FINALLY fix gh-pages deployment???

yinchi · May 4, 2024 · 2c6c49c · 2c6c49c
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diff --git a/.github/workflows/html_dir_to_gh_pages.yaml b/.github/workflows/html_dir_to_gh_pages.yaml
@@ -37,7 +37,7 @@ jobs:
         uses: actions/upload-pages-artifact@v3
         with:
           name: html-docs
-          path: docs/_build/html/
+          path: docs/html/
       - name: Deploy to GitHub Pages
         id: deployment
         uses: actions/deploy-pages@v4
diff --git a/docs.sh b/docs.sh
@@ -3,6 +3,7 @@ build-docs() {
     poetry run sphinx-apidoc -fe -o docs/apidoc/ histopath_bim_des/
     cd docs
     poetry run make html
+    cp -r _build/html html
     popd
 }
 

diff --git a/docs/html/.buildinfo b/docs/html/.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: 661ee7406388d085c75b2b522d567f0f
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/html/.nojekyll b/docs/html/.nojekyll
diff --git a/docs/html/_images/Config.erd.png b/docs/html/_images/Config.erd.png
diff --git a/docs/html/_images/uml_flowchart.png b/docs/html/_images/uml_flowchart.png
diff --git a/docs/html/_modules/histopath_bim_des/bim.html b/docs/html/_modules/histopath_bim_des/bim.html
diff --git a/docs/html/_modules/histopath_bim_des/config/arrivals.html b/docs/html/_modules/histopath_bim_des/config/arrivals.html
@@ -0,0 +1,195 @@
+<!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>histopath_bim_des.config.arrivals &mdash; histopath-bim-des 0.0.0 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=7026087e"></script>
+        <script src="../../../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></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">
+            histopath-bim-des
+          </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">
+              <p class="caption" role="heading"><span class="caption-text">Contents</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../../../apidoc/histopath_bim_des.html">histopath_bim_des package</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">histopath-bim-des</a>
+      </nav>
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+          <div role="navigation" aria-label="Page navigation">
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+      <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">histopath_bim_des.config.arrivals</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 histopath_bim_des.config.arrivals</h1><div class="highlight"><pre>
+<span></span><span class="sd">&quot;&quot;&quot;Arrival process configuration module for the histopath simulation model.&quot;&quot;&quot;</span>
+
+<span class="kn">import</span> <span class="nn">typing</span> <span class="k">as</span> <span class="nn">ty</span>
+
+<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+<span class="kn">import</span> <span class="nn">pydantic</span> <span class="k">as</span> <span class="nn">pyd</span>
+<span class="kn">from</span> <span class="nn">annotated_types</span> <span class="kn">import</span> <span class="n">Annotated</span><span class="p">,</span> <span class="n">Len</span>
+<span class="kn">from</span> <span class="nn">openpyxl</span> <span class="kn">import</span> <span class="n">Workbook</span>
+
+<span class="kn">from</span> <span class="nn">..</span> <span class="kn">import</span> <span class="n">excel</span>
+
+
+<div class="viewcode-block" id="ArrivalSchedule">
+<a class="viewcode-back" href="../../../apidoc/histopath_bim_des.config.arrivals.html#histopath_bim_des.config.arrivals.ArrivalSchedule">[docs]</a>
+<span class="k">class</span> <span class="nc">ArrivalSchedule</span><span class="p">(</span><span class="n">pyd</span><span class="o">.</span><span class="n">BaseModel</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;An arrival schedule for specimens.&quot;&quot;&quot;</span>
+
+    <span class="n">rates</span><span class="p">:</span> <span class="n">Annotated</span><span class="p">[</span><span class="n">ty</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="n">pyd</span><span class="o">.</span><span class="n">NonNegativeFloat</span><span class="p">],</span> <span class="n">Len</span><span class="p">(</span><span class="mi">168</span><span class="p">,</span> <span class="mi">168</span><span class="p">)]</span>
+    <span class="s2">&quot;Hourly arrival rates for the arrival process, for one week (168 hours).&quot;</span>
+
+<div class="viewcode-block" id="ArrivalSchedule.from_pd">
+<a class="viewcode-back" href="../../../apidoc/histopath_bim_des.config.arrivals.html#histopath_bim_des.config.arrivals.ArrivalSchedule.from_pd">[docs]</a>
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">from_pd</span><span class="p">(</span><span class="n">df</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="s1">&#39;ArrivalSchedule&#39;</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Construct an arrival schedule from a dataframe with the 24 hours the day as rows</span>
+<span class="sd">        and the seven days of the week as columns (starting on Monday).  Each value is the</span>
+<span class="sd">        arrival rate for one hour of the week</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            df: The dataframe containing the arrival schedule information.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            The ArrivalSchedule object.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">return</span> <span class="vm">__class__</span><span class="p">(</span><span class="n">rates</span><span class="o">=</span><span class="n">df</span><span class="o">.</span><span class="n">to_numpy</span><span class="p">()</span><span class="o">.</span><span class="n">flatten</span><span class="p">(</span><span class="s1">&#39;F&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">tolist</span><span class="p">())</span>  <span class="c1"># F = column-major order</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="ArrivalSchedules">
+<a class="viewcode-back" href="../../../apidoc/histopath_bim_des.config.arrivals.html#histopath_bim_des.config.arrivals.ArrivalSchedules">[docs]</a>
+<span class="k">class</span> <span class="nc">ArrivalSchedules</span><span class="p">(</span><span class="n">pyd</span><span class="o">.</span><span class="n">BaseModel</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Dataclass for tracking the specimen arrival schedules of the histopathology model.&quot;&quot;&quot;</span>
+
+    <span class="n">cancer</span><span class="p">:</span> <span class="n">ArrivalSchedule</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Arrival schedule for cancer pathway specimens.&quot;&quot;&quot;</span>
+
+    <span class="n">noncancer</span><span class="p">:</span> <span class="n">ArrivalSchedule</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Arrival schedule for non-cancer pathway specimens.&quot;&quot;&quot;</span>
+
+<div class="viewcode-block" id="ArrivalSchedules.from_workbook">
+<a class="viewcode-back" href="../../../apidoc/histopath_bim_des.config.arrivals.html#histopath_bim_des.config.arrivals.ArrivalSchedules.from_workbook">[docs]</a>
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">from_workbook</span><span class="p">(</span><span class="n">wbook</span><span class="p">:</span> <span class="n">Workbook</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="s1">&#39;ArrivalSchedules&#39;</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Construct a dataclass instance from an Excel workbook.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            wbook: The Excel workbook to parse.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            The parsed dataclass instance.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">arrival_schedule_cancer_df</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">df</span> <span class="o">:=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="n">table</span> <span class="o">:=</span> <span class="n">excel</span><span class="o">.</span><span class="n">get_table</span><span class="p">(</span><span class="n">wbook</span><span class="p">,</span> <span class="s1">&#39;Arrival Schedules&#39;</span><span class="p">,</span> <span class="s1">&#39;ArrivalScheduleCancer&#39;</span><span class="p">)</span>
+                <span class="p">)[</span><span class="mi">1</span><span class="p">:],</span>
+                <span class="n">columns</span><span class="o">=</span><span class="n">table</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s1">&#39;Hour&#39;</span><span class="p">)</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">df</span><span class="o">.</span><span class="n">index</span> <span class="o">!=</span> <span class="s1">&#39;Total&#39;</span><span class="p">]</span>
+
+        <span class="n">arrival_schedule_noncancer_df</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">df</span> <span class="o">:=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="n">table</span> <span class="o">:=</span> <span class="n">excel</span><span class="o">.</span><span class="n">get_table</span><span class="p">(</span><span class="n">wbook</span><span class="p">,</span> <span class="s1">&#39;Arrival Schedules&#39;</span><span class="p">,</span> <span class="s1">&#39;ArrivalScheduleNonCancer&#39;</span><span class="p">)</span>
+                <span class="p">)[</span><span class="mi">1</span><span class="p">:],</span>
+                <span class="n">columns</span><span class="o">=</span><span class="n">table</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s1">&#39;Hour&#39;</span><span class="p">)</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">df</span><span class="o">.</span><span class="n">index</span> <span class="o">!=</span> <span class="s1">&#39;Total&#39;</span><span class="p">]</span>
+
+        <span class="k">return</span> <span class="n">ArrivalSchedules</span><span class="p">(</span>
+            <span class="n">cancer</span><span class="o">=</span><span class="n">ArrivalSchedule</span><span class="o">.</span><span class="n">from_pd</span><span class="p">(</span><span class="n">arrival_schedule_cancer_df</span><span class="p">),</span>
+            <span class="n">noncancer</span><span class="o">=</span><span class="n">ArrivalSchedule</span><span class="o">.</span><span class="n">from_pd</span><span class="p">(</span><span class="n">arrival_schedule_noncancer_df</span><span class="p">),</span>
+        <span class="p">)</span></div>
+</div>
+
+</pre></div>
+
+           </div>
+          </div>
+          <footer>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2024, Yin-Chi Chan, Nicola Moretti.</p>
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+</html>
-Original file line number
+Diff line change
@@ Expand Up / @@ -3,6 +3,7 @@ build-docs() { @@
         poetry run sphinx-apidoc -fe -o docs/apidoc/ histopath_bim_des/
         cd docs
         poetry run make html
+        cp -r _build/html html
         popd
     }
@@ Expand Down @@