publish: Remove manual installation of Python 3.11 in workflow jobs a…

…nd specify `basepython` in `tox.ini` (#931) generated from commit 5655119
UCL · Apr 6, 2023 · 32dd2c4 · 32dd2c4
1 parent 76c5676
commit 32dd2c4
Show file tree

Hide file tree

Showing 291 changed files with 24,573 additions and 26,808 deletions.
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.
-config: 114663019e0142458c362f53d0079617
+config: f9c90ae0e08057c6bd68d9d329e600d1
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.doctrees/_data_sources.doctree b/.doctrees/_data_sources.doctree
diff --git a/.doctrees/_hsi_events.doctree b/.doctrees/_hsi_events.doctree
diff --git a/.doctrees/aims.doctree b/.doctrees/aims.doctree
diff --git a/.doctrees/authors.doctree b/.doctrees/authors.doctree
diff --git a/.doctrees/azure_batch.doctree b/.doctrees/azure_batch.doctree
diff --git a/.doctrees/background.doctree b/.doctrees/background.doctree
diff --git a/.doctrees/contributing.doctree b/.doctrees/contributing.doctree
diff --git a/.doctrees/data_sources.doctree b/.doctrees/data_sources.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/hsi_events.doctree b/.doctrees/hsi_events.doctree
diff --git a/.doctrees/index.doctree b/.doctrees/index.doctree
diff --git a/.doctrees/publications.doctree b/.doctrees/publications.doctree
diff --git a/.doctrees/readme.doctree b/.doctrees/readme.doctree
diff --git a/.doctrees/reference/index.doctree b/.doctrees/reference/index.doctree
diff --git a/.doctrees/reference/modules.doctree b/.doctrees/reference/modules.doctree
diff --git a/.doctrees/reference/tlo.analysis.doctree b/.doctrees/reference/tlo.analysis.doctree
diff --git a/.doctrees/reference/tlo.analysis.hsi_events.doctree b/.doctrees/reference/tlo.analysis.hsi_events.doctree
diff --git a/.doctrees/reference/tlo.analysis.utils.doctree b/.doctrees/reference/tlo.analysis.utils.doctree
diff --git a/.doctrees/reference/tlo.cli.doctree b/.doctrees/reference/tlo.cli.doctree
diff --git a/.doctrees/reference/tlo.core.doctree b/.doctrees/reference/tlo.core.doctree
diff --git a/.doctrees/reference/tlo.dependencies.doctree b/.doctrees/reference/tlo.dependencies.doctree
diff --git a/.doctrees/reference/tlo.docs.doctree b/.doctrees/reference/tlo.docs.doctree
diff --git a/.doctrees/reference/tlo.doctree b/.doctrees/reference/tlo.doctree
diff --git a/.doctrees/reference/tlo.events.doctree b/.doctrees/reference/tlo.events.doctree
diff --git a/.doctrees/reference/tlo.lm.doctree b/.doctrees/reference/tlo.lm.doctree
diff --git a/.doctrees/reference/tlo.lm_play.doctree b/.doctrees/reference/tlo.lm_play.doctree
diff --git a/.doctrees/reference/tlo.logging.core.doctree b/.doctrees/reference/tlo.logging.core.doctree
diff --git a/.doctrees/reference/tlo.logging.doctree b/.doctrees/reference/tlo.logging.doctree
diff --git a/.doctrees/reference/tlo.logging.encoding.doctree b/.doctrees/reference/tlo.logging.encoding.doctree
diff --git a/.doctrees/reference/tlo.logging.helpers.doctree b/.doctrees/reference/tlo.logging.helpers.doctree
diff --git a/.doctrees/reference/tlo.logging.reader.doctree b/.doctrees/reference/tlo.logging.reader.doctree
diff --git a/.doctrees/reference/tlo.methods.alri.doctree b/.doctrees/reference/tlo.methods.alri.doctree
diff --git a/.doctrees/reference/tlo.methods.bed_days.doctree b/.doctrees/reference/tlo.methods.bed_days.doctree
diff --git a/.doctrees/reference/tlo.methods.bladder_cancer.doctree b/.doctrees/reference/tlo.methods.bladder_cancer.doctree
diff --git a/.doctrees/reference/tlo.methods.breast_cancer.doctree b/.doctrees/reference/tlo.methods.breast_cancer.doctree
diff --git a/.doctrees/reference/tlo.methods.cardio_metabolic_disorders.doctree b/.doctrees/reference/tlo.methods.cardio_metabolic_disorders.doctree
diff --git a/.doctrees/reference/tlo.methods.care_of_women_during_pregnancy.doctree b/.doctrees/reference/tlo.methods.care_of_women_during_pregnancy.doctree
diff --git a/.doctrees/reference/tlo.methods.causes.doctree b/.doctrees/reference/tlo.methods.causes.doctree
diff --git a/.doctrees/reference/tlo.methods.chronicsyndrome.doctree b/.doctrees/reference/tlo.methods.chronicsyndrome.doctree
diff --git a/.doctrees/reference/tlo.methods.consumables.doctree b/.doctrees/reference/tlo.methods.consumables.doctree
diff --git a/.doctrees/reference/tlo.methods.contraception.doctree b/.doctrees/reference/tlo.methods.contraception.doctree
diff --git a/.doctrees/reference/tlo.methods.demography.doctree b/.doctrees/reference/tlo.methods.demography.doctree
diff --git a/.doctrees/reference/tlo.methods.depression.doctree b/.doctrees/reference/tlo.methods.depression.doctree
diff --git a/.doctrees/reference/tlo.methods.diarrhoea.doctree b/.doctrees/reference/tlo.methods.diarrhoea.doctree
diff --git a/.doctrees/reference/tlo.methods.doctree b/.doctrees/reference/tlo.methods.doctree
diff --git a/.doctrees/reference/tlo.methods.dxmanager.doctree b/.doctrees/reference/tlo.methods.dxmanager.doctree
diff --git a/.doctrees/reference/tlo.methods.enhanced_lifestyle.doctree b/.doctrees/reference/tlo.methods.enhanced_lifestyle.doctree
diff --git a/.doctrees/reference/tlo.methods.epi.doctree b/.doctrees/reference/tlo.methods.epi.doctree
diff --git a/.doctrees/reference/tlo.methods.epilepsy.doctree b/.doctrees/reference/tlo.methods.epilepsy.doctree
diff --git a/.doctrees/reference/tlo.methods.fullmodel.doctree b/.doctrees/reference/tlo.methods.fullmodel.doctree
diff --git a/.doctrees/reference/tlo.methods.healthburden.doctree b/.doctrees/reference/tlo.methods.healthburden.doctree
diff --git a/.doctrees/reference/tlo.methods.healthseekingbehaviour.doctree b/.doctrees/reference/tlo.methods.healthseekingbehaviour.doctree
diff --git a/.doctrees/reference/tlo.methods.healthsystem.doctree b/.doctrees/reference/tlo.methods.healthsystem.doctree
diff --git a/.doctrees/reference/tlo.methods.hiv.doctree b/.doctrees/reference/tlo.methods.hiv.doctree
diff --git a/.doctrees/reference/tlo.methods.hiv_tb_calibration.doctree b/.doctrees/reference/tlo.methods.hiv_tb_calibration.doctree
diff --git a/.doctrees/reference/tlo.methods.hsi_generic_first_appts.doctree b/.doctrees/reference/tlo.methods.hsi_generic_first_appts.doctree
diff --git a/.doctrees/reference/tlo.methods.labour.doctree b/.doctrees/reference/tlo.methods.labour.doctree
diff --git a/.doctrees/reference/tlo.methods.labour_lm.doctree b/.doctrees/reference/tlo.methods.labour_lm.doctree
diff --git a/.doctrees/reference/tlo.methods.malaria.doctree b/.doctrees/reference/tlo.methods.malaria.doctree
diff --git a/.doctrees/reference/tlo.methods.measles.doctree b/.doctrees/reference/tlo.methods.measles.doctree
diff --git a/.doctrees/reference/tlo.methods.mockitis.doctree b/.doctrees/reference/tlo.methods.mockitis.doctree
diff --git a/.doctrees/reference/tlo.methods.newborn_outcomes.doctree b/.doctrees/reference/tlo.methods.newborn_outcomes.doctree
diff --git a/.doctrees/reference/tlo.methods.newborn_outcomes_lm.doctree b/.doctrees/reference/tlo.methods.newborn_outcomes_lm.doctree
diff --git a/.doctrees/reference/tlo.methods.oesophagealcancer.doctree b/.doctrees/reference/tlo.methods.oesophagealcancer.doctree
diff --git a/.doctrees/reference/tlo.methods.other_adult_cancers.doctree b/.doctrees/reference/tlo.methods.other_adult_cancers.doctree
diff --git a/.doctrees/reference/tlo.methods.postnatal_supervisor.doctree b/.doctrees/reference/tlo.methods.postnatal_supervisor.doctree
diff --git a/.doctrees/reference/tlo.methods.postnatal_supervisor_lm.doctree b/.doctrees/reference/tlo.methods.postnatal_supervisor_lm.doctree
diff --git a/.doctrees/reference/tlo.methods.pregnancy_helper_functions.doctree b/.doctrees/reference/tlo.methods.pregnancy_helper_functions.doctree
diff --git a/.doctrees/reference/tlo.methods.pregnancy_supervisor.doctree b/.doctrees/reference/tlo.methods.pregnancy_supervisor.doctree
diff --git a/.doctrees/reference/tlo.methods.pregnancy_supervisor_lm.doctree b/.doctrees/reference/tlo.methods.pregnancy_supervisor_lm.doctree
diff --git a/.doctrees/reference/tlo.methods.prostate_cancer.doctree b/.doctrees/reference/tlo.methods.prostate_cancer.doctree
diff --git a/.doctrees/reference/tlo.methods.rti.doctree b/.doctrees/reference/tlo.methods.rti.doctree
diff --git a/.doctrees/reference/tlo.methods.schisto.doctree b/.doctrees/reference/tlo.methods.schisto.doctree
diff --git a/.doctrees/reference/tlo.methods.simplified_births.doctree b/.doctrees/reference/tlo.methods.simplified_births.doctree
diff --git a/.doctrees/reference/tlo.methods.skeleton.doctree b/.doctrees/reference/tlo.methods.skeleton.doctree
diff --git a/.doctrees/reference/tlo.methods.stunting.doctree b/.doctrees/reference/tlo.methods.stunting.doctree
diff --git a/.doctrees/reference/tlo.methods.symptommanager.doctree b/.doctrees/reference/tlo.methods.symptommanager.doctree
diff --git a/.doctrees/reference/tlo.methods.tb.doctree b/.doctrees/reference/tlo.methods.tb.doctree
diff --git a/.doctrees/reference/tlo.methods.wasting.doctree b/.doctrees/reference/tlo.methods.wasting.doctree
diff --git a/.doctrees/reference/tlo.population.doctree b/.doctrees/reference/tlo.population.doctree
diff --git a/.doctrees/reference/tlo.progressbar.doctree b/.doctrees/reference/tlo.progressbar.doctree
diff --git a/.doctrees/reference/tlo.scenario.doctree b/.doctrees/reference/tlo.scenario.doctree
diff --git a/.doctrees/reference/tlo.simulation.doctree b/.doctrees/reference/tlo.simulation.doctree
diff --git a/.doctrees/reference/tlo.test.doctree b/.doctrees/reference/tlo.test.doctree
diff --git a/.doctrees/reference/tlo.test.random_birth.doctree b/.doctrees/reference/tlo.test.random_birth.doctree
diff --git a/.doctrees/reference/tlo.test.random_death.doctree b/.doctrees/reference/tlo.test.random_death.doctree
diff --git a/.doctrees/reference/tlo.util.doctree b/.doctrees/reference/tlo.util.doctree
diff --git a/.doctrees/writeups.doctree b/.doctrees/writeups.doctree
diff --git a/_data_sources.html b/_data_sources.html
diff --git a/_downloads/23adaf6cf93219b8c57f084eec0ccd41/Epilepsy.docx b/_downloads/23adaf6cf93219b8c57f084eec0ccd41/Epilepsy.docx
diff --git a/_downloads/d259ee2478d4ac9e09a19cb71e63d1a9/hsi_events.csv b/_downloads/d259ee2478d4ac9e09a19cb71e63d1a9/hsi_events.csv
diff --git a/_downloads/db7bd2398d1bf8be50deed61b70cde9a/Measles.docx b/_downloads/db7bd2398d1bf8be50deed61b70cde9a/Measles.docx
diff --git a/_hsi_events.html b/_hsi_events.html
diff --git a/_modules/index.html b/_modules/index.html
@@ -1,96 +1,45 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" >
 <head>
   <meta charset="utf-8" />
-
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-
   <title>Overview: module code &mdash; TLOmodel 0.1.0 documentation</title>
-
-
-
-  <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
-  <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-  <link rel="stylesheet" href="../_static/theme_overrides.css" type="text/css" />
-
-
-
+      <link rel="stylesheet" href="../_static/theme_overrides.css" type="text/css" />
     <link rel="shortcut icon" href="../_static/favicon.png"/>
-
-
-
-
-
-
-
-
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-
-      <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
         <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
-        <script src="../_static/jquery.js"></script>
-        <script src="../_static/underscore.js"></script>
-        <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
         <script src="../_static/doctools.js"></script>
-
-    <script type="text/javascript" src="../_static/js/theme.js"></script>
-
-
+        <script src="../_static/sphinx_highlight.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">
-
-
+<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"> TLOmodel
-
-
 
+          <a href="../index.html" class="icon icon-home">
+            TLOmodel
           </a>
-
-
-
-
               <div class="version">
                 0.1.0
               </div>
-
-
-
-
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" />
+    <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="main navigation">
-
-
-
-
-
-
+        </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="../index.html">Welcome</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../aims.html">Aims &amp; Objectives</a></li>
@@ -105,67 +54,29 @@
 <li class="toctree-l1"><a class="reference internal" href="../contributing.html">Contributing</a></li>
 </ul>
 
-
-
         </div>
-
       </div>
     </nav>
 
-    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
-
-
-      <nav class="wy-nav-top" aria-label="top navigation">
-
+    <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">TLOmodel</a>
-
       </nav>
 
-
       <div class="wy-nav-content">
-
         <div class="rst-content">
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-<div role="navigation" aria-label="breadcrumbs navigation">
-
+          <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-
-      <li><a href="../index.html" class="icon icon-home"></a> &raquo;</li>
-
-      <li>Overview: module code</li>
-
-
+      <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li class="breadcrumb-item active">Overview: module code</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>All modules for which code is available</h1>
 <ul><li><a href="tlo/analysis/hsi_events.html">tlo.analysis.hsi_events</a></li>
 <li><a href="tlo/analysis/utils.html">tlo.analysis.utils</a></li>
@@ -175,6 +86,7 @@ <h1>All modules for which code is available</h1>
 <li><a href="tlo/docs.html">tlo.docs</a></li>
 <li><a href="tlo/events.html">tlo.events</a></li>
 <li><a href="tlo/lm.html">tlo.lm</a></li>
+<li><a href="tlo/lm_play.html">tlo.lm_play</a></li>
 <li><a href="tlo/logging/core.html">tlo.logging.core</a></li>
 <li><a href="tlo/logging/encoding.html">tlo.logging.encoding</a></li>
 <li><a href="tlo/logging/helpers.html">tlo.logging.helpers</a></li>
@@ -197,6 +109,7 @@ <h1>All modules for which code is available</h1>
 <li><a href="tlo/methods/healthseekingbehaviour.html">tlo.methods.healthseekingbehaviour</a></li>
 <li><a href="tlo/methods/healthsystem.html">tlo.methods.healthsystem</a></li>
 <li><a href="tlo/methods/hiv.html">tlo.methods.hiv</a></li>
+<li><a href="tlo/methods/hiv_tb_calibration.html">tlo.methods.hiv_tb_calibration</a></li>
 <li><a href="tlo/methods/hsi_generic_first_appts.html">tlo.methods.hsi_generic_first_appts</a></li>
 <li><a href="tlo/methods/labour.html">tlo.methods.labour</a></li>
 <li><a href="tlo/methods/malaria.html">tlo.methods.malaria</a></li>
@@ -226,48 +139,32 @@ <h1>All modules for which code is available</h1>
 </ul>
 
            </div>
-
           </div>
           <footer>
 
   <hr/>
 
   <div role="contentinfo">
     <p>
-      <span class="lastupdated">
-        Last updated on Dec 01, 2022.
-      </span>
-
-    </p>
+      <span class="lastupdated">Last updated on Apr 06, 2023.
+      </span></p>
   </div>
-
-
-
-    Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
-
+
+  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>. 
+    provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
 
 </footer>
         </div>
       </div>
-
     </section>
-
   </div>
-
-
-  <script type="text/javascript">
+  <script>
       jQuery(function () {
           SphinxRtdTheme.Navigation.enable(true);
       });
-  </script>
-
-
-
-
-
+  </script> 
 
 </body>
 </html>