modified-sort="1709062041706" data-listing-reading-time-sort="1" data-listing-title-sort="Install Machine Learning Plugins" data-listing-filename-sort="install-ml-plugins.qmd">
 <td>
 <a href="../../guide/how-to/install-ml-plugins.html" class="title listing-title">Install Machine Learning Plugins</a>
 </td>
 <td>
 <span class="listing-author">&nbsp;</span>
 </td>
 </tr>
-<tr data-index="4" data-listing-file-modified-sort="1709047597697" data-listing-reading-time-sort="1" data-listing-title-sort="Reaction only" data-listing-filename-sort="reaction_only.qmd">
+<tr data-index="4" data-listing-file-modified-sort="1709062041706" data-listing-reading-time-sort="1" data-listing-title-sort="Reaction only" data-listing-filename-sort="reaction_only.qmd">
 <td>
 <a href="../../guide/how-to/reaction_only.html" class="title listing-title">Reaction only</a>
 </td>

docs/guide/tutorials/getting-started.html

@@ -603,7 +603,7 @@ <h2 class="anchored" data-anchor-id="setup-the-simulation">Setup the Simulation<
 <p>Our starting structure is a simple ACE/NME-capped Alanine molecule in a box of water. Note, how it has a missing hydrogen atom on the alpha carbon. This is a radical. We will use the builtin <code>hat_reaction</code> to simulate hydrogen atom transfer reactions from nearby hydrogens to the radical position.</p>
     <div id="app-./getting-started-files/vis-ala.molj" class="molstar-app"></div>
     <script type="text/javascript">
-    molstar.Viewer.create("app-./getting-started-files/vis-ala.molj", {"layoutShowRemoteState":false,"layoutShowSequence":false,"layoutShowLog":false,"viewportShowAnimation":true,"viewportShowExpand":true,"layoutIsExpanded":false,"layoutShowControls":false,"emdbProvider":"rcsb","pdbProvider":"rcsb","layoutShowLeftPanel":true,"viewportShowSelectionMode":false}).then(viewer => {
+    molstar.Viewer.create("app-./getting-started-files/vis-ala.molj", {"layoutShowSequence":false,"pdbProvider":"rcsb","layoutShowLog":false,"emdbProvider":"rcsb","viewportShowExpand":true,"viewportShowSelectionMode":false,"viewportShowAnimation":true,"layoutShowRemoteState":false,"layoutShowControls":false,"layoutIsExpanded":false,"layoutShowLeftPanel":true}).then(viewer => {
     viewer.loadSnapshotFromUrl(url="./getting-started-files/vis-ala.molj", "molj");    });
     </script>
 

docs/guide/tutorials/index.html

@@ -507,7 +507,7 @@ <h1 class="title">Tutorials</h1>
 
 <div class="quarto-listing quarto-listing-container-default" id="listing-listing">
 <div class="list quarto-listing-default">
-<div class="quarto-post image-right" data-index="0" data-categories="user" data-listing-file-modified-sort="1709047597701" data-listing-reading-time-sort="3">
+<div class="quarto-post image-right" data-index="0" data-categories="user" data-listing-file-modified-sort="1709062041706" data-listing-reading-time-sort="3">
 <div class="thumbnail">
 <p><a href="../../guide/tutorials/getting-started.html"> <img src="../../guide/tutorials/img/getting-started-vmd-radicals.png" class="thumbnail-image"> </a></p>
 </div>
@@ -539,7 +539,7 @@ <h3 class="no-anchor listing-title">
 </a>
 </div>
 </div>
-<div class="quarto-post image-right" data-index="1" data-categories="user" data-listing-file-modified-sort="1709047597697" data-listing-reading-time-sort="6">
+<div class="quarto-post image-right" data-index="1" data-categories="user" data-listing-file-modified-sort="1709062041706" data-listing-reading-time-sort="6">
 <div class="thumbnail">
 <p><a href="../../guide/tutorials/colbuilder.html"> <img src="../../guide/tutorials/img/colbuilder.png" class="thumbnail-image"> </a></p>
 </div>
@@ -571,7 +571,7 @@ <h3 class="no-anchor listing-title">
 </a>
 </div>
 </div>
-<div class="quarto-post image-right" data-index="2" data-categories="developer" data-listing-file-modified-sort="1709047597705" data-listing-reading-time-sort="6">
+<div class="quarto-post image-right" data-index="2" data-categories="developer" data-listing-file-modified-sort="1709062041710" data-listing-reading-time-sort="6">
 <div class="thumbnail">
 <p><a href="../../guide/tutorials/write-plugin.html"> <div class="listing-item-img-placeholder card-img-top" >&nbsp;</div> </a></p>
 </div>

docs/sitemap.xml

@@ -2,154 +2,154 @@
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/explanation/topology.html</loc>
-    <lastmod>2024-02-27T15:26:37.697Z</lastmod>
+    <lastmod>2024-02-27T19:27:21.706Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/references/cmd_ref.html</loc>
-    <lastmod>2024-02-27T15:26:37.697Z</lastmod>
+    <lastmod>2024-02-27T19:27:21.706Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/reaction_only.html</loc>
-    <lastmod>2024-02-27T15:26:37.697Z</lastmod>
+    <lastmod>2024-02-27T19:27:21.706Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/contribute.html</loc>
-    <lastmod>2024-02-27T15:26:37.697Z</lastmod>
+    <lastmod>2024-02-27T19:27:21.706Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/install-ml-plugins.html</loc>
-    <lastmod>2024-02-27T15:26:37.697Z</lastmod>
+    <lastmod>2024-02-27T19:27:21.706Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/tutorials/getting-started.html</loc>
-    <lastmod>2024-02-27T15:26:37.701Z</lastmod>
+    <lastmod>2024-02-27T19:27:21.706Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/tutorials/index.html</loc>
-    <lastmod>2024-02-27T15:26:37.705Z</lastmod>
+    <lastmod>2024-02-27T19:27:21.710Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/schema.html</loc>
-    <lastmod>2024-02-27T15:27:32.981Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.330Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/homolysis.reaction.Homolysis.html</loc>
-    <lastmod>2024-02-27T15:27:33.049Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.398Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/topology.topology.html</loc>
-    <lastmod>2024-02-27T15:27:32.681Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.030Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/hat_naive.reaction.NaiveHAT.html</loc>
-    <lastmod>2024-02-27T15:27:33.049Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.398Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/topology.ff.html</loc>
-    <lastmod>2024-02-27T15:27:32.685Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.034Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/coordinates.html</loc>
-    <lastmod>2024-02-27T15:27:32.849Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.198Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/runmanager.html</loc>
-    <lastmod>2024-02-27T15:27:32.965Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.314Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/kmc.html</loc>
-    <lastmod>2024-02-27T15:27:32.869Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.218Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/analysis.html</loc>
-    <lastmod>2024-02-27T15:27:32.805Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.154Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/tasks.html</loc>
-    <lastmod>2024-02-27T15:27:32.997Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.346Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/utils.html</loc>
-    <lastmod>2024-02-27T15:27:33.045Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.394Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/parsing.TopologyDict.html</loc>
-    <lastmod>2024-02-27T15:27:32.773Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.122Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/index.html</loc>
-    <lastmod>2024-02-27T15:26:37.705Z</lastmod>
+    <lastmod>2024-02-27T19:27:21.710Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/cmd.html</loc>
-    <lastmod>2024-02-27T15:27:32.653Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.006Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/constants.html</loc>
-    <lastmod>2024-02-27T15:27:32.829Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.178Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/index.html</loc>
-    <lastmod>2024-02-27T15:27:32.633Z</lastmod>
+    <lastmod>2024-02-27T19:28:18.982Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/parsing.html</loc>
-    <lastmod>2024-02-27T15:27:32.897Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.246Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/topology.atomic.html</loc>
-    <lastmod>2024-02-27T15:27:32.773Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.122Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/plugins.html</loc>
-    <lastmod>2024-02-27T15:27:32.905Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.258Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/topology.utils.html</loc>
-    <lastmod>2024-02-27T15:27:32.713Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.062Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/tools.html</loc>
-    <lastmod>2024-02-27T15:27:33.017Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.366Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/dummyreaction.reaction.DummyReaction.html</loc>
-    <lastmod>2024-02-27T15:27:33.053Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.402Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/config.html</loc>
-    <lastmod>2024-02-27T15:27:32.825Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.174Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/recipe.html</loc>
-    <lastmod>2024-02-27T15:27:32.953Z</lastmod>
+    <lastmod>2024-02-27T19:28:19.302Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/tutorials/write-plugin.html</loc>
-    <lastmod>2024-02-27T15:26:37.705Z</lastmod>
+    <lastmod>2024-02-27T19:27:21.710Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/tutorials/colbuilder.html</loc>
-    <lastmod>2024-02-27T15:26:37.697Z</lastmod>
+    <lastmod>2024-02-27T19:27:21.706Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/hcp.html</loc>
-    <lastmod>2024-02-27T15:26:37.697Z</lastmod>
+    <lastmod>2024-02-27T19:27:21.706Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/index.html</loc>
-    <lastmod>2024-02-27T15:26:37.697Z</lastmod>
+    <lastmod>2024-02-27T19:27:21.706Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/examples.html</loc>
-    <lastmod>2024-02-27T15:26:37.697Z</lastmod>
+    <lastmod>2024-02-27T19:27:21.706Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/references/input.html</loc>
-    <lastmod>2024-02-27T15:26:37.697Z</lastmod>
+    <lastmod>2024-02-27T19:27:21.706Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/explanation/index.html</loc>
-    <lastmod>2024-02-27T15:26:37.697Z</lastmod>
+    <lastmod>2024-02-27T19:27:21.706Z</lastmod>
   </url>
 </urlset>

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = kimmdy
-version = 6.2.4
+version = 6.2.5
 license = MIT
 description = Kinetic Monte Carlo Molecular Dynamics
 description_content_type = text/markdown