Sphinx build from commit f8fed4e by GitHub Action

CovertLab · Jul 20, 2024 · 6d9a1bf · 6d9a1bf
commit 6d9a1bf
Show file tree

Hide file tree

Showing 785 changed files with 193,865 additions and 0 deletions.
diff --git a/.buildinfo b/.buildinfo
@@ -0,0 +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.
+config: 817303359296854b7383a52c37e685d9
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.nojekyll b/.nojekyll
diff --git a/_images/ecoli_master_topology.png b/_images/ecoli_master_topology.png
diff --git a/_modules/ecoli/analysis/antibiotics_colony.html b/_modules/ecoli/analysis/antibiotics_colony.html
diff --git a/_modules/ecoli/analysis/antibiotics_colony/amp_plots.html b/_modules/ecoli/analysis/antibiotics_colony/amp_plots.html
diff --git a/_modules/ecoli/analysis/antibiotics_colony/exploration.html b/_modules/ecoli/analysis/antibiotics_colony/exploration.html
diff --git a/_modules/ecoli/analysis/antibiotics_colony/load_data.html b/_modules/ecoli/analysis/antibiotics_colony/load_data.html
diff --git a/_modules/ecoli/analysis/antibiotics_colony/metrics.html b/_modules/ecoli/analysis/antibiotics_colony/metrics.html
diff --git a/_modules/ecoli/analysis/antibiotics_colony/plot.html b/_modules/ecoli/analysis/antibiotics_colony/plot.html
diff --git a/_modules/ecoli/analysis/antibiotics_colony/plot_utils.html b/_modules/ecoli/analysis/antibiotics_colony/plot_utils.html
diff --git a/_modules/ecoli/analysis/antibiotics_colony/snapshot_and_hist_plot.html b/_modules/ecoli/analysis/antibiotics_colony/snapshot_and_hist_plot.html
diff --git a/_modules/ecoli/analysis/antibiotics_colony/spatial_correlation.html b/_modules/ecoli/analysis/antibiotics_colony/spatial_correlation.html
diff --git a/_modules/ecoli/analysis/antibiotics_colony/tet_dry_mass.html b/_modules/ecoli/analysis/antibiotics_colony/tet_dry_mass.html
diff --git a/_modules/ecoli/analysis/antibiotics_colony/timeseries.html b/_modules/ecoli/analysis/antibiotics_colony/timeseries.html
diff --git a/_modules/ecoli/analysis/antibiotics_colony/validation.html b/_modules/ecoli/analysis/antibiotics_colony/validation.html
diff --git a/_modules/ecoli/analysis/causality_network/buildCausalityNetwork.html b/_modules/ecoli/analysis/causality_network/buildCausalityNetwork.html
diff --git a/_modules/ecoli/analysis/causality_network/build_network.html b/_modules/ecoli/analysis/causality_network/build_network.html
diff --git a/_modules/ecoli/analysis/causality_network/network_components.html b/_modules/ecoli/analysis/causality_network/network_components.html
diff --git a/_modules/ecoli/analysis/causality_network/read_dynamics.html b/_modules/ecoli/analysis/causality_network/read_dynamics.html
diff --git a/_modules/ecoli/analysis/colony/snapshots.html b/_modules/ecoli/analysis/colony/snapshots.html
diff --git a/_modules/ecoli/analysis/multigeneration/new_gene_counts.html b/_modules/ecoli/analysis/multigeneration/new_gene_counts.html
diff --git a/_modules/ecoli/analysis/multiseed/ecocyc_table.html b/_modules/ecoli/analysis/multiseed/ecocyc_table.html
diff --git a/_modules/ecoli/analysis/multiseed/subgenerational_expression_table.html b/_modules/ecoli/analysis/multiseed/subgenerational_expression_table.html
diff --git a/_modules/ecoli/analysis/multivariant/average_monomer_counts.html b/_modules/ecoli/analysis/multivariant/average_monomer_counts.html
diff --git a/_modules/ecoli/analysis/multivariant/new_gene_translation_efficiency_heatmaps.html b/_modules/ecoli/analysis/multivariant/new_gene_translation_efficiency_heatmaps.html
diff --git a/_modules/ecoli/analysis/single/blame.html b/_modules/ecoli/analysis/single/blame.html
diff --git a/_modules/ecoli/analysis/single/mass_fraction_summary.html b/_modules/ecoli/analysis/single/mass_fraction_summary.html
diff --git a/_modules/ecoli/composites/chemotaxis_minimal.html b/_modules/ecoli/composites/chemotaxis_minimal.html
diff --git a/_modules/ecoli/composites/ecoli_master.html b/_modules/ecoli/composites/ecoli_master.html
diff --git a/_modules/ecoli/composites/ecoli_master_tests.html b/_modules/ecoli/composites/ecoli_master_tests.html
diff --git a/_modules/ecoli/composites/ecoli_spatial.html b/_modules/ecoli/composites/ecoli_spatial.html
diff --git a/_modules/ecoli/composites/environment/grow_divide.html b/_modules/ecoli/composites/environment/grow_divide.html
diff --git a/_modules/ecoli/composites/environment/lattice.html b/_modules/ecoli/composites/environment/lattice.html
diff --git a/_modules/ecoli/experiments/antibiotics_tests.html b/_modules/ecoli/experiments/antibiotics_tests.html
diff --git a/_modules/ecoli/experiments/ecoli_engine_process.html b/_modules/ecoli/experiments/ecoli_engine_process.html
diff --git a/_modules/ecoli/experiments/ecoli_master_sim.html b/_modules/ecoli/experiments/ecoli_master_sim.html
diff --git a/_modules/ecoli/experiments/glt_division.html b/_modules/ecoli/experiments/glt_division.html
diff --git a/_modules/ecoli/experiments/metabolism_exchanger.html b/_modules/ecoli/experiments/metabolism_exchanger.html
diff --git a/_modules/ecoli/experiments/metabolism_redux_sim.html b/_modules/ecoli/experiments/metabolism_redux_sim.html
diff --git a/_modules/ecoli/experiments/tet_amp_sim.html b/_modules/ecoli/experiments/tet_amp_sim.html
diff --git a/_modules/ecoli/library/cell_wall/column_sampler.html b/_modules/ecoli/library/cell_wall/column_sampler.html
diff --git a/_modules/ecoli/library/cell_wall/fit_lysis_time.html b/_modules/ecoli/library/cell_wall/fit_lysis_time.html
diff --git a/_modules/ecoli/library/cell_wall/hole_detection.html b/_modules/ecoli/library/cell_wall/hole_detection.html
diff --git a/_modules/ecoli/library/cell_wall/lattice.html b/_modules/ecoli/library/cell_wall/lattice.html
diff --git a/_modules/ecoli/library/create_timeline.html b/_modules/ecoli/library/create_timeline.html
diff --git a/_modules/ecoli/library/data_predicates.html b/_modules/ecoli/library/data_predicates.html
diff --git a/_modules/ecoli/library/initial_conditions.html b/_modules/ecoli/library/initial_conditions.html
diff --git a/_modules/ecoli/library/json_state.html b/_modules/ecoli/library/json_state.html
diff --git a/_modules/ecoli/library/kinetic_rate_laws.html b/_modules/ecoli/library/kinetic_rate_laws.html
diff --git a/_modules/ecoli/library/lattice_utils.html b/_modules/ecoli/library/lattice_utils.html
diff --git a/_modules/ecoli/library/logging_tools.html b/_modules/ecoli/library/logging_tools.html
@@ -0,0 +1,148 @@
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../../../">
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>ecoli.library.logging_tools &mdash; Vivarium E. coli 1.0.0 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
+
+
+  <!--[if lt IE 9]>
+    <script src="../../../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+
+        <script src="../../../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../../../_static/documentation_options.js?v=8d563738"></script>
+        <script src="../../../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
+    <script src="../../../_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="../../../genindex.html" />
+    <link rel="search" title="Search" href="../../../search.html" /> 
+</head>
+
+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+
+
+
+          <a href="../../../index.html" class="icon icon-home">
+            Vivarium E. coli
+          </a>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="../../../stores.html">Stores</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Processes</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../composites.html">Composites</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../experiments.html">Experiments</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../workflows.html">Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../output.html">Output</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../tutorial.html">Tutorial</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../docs.html">Documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../reference/api_ref.html">API Reference</a></li>
+</ul>
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../../../index.html">Vivarium E. coli</a>
+      </nav>
+
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="Page navigation">
+  <ul class="wy-breadcrumbs">
+      <li><a href="../../../index.html" class="icon icon-home" aria-label="Home"></a></li>
+          <li class="breadcrumb-item"><a href="../../index.html">Module code</a></li>
+      <li class="breadcrumb-item active">ecoli.library.logging_tools</li>
+      <li class="wy-breadcrumbs-aside">
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+  <h1>Source code for ecoli.library.logging_tools</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">json</span>
+
+<span class="kn">from</span> <span class="nn">vivarium.core.serialize</span> <span class="kn">import</span> <span class="n">serialize_value</span>
+
+
+<div class="viewcode-block" id="make_logging_process">
+<a class="viewcode-back" href="../../../reference/api/ecoli/ecoli.library.logging_tools.html#ecoli.library.logging_tools.make_logging_process">[docs]</a>
+<span class="k">def</span> <span class="nf">make_logging_process</span><span class="p">(</span><span class="n">process_class</span><span class="p">):</span>
+    <span class="k">class</span> <span class="nc">LoggingProcess</span><span class="p">(</span><span class="n">process_class</span><span class="p">):</span>
+        <span class="k">def</span> <span class="nf">ports_schema</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+            <span class="n">ports</span> <span class="o">=</span> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="n">ports_schema</span><span class="p">()</span>  <span class="c1"># original port structure</span>
+            <span class="n">ports</span><span class="p">[</span><span class="s2">&quot;log_update&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s2">&quot;_default&quot;</span><span class="p">:</span> <span class="p">{},</span>
+                <span class="s2">&quot;_updater&quot;</span><span class="p">:</span> <span class="s2">&quot;set&quot;</span><span class="p">,</span>
+                <span class="s2">&quot;_emit&quot;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="p">}</span>  <span class="c1"># add a new port</span>
+            <span class="k">return</span> <span class="n">ports</span>
+
+        <span class="k">def</span> <span class="nf">next_update</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">timestep</span><span class="p">,</span> <span class="n">states</span><span class="p">):</span>
+            <span class="n">update</span> <span class="o">=</span> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="n">next_update</span><span class="p">(</span><span class="n">timestep</span><span class="p">,</span> <span class="n">states</span><span class="p">)</span>  <span class="c1"># original update</span>
+            <span class="n">log_update</span> <span class="o">=</span> <span class="p">{</span><span class="s2">&quot;log_update&quot;</span><span class="p">:</span> <span class="n">update</span><span class="p">}</span>  <span class="c1"># log the update</span>
+            <span class="k">return</span> <span class="p">{</span><span class="o">**</span><span class="n">update</span><span class="p">,</span> <span class="o">**</span><span class="n">log_update</span><span class="p">}</span>
+
+    <span class="n">LoggingProcess</span><span class="o">.</span><span class="vm">__name__</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;Logging_</span><span class="si">{</span><span class="n">process_class</span><span class="o">.</span><span class="vm">__name__</span><span class="si">}</span><span class="s2">&quot;</span>
+    <span class="k">return</span> <span class="n">LoggingProcess</span></div>
+
+
+
+<div class="viewcode-block" id="write_json">
+<a class="viewcode-back" href="../../../reference/api/ecoli/ecoli.library.logging_tools.html#ecoli.library.logging_tools.write_json">[docs]</a>
+<span class="k">def</span> <span class="nf">write_json</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">numpy_dict</span><span class="p">):</span>
+    <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">path</span><span class="p">),</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s2">&quot;w&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">outfile</span><span class="p">:</span>
+        <span class="n">json</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">serialize_value</span><span class="p">(</span><span class="n">numpy_dict</span><span class="p">),</span> <span class="n">outfile</span><span class="p">)</span></div>
+
+</pre></div>
+
+           </div>
+          </div>
+          <footer>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2021-2024, The Vivarium E. coli Authors.</p>
+  </div>
+
+  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
+    provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+
+</footer>
+        </div>
+      </div>
+    </section>
+  </div>
+  <script>
+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script> 
+
+</body>
+</html>