added auto doc req file and updated steps for setup

quanted · Jul 18, 2024 · 3757d0c · 3757d0c
1 parent c1e58ce
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Showing 38 changed files with 307 additions and 1,905 deletions.
diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -14,8 +14,13 @@ jobs:
       - name: Install dependencies
         run: |
           pip install sphinx sphinx_rtd_theme myst_parser sphinx-click
+          pip install -r doc-requirements.txt
       - name: Sphinx build
         run: |
+          python -m build
+          pip install dist\esat-2024.0.1-cp312-cp312-linux_x86_64.whl
+          sphinx-apidoc -o docs esat
+          sphinx-apidoc -o docs eval
           sphinx-build -M html . docs
       - name: Deploy to GitHub Pages
         uses: peaceiris/actions-gh-pages@v3

diff --git a/conf.py b/conf.py
@@ -5,10 +5,10 @@
 import os
 import sys
 from datetime import datetime
-sys.path.insert(0, os.path.abspath('.'))
-sys.path.insert(1, os.path.abspath('..'))
-sys.path.insert(2, os.path.abspath(os.path.join("..", "esat")))
-sys.path.insert(3, os.path.abspath(os.path.join("..", "eval")))
+sys.path.insert(0, os.path.abspath("."))
+sys.path.insert(1, os.path.abspath(os.path.join('.', 'esat')))
+# sys.path.insert(2, os.path.abspath(os.path.join(".", "esat")))
+sys.path.insert(2, os.path.abspath(os.path.join(".", "eval")))
 
 
 # -- Project information -----------------------------------------------------
@@ -17,7 +17,8 @@
 project = 'Environmental Source Apportionment Toolkit (ESAT)'
 copyright = '2024, EPA'
 author = 'Deron Smith'
-release = datetime.now().strftime("%m/%d/%Y")
+version = str(datetime.now().year)
+release = "0.1a"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

diff --git a/doc-requirements.txt b/doc-requirements.txt
@@ -0,0 +1,11 @@
+fastcluster==1.2.6
+fuzzy-c-means==1.7.0
+myst_parser==3.0.1
+numpy==1.26.4
+pandas==2.2.0
+plotly==5.22.0
+scipy==1.14.0
+sphinx==7.4.6
+sphinx-click==6.0.0
+sphinx_rtd_theme==2.0.0
+tqdm==4.66.4
diff --git a/docs/doctrees/.pytest_cache/README.doctree b/docs/doctrees/.pytest_cache/README.doctree
diff --git a/docs/doctrees/README.doctree b/docs/doctrees/README.doctree
diff --git a/docs/doctrees/docs/cli.doctree b/docs/doctrees/docs/cli.doctree
diff --git a/docs/doctrees/docs/esat.cli.doctree b/docs/doctrees/docs/esat.cli.doctree
diff --git a/docs/doctrees/docs/esat.data.doctree b/docs/doctrees/docs/esat.data.doctree
diff --git a/docs/doctrees/docs/esat.doctree b/docs/doctrees/docs/esat.doctree
diff --git a/docs/doctrees/docs/esat.error.doctree b/docs/doctrees/docs/esat.error.doctree
diff --git a/docs/doctrees/docs/esat.model.doctree b/docs/doctrees/docs/esat.model.doctree
diff --git a/docs/doctrees/docs/esat.rotational.doctree b/docs/doctrees/docs/esat.rotational.doctree
diff --git a/docs/doctrees/docs/eval.doctree b/docs/doctrees/docs/eval.doctree
diff --git a/docs/doctrees/docs/modules.doctree b/docs/doctrees/docs/modules.doctree
diff --git a/docs/doctrees/environment.pickle b/docs/doctrees/environment.pickle
diff --git a/docs/doctrees/index.doctree b/docs/doctrees/index.doctree
diff --git a/docs/html/.buildinfo b/docs/html/.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: 905dd1daf8b115872569f488ac4a69b1
+config: 0c27b2fe9c7950e44a6a7aa429929cac
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/html/.pytest_cache/README.html b/docs/html/.pytest_cache/README.html
@@ -0,0 +1,116 @@
+<!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" />
+
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>pytest cache directory &mdash; Environmental Source Apportionment Toolkit (ESAT) 0.1a 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=88a2ef70"></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">
+            Environmental Source Apportionment Toolkit (ESAT)
+          </a>
+              <div class="version">
+                2024
+              </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" 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">Documentation</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../index.html">Welcome to EPA ESAT’s Documentation!</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../README.html">Environmental Source Apportionment Toolkit (ESAT)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../docs/modules.html">Python API</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../docs/cli.html">Command Line Interface</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">Environmental Source Apportionment Toolkit (ESAT)</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 active">pytest cache directory</li>
+      <li class="wy-breadcrumbs-aside">
+            <a href="../_sources/.pytest_cache/README.md.txt" rel="nofollow"> View page source</a>
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+  <section id="pytest-cache-directory">
+<h1>pytest cache directory<a class="headerlink" href="#pytest-cache-directory" title="Link to this heading"></a></h1>
+<p>This directory contains data from the pytest’s cache plugin,
+which provides the <code class="docutils literal notranslate"><span class="pre">--lf</span></code> and <code class="docutils literal notranslate"><span class="pre">--ff</span></code> options, as well as the <code class="docutils literal notranslate"><span class="pre">cache</span></code> fixture.</p>
+<p><strong>Do not</strong> commit this to version control.</p>
+<p>See <a class="reference external" href="https://docs.pytest.org/en/stable/how-to/cache.html">the docs</a> for more information.</p>
+</section>
+
+
+           </div>
+          </div>
+          <footer>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2024, EPA.</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>
diff --git a/docs/html/README.html b/docs/html/README.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Environmental Source Apportionment Toolkit (ESAT) &mdash; Environmental Source Apportionment Toolkit (ESAT) 06/03/2024 documentation</title>
+  <title>Environmental Source Apportionment Toolkit (ESAT) &mdash; Environmental Source Apportionment Toolkit (ESAT) 0.1a 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" />
 
@@ -15,7 +15,7 @@
 
         <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=f6960e4d"></script>
+        <script src="_static/documentation_options.js?v=88a2ef70"></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>
@@ -36,6 +36,9 @@
           <a href="index.html" class="icon icon-home">
             Environmental Source Apportionment Toolkit (ESAT)
           </a>
+              <div class="version">
+                2024
+              </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" aria-label="Search docs" />

diff --git a/docs/html/_sources/.pytest_cache/README.md.txt b/docs/html/_sources/.pytest_cache/README.md.txt
@@ -0,0 +1,8 @@
+# pytest cache directory #
+
+This directory contains data from the pytest's cache plugin,
+which provides the `--lf` and `--ff` options, as well as the `cache` fixture.
+
+**Do not** commit this to version control.
+
+See [the docs](https://docs.pytest.org/en/stable/how-to/cache.html) for more information.
diff --git a/docs/html/_static/documentation_options.js b/docs/html/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '06/03/2024',
+    VERSION: '0.1a',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/html/_static/searchtools.js b/docs/html/_static/searchtools.js
@@ -178,7 +178,7 @@ const Search = {
 
   htmlToText: (htmlString, anchor) => {
     const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
-    for (const removalQuery of [".headerlinks", "script", "style"]) {
+    for (const removalQuery of [".headerlink", "script", "style"]) {
       htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() });
     }
     if (anchor) {
@@ -328,13 +328,14 @@ const Search = {
     for (const [title, foundTitles] of Object.entries(allTitles)) {
       if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) {
         for (const [file, id] of foundTitles) {
-          let score = Math.round(100 * queryLower.length / title.length)
+          const score = Math.round(Scorer.title * queryLower.length / title.length);
+          const boost = titles[file] === title ? 1 : 0;  // add a boost for document titles
           normalResults.push([
             docNames[file],
             titles[file] !== title ? `${titles[file]} > ${title}` : title,
             id !== null ? "#" + id : "",
             null,
-            score,
+            score + boost,
             filenames[file],
           ]);
         }