v1.0.7

danielfrees · Sep 14, 2023 · 1bbd7e9 · 1bbd7e9
1 parent 5bfbe15
commit 1bbd7e9
Show file tree

Hide file tree

Showing 11 changed files with 785 additions and 780 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,8 +6,8 @@ repos:
       language_version: python3.11
   - repo: local
     hooks:
-      - id: pytest-check
-        name: pytest-check
+      - id: pytest
+        name: pytest
         entry: pytest
         language: system
         pass_filenames: false

diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
@@ -9,25 +9,25 @@
   <!--[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=e2a723ec"></script>
         <script src="../_static/doctools.js?v=888ff710"></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" /> 
+    <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">
             scrapemed
           </a>
@@ -66,7 +66,7 @@
 </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="scrapemed/paper.html">scrapemed.paper</a></li>
 <li><a href="scrapemed/paperSet.html">scrapemed.paperSet</a></li>
@@ -88,7 +88,7 @@ <h1>All modules for which code is available</h1>
   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>
@@ -99,7 +99,7 @@ <h1>All modules for which code is available</h1>
       jQuery(function () {
           SphinxRtdTheme.Navigation.enable(true);
       });
-  </script> 
+  </script>
 
 </body>
 </html>
diff --git a/docs/build/html/_modules/scrapemed/trees.html b/docs/build/html/_modules/scrapemed/trees.html
@@ -9,25 +9,25 @@
   <!--[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=e2a723ec"></script>
         <script src="../../_static/doctools.js?v=888ff710"></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" /> 
+    <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">
             scrapemed
           </a>
@@ -67,7 +67,7 @@
 </div>
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
-             
+
   <h1>Source code for scrapemed.trees</h1><div class="highlight"><pre>
 <span></span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">Scrapemed&#39;s &quot;trees&quot; module handles PMC article tree visualizations,</span>
@@ -216,7 +216,7 @@ <h1>Source code for scrapemed.trees</h1><div class="highlight"><pre>
   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>
@@ -227,7 +227,7 @@ <h1>Source code for scrapemed.trees</h1><div class="highlight"><pre>
       jQuery(function () {
           SphinxRtdTheme.Navigation.enable(true);
       });
-  </script> 
+  </script>
 
 </body>
 </html>
diff --git a/docs/build/html/_static/css/fonts/fontawesome-webfont.svg b/docs/build/html/_static/css/fonts/fontawesome-webfont.svg
diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html
@@ -9,25 +9,25 @@
   <!--[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=e2a723ec"></script>
         <script src="_static/doctools.js?v=888ff710"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="#" />
-    <link rel="search" title="Search" href="search.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">
             scrapemed
           </a>
@@ -66,7 +66,7 @@
 </div>
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
-             
+
 
 <h1 id="index">Index</h1>
 
@@ -86,7 +86,7 @@ <h1 id="index">Index</h1>
  | <a href="#T"><strong>T</strong></a>
  | <a href="#V"><strong>V</strong></a>
  | <a href="#X"><strong>X</strong></a>
- 
+
 </div>
 <h2 id="A">A</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
@@ -344,7 +344,7 @@ <h2 id="X">X</h2>
   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>
@@ -355,7 +355,7 @@ <h2 id="X">X</h2>
       jQuery(function () {
           SphinxRtdTheme.Navigation.enable(true);
       });
-  </script> 
+  </script>
 
 </body>
 </html>
diff --git a/docs/build/html/index.html b/docs/build/html/index.html
@@ -10,7 +10,7 @@
   <!--[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=e2a723ec"></script>
@@ -19,17 +19,17 @@
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="scrapemed" href="modules.html" /> 
+    <link rel="next" title="scrapemed" href="modules.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="#" class="icon icon-home">
             scrapemed
           </a>
@@ -69,7 +69,7 @@
 </div>
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
-             
+
   <section id="welcome-to-scrapemed-s-documentation">
 <h1>Welcome to scrapemed’s documentation!<a class="headerlink" href="#welcome-to-scrapemed-s-documentation" title="Link to this heading"></a></h1>
 <p>ScrapeMed is a powerful, easy to use, data scraping tool for PubMed Central (PMC) data.
@@ -135,7 +135,7 @@ <h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Li
   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>
@@ -146,7 +146,7 @@ <h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Li
       jQuery(function () {
           SphinxRtdTheme.Navigation.enable(true);
       });
-  </script> 
+  </script>
 
 </body>
 </html>
diff --git a/docs/build/html/modules.html b/docs/build/html/modules.html
@@ -10,7 +10,7 @@
   <!--[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=e2a723ec"></script>
@@ -20,17 +20,17 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="scrapemed package" href="scrapemed.html" />
-    <link rel="prev" title="Welcome to scrapemed’s documentation!" href="index.html" /> 
+    <link rel="prev" title="Welcome to scrapemed’s documentation!" href="index.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">
             scrapemed
           </a>
@@ -73,7 +73,7 @@
 </div>
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
-             
+
   <section id="scrapemed">
 <h1>scrapemed<a class="headerlink" href="#scrapemed" title="Link to this heading"></a></h1>
 <div class="toctree-wrapper compound">
@@ -159,7 +159,7 @@ <h1>scrapemed<a class="headerlink" href="#scrapemed" title="Link to this heading
   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>
@@ -170,7 +170,7 @@ <h1>scrapemed<a class="headerlink" href="#scrapemed" title="Link to this heading
       jQuery(function () {
           SphinxRtdTheme.Navigation.enable(true);
       });
-  </script> 
+  </script>
 
 </body>
 </html>
diff --git a/docs/build/html/py-modindex.html b/docs/build/html/py-modindex.html
@@ -9,7 +9,7 @@
   <!--[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=e2a723ec"></script>
@@ -18,19 +18,19 @@
     <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">
             scrapemed
           </a>
@@ -69,7 +69,7 @@
 </div>
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
-             
+
 
    <h1>Python Module Index</h1>
 
@@ -128,7 +128,7 @@ <h1>Python Module Index</h1>
   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>
@@ -139,7 +139,7 @@ <h1>Python Module Index</h1>
       jQuery(function () {
           SphinxRtdTheme.Navigation.enable(true);
       });
-  </script> 
+  </script>
 
 </body>
 </html>