chore(main): release 5.1.10 (#324)

* chore(main): release 5.1.10

* 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>

CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+## [5.1.10](https://github.com/hits-mbm-dev/kimmdy/compare/v5.1.9...v5.1.10) (2023-11-08)
+
+
+### Bug Fixes
+
+* discover plugins for building docs ([22018e4](https://github.com/hits-mbm-dev/kimmdy/commit/22018e42d0ccb3768379f82d68a5521f1985101e))
+
 ## [5.1.9](https://github.com/hits-mbm-dev/kimmdy/compare/v5.1.8...v5.1.9) (2023-11-08)
 
 

docs/guide/how_to/options.html

@@ -765,6 +765,76 @@ <h2 class="anchored" data-anchor-id="all-options">All Options</h2>
 <td></td>
 </tr>
 <tr class="odd">
+<td>reactions.homolysis.edis</td>
+<td>Dissociation energies data file</td>
+<td>Path</td>
+<td>edissoc.dat</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>reactions.homolysis.itp</td>
+<td>Additional itp file with bonded parameters</td>
+<td>Path</td>
+<td>ffbonded.itp</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>reactions.homolysis.kmc</td>
+<td>KMC algorithm for this reaction.</td>
+<td>str</td>
+<td>rfkmc</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>reactions.hat_naive.frequency_factor</td>
+<td>Frequency factor</td>
+<td>float</td>
+<td>1</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>reactions.hat_naive.h_cutoff</td>
+<td>Cutoff for H atom</td>
+<td>float</td>
+<td>4</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>reactions.hat_naive.polling_rate</td>
+<td>Polling rate</td>
+<td>float</td>
+<td>1</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>reactions.hat_naive.kmc</td>
+<td>KMC algorithm for this reaction.</td>
+<td>str</td>
+<td>extrande_mod</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>reactions.dummyreaction.example</td>
+<td>This is an example of an option for a reaction.</td>
+<td>float</td>
+<td>0.0</td>
+<td></td>
+</tr>
+<tr class="odd">
+<td>reactions.dummyreaction.example2</td>
+<td>This is another example of an option for a reaction.</td>
+<td>str</td>
+<td>hello</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>reactions.dummyreaction.kmc</td>
+<td>KMC algorithm for this reaction.</td>
+<td>str</td>
+<td>extrande_mod</td>
+<td></td>
+</tr>
+<tr class="odd">
 <td>plot_rates</td>
 <td>Plot the reaction rates during the reactions step</td>
 <td>bool</td>

docs/guide/how_to/topology.html

@@ -506,13 +506,13 @@ <h1 class="title">Visualize Topologies</h1>
 
 <section id="hexala" class="level1">
 <h1>Hexala</h1>
-<div id="4a34c090" class="cell" data-execution_count="1">
+<div id="e88c47a8" class="cell" data-execution_count="1">
 <div class="sourceCode cell-code" id="cb1"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> kimmdy.parsing <span class="im">import</span> read_top</span>
 <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> kimmdy.topology.topology <span class="im">import</span> Topology</span>
 <span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> pathlib <span class="im">import</span> Path</span>
 <span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> kimmdy.tools <span class="im">import</span> write_top_as_dot</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
-<div id="2f8ac499" class="cell" data-execution_count="2">
+<div id="b016da6a" class="cell" data-execution_count="2">
 <div class="sourceCode cell-code" id="cb2"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>ala_top <span class="op">=</span> read_top(Path(<span class="st">'../../tests/test_files/test_topology/urea.top'</span>), use_gmx_dir<span class="op">=</span><span class="va">False</span>)</span>
 <span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>top <span class="op">=</span> Topology(ala_top)</span>
 <span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a></span>

docs/guide/tutorials/getting-started.html

@@ -583,7 +583,7 @@ <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.</p>
     <div id="app-vis-ala.molj" class="molstar-app"></div>
     <script type="text/javascript">
-    molstar.Viewer.create("app-vis-ala.molj", {"layoutShowLog":false,"emdbProvider":"rcsb","viewportShowSelectionMode":false,"pdbProvider":"rcsb","layoutShowControls":false,"layoutShowSequence":false,"viewportShowAnimation":true,"viewportShowExpand":true,"layoutIsExpanded":false,"layoutShowRemoteState":false,"layoutShowLeftPanel":true}).then(viewer => {
+    molstar.Viewer.create("app-vis-ala.molj", {"layoutShowControls":false,"layoutShowLog":false,"emdbProvider":"rcsb","layoutShowSequence":false,"layoutShowRemoteState":false,"pdbProvider":"rcsb","layoutIsExpanded":false,"viewportShowAnimation":true,"viewportShowSelectionMode":false,"viewportShowExpand":true,"layoutShowLeftPanel":true}).then(viewer => {
     viewer.loadSnapshotFromUrl(url="vis-ala.molj", "molj");    });
     </script>
 

docs/guide/tutorials/write-plugin.html

@@ -522,7 +522,7 @@ <h2 class="anchored" data-anchor-id="adding-the-functionality-of-the-plugin">Add
 <h3 class="anchored" data-anchor-id="main-code">Main code</h3>
 <p>A reaction plugin has to be a derived class from the <code>ReactionPlugin</code> base class. Such a class has the attributes <code>name</code>, <code>runmng</code> and <code>config</code> and the method <code>get_recipe_collection</code>, which takes a <code>TaskFiles</code> object as argument and returns a <code>RecipeCollection</code>.</p>
 <p>The <code>name</code> is a simple string and may be useful for logging. <code>runmng</code> is the central <code>RunManager</code> of a kimmdy run and has plenty of useful attributes for your plugin, especially the system <code>Topology</code>, which can be accessed via <code>self.runmg.top</code>. <code>config</code> contains the reaction plugin configuration as specified in the kimmdy configuration file (typically named kimmdy.yml). A <code>RecipeCollection</code> contains <code>Recipe</code>s with predefined <code>RecipeStep</code>s that can be used to define the modification to the system for the reaction. A <code>Recipe</code> also contains the <code>rates</code> of the specified reaction and the <code>timespans</code> during which the corresponding rates are valid. An example plugin can be seen below.</p>
-<div id="97ab4179" class="cell" data-execution_count="1">
+<div id="8638d43e" class="cell" data-execution_count="1">
 <details>
 <summary>Plugin main code (reaction.py)</summary>
 <div class="sourceCode cell-code" id="cb1"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> kimmdy.recipe <span class="im">import</span> (</span>
@@ -582,7 +582,7 @@ <h3 class="anchored" data-anchor-id="main-code">Main code</h3>
 <section id="configuration-file-schema" class="level3">
 <h3 class="anchored" data-anchor-id="configuration-file-schema">Configuration file schema</h3>
 <p>A plugin defines which variables it needs in a schema. The schema can contain default values and types of these variables. For a Kimmdy run, reaction plugin variables are defined in the configuration file (kimmdy.yml). An example schema can be seen below.</p>
-<div id="6dee472f" class="cell" data-execution_count="2">
+<div id="4bdbbb35" class="cell" data-execution_count="2">
 <details>
 <summary>Plugin schema (kimmdy-yaml-schema.json)</summary>
 <div class="sourceCode cell-code" id="cb2"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>{</span>
@@ -614,15 +614,15 @@ <h3 class="anchored" data-anchor-id="configuration-file-schema">Configuration fi
 <section id="making-a-python-package" class="level2">
 <h2 class="anchored" data-anchor-id="making-a-python-package">Making a python package</h2>
 <p>It is necessary to make the plugin a python package to interface with Kimmdy. For this, package setup configuration files are necessary, for example <code>setup.py</code> and <code>setup.cfg</code>. In <code>setup.cfg</code> dependencies can be specified, which will be installed alongside the plugin. The interface with kimmdy is specified in the <code>[options.entry_points]</code> section. This section needs to refer to the class we created in the plugin main code and assign it to <code>kimmdy.reaction_plugins</code>, i.e.&nbsp;<code>kimmdy.reaction_plugins = bind = &lt;path&gt;.&lt;to&gt;.&lt;main file&gt;:&lt;ClassName&gt;</code>. Also, the directory containing the source code (typically <code>src</code>) is defined in <code>[options.packages.find]</code>. An example for <code>setup.py</code> and <code>setup.cfg</code> can be found below.</p>
-<div id="bd1ad0da" class="cell" data-execution_count="3">
+<div id="dc370d68" class="cell" data-execution_count="3">
 <details>
 <summary>setup.py</summary>
 <div class="sourceCode cell-code" id="cb3"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> setuptools <span class="im">import</span> setup</span>
 <span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a>setup()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </details>
 </div>
-<div id="41c88431" class="cell" data-execution_count="4">
+<div id="0d87dad9" class="cell" data-execution_count="4">
 <details>
 <summary>setup.cfg</summary>
 <div class="sourceCode cell-code" id="cb4"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a>[metadata]</span>

docs/search.json

@@ -39,7 +39,7 @@
     "href": "guide/how_to/options.html#all-options",
     "title": "KIMMDY Options",
     "section": "All Options",
-    "text": "All Options\nThe following is a list of the options that can be set in the kimmdy.yml file. It includes reactions currently available in KIMMDY as plugins. Nested options are separated by a .. * denotes an arbitrary name for a section. The key for a section is bold.\n\n\nTable 1: KIMMDY options\n\n\n\n\n\n\n\n\n\nOption\nDescription\nType\nDefault\n\n\n\n\n\ndryrun\nDon’t run the actual simulations, just print the tasks\nbool\nFalse\n\n\n\nwrite_checkpoint\nWrite checkpoints to continue a KIMMDY run from. Default True\nbool\nTrue\n\n\n\ncwd\nWorking directory. Default is current working directory\nPath\n\n\n\n\nname\nUsed for output folder if out is not specified\nstr\nkimmdy\n\n\n\nout\nOutput folder\nPath\n\n\n\n\nlog\nSettings for logging\n\n\n\n\n\nmax_tasks\nMaximum number of tasks to run. This is useful when a task in the sequence can dymanically add more tasks. 0 means no limit.\nint\n0\n\n\n\nmax_hours\nStop KIMMDY after max_hours hours. Set this lower than the limit of your HPC cluster for use with a re-submit jobscript. 0 Means no limit.\nint\n0\n\n\n\nkmc\nKMC algorithm overwrite. Should be set by the reactions, but can be changed here.\nstr\n\n\n\n\ntau_scale\nScaling parameter for tau in the extrande kmc algorithm.\nfloat\n1.0\n\n\n\ntop\nTopology file\nPath\ntopol.top\n\n\n\ngro\nCoordinate file\nPath\nconf.gro\n\n\n\nndx\nGromaxs index file\nPath\nindex.ndx\n\n\n\ngromacs_alias\nGromacs alias. e.g. gmx or mpirun gmx_mpi\nstr\ngmx\n\n\n\ngmx_mdrun_flags\nFlags passed to gmx mdrun. Default -maxh 24 -dlb yes\nstr\n-maxh 24 -dlb yes\n\n\n\nff\nForce field directory (looks for .ff in cwd if not set)\nPath\n*.ff\n\n\n\nplumed\n.dat file containing plumed config\nPath\n\n\n\n\ntpr\n.tpr file of a finished simulation for starting directly with a reaction\nPath\n\n\n\n\ntrr\n.trr file of a finished simulation for starting directly with a reaction\nPath\n\n\n\n\nmds\nSettings for MD steps, e.g. mdp files, plumed files, etc.\n\n\n\n\n\nmds.*.mdp\nMDP file for the MD step\nPath\n\n\n\n\nmds.*.use_plumed\nWhether plumed should be used for this run or not\nbool\nFalse\n\n\n\nchanger\nSettings for applying a reaction recipe\n\n\n\n\n\nchanger.coordinates.md\nMD step from the ‘mds’ section that is used for relaxation MDs\nstr\n\n\n\n\nchanger.coordinates.slow_growth\nWhether the chosen MD step is a slow growth/free-energy simulation\nbool\nFalse\n\n\n\nchanger.topology.parameterization\nParameterization scheme that is used on the topology file after changes to it\nstr\nbasic\n\n\n\nsequence\nList of tasks. Each task can be a string (the name of the task) or an object with the task name and a multiplicity mult: <int>\nSequence\n\n\n\n\nreactions\nSettings for reactions\n\n\n\n\n\nplot_rates\nPlot the reaction rates during the reactions step\nbool\nTrue\n\n\n\nsave_recipes\nSave recipes as csv during the reactions step\nbool\nTrue"
+    "text": "All Options\nThe following is a list of the options that can be set in the kimmdy.yml file. It includes reactions currently available in KIMMDY as plugins. Nested options are separated by a .. * denotes an arbitrary name for a section. The key for a section is bold.\n\n\nTable 1: KIMMDY options\n\n\n\n\n\n\n\n\n\nOption\nDescription\nType\nDefault\n\n\n\n\n\ndryrun\nDon’t run the actual simulations, just print the tasks\nbool\nFalse\n\n\n\nwrite_checkpoint\nWrite checkpoints to continue a KIMMDY run from. Default True\nbool\nTrue\n\n\n\ncwd\nWorking directory. Default is current working directory\nPath\n\n\n\n\nname\nUsed for output folder if out is not specified\nstr\nkimmdy\n\n\n\nout\nOutput folder\nPath\n\n\n\n\nlog\nSettings for logging\n\n\n\n\n\nmax_tasks\nMaximum number of tasks to run. This is useful when a task in the sequence can dymanically add more tasks. 0 means no limit.\nint\n0\n\n\n\nmax_hours\nStop KIMMDY after max_hours hours. Set this lower than the limit of your HPC cluster for use with a re-submit jobscript. 0 Means no limit.\nint\n0\n\n\n\nkmc\nKMC algorithm overwrite. Should be set by the reactions, but can be changed here.\nstr\n\n\n\n\ntau_scale\nScaling parameter for tau in the extrande kmc algorithm.\nfloat\n1.0\n\n\n\ntop\nTopology file\nPath\ntopol.top\n\n\n\ngro\nCoordinate file\nPath\nconf.gro\n\n\n\nndx\nGromaxs index file\nPath\nindex.ndx\n\n\n\ngromacs_alias\nGromacs alias. e.g. gmx or mpirun gmx_mpi\nstr\ngmx\n\n\n\ngmx_mdrun_flags\nFlags passed to gmx mdrun. Default -maxh 24 -dlb yes\nstr\n-maxh 24 -dlb yes\n\n\n\nff\nForce field directory (looks for .ff in cwd if not set)\nPath\n*.ff\n\n\n\nplumed\n.dat file containing plumed config\nPath\n\n\n\n\ntpr\n.tpr file of a finished simulation for starting directly with a reaction\nPath\n\n\n\n\ntrr\n.trr file of a finished simulation for starting directly with a reaction\nPath\n\n\n\n\nmds\nSettings for MD steps, e.g. mdp files, plumed files, etc.\n\n\n\n\n\nmds.*.mdp\nMDP file for the MD step\nPath\n\n\n\n\nmds.*.use_plumed\nWhether plumed should be used for this run or not\nbool\nFalse\n\n\n\nchanger\nSettings for applying a reaction recipe\n\n\n\n\n\nchanger.coordinates.md\nMD step from the ‘mds’ section that is used for relaxation MDs\nstr\n\n\n\n\nchanger.coordinates.slow_growth\nWhether the chosen MD step is a slow growth/free-energy simulation\nbool\nFalse\n\n\n\nchanger.topology.parameterization\nParameterization scheme that is used on the topology file after changes to it\nstr\nbasic\n\n\n\nsequence\nList of tasks. Each task can be a string (the name of the task) or an object with the task name and a multiplicity mult: <int>\nSequence\n\n\n\n\nreactions\nSettings for reactions\n\n\n\n\n\nreactions.homolysis.edis\nDissociation energies data file\nPath\nedissoc.dat\n\n\n\nreactions.homolysis.itp\nAdditional itp file with bonded parameters\nPath\nffbonded.itp\n\n\n\nreactions.homolysis.kmc\nKMC algorithm for this reaction.\nstr\nrfkmc\n\n\n\nreactions.hat_naive.frequency_factor\nFrequency factor\nfloat\n1\n\n\n\nreactions.hat_naive.h_cutoff\nCutoff for H atom\nfloat\n4\n\n\n\nreactions.hat_naive.polling_rate\nPolling rate\nfloat\n1\n\n\n\nreactions.hat_naive.kmc\nKMC algorithm for this reaction.\nstr\nextrande_mod\n\n\n\nreactions.dummyreaction.example\nThis is an example of an option for a reaction.\nfloat\n0.0\n\n\n\nreactions.dummyreaction.example2\nThis is another example of an option for a reaction.\nstr\nhello\n\n\n\nreactions.dummyreaction.kmc\nKMC algorithm for this reaction.\nstr\nextrande_mod\n\n\n\nplot_rates\nPlot the reaction rates during the reactions step\nbool\nTrue\n\n\n\nsave_recipes\nSave recipes as csv during the reactions step\nbool\nTrue"
   },
   {
     "objectID": "guide/how_to/options.html#example-kimmdy.yml-files",