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titipata · Aug 30, 2024 · 3f7c503 · 3f7c503
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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: 9dca3470b2ad9c246eea0133284e2a44
+config: 58d48bb294faa78a8aa123aa8ed28651
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/_modules/index.html b/_modules/index.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Overview: module code &mdash; Pubmed Parser 0.6.dev3+ga6e846d documentation</title>
+  <title>Overview: module code &mdash; Pubmed Parser 0.5.2.dev1+ga7e88c8 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" />
 
@@ -14,7 +14,7 @@
 
         <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=cd3e8eb9"></script>
+        <script src="../_static/documentation_options.js?v=25fc7194"></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>
@@ -34,7 +34,7 @@
             Pubmed Parser
           </a>
               <div class="version">
-                0.6.dev3+ga6e846d
+                0.5.2.dev1+ga7e88c8
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">

diff --git a/_modules/pubmed_parser/medline_parser.html b/_modules/pubmed_parser/medline_parser.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pubmed_parser.medline_parser &mdash; Pubmed Parser 0.6.dev3+ga6e846d documentation</title>
+  <title>pubmed_parser.medline_parser &mdash; Pubmed Parser 0.5.2.dev1+ga7e88c8 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" />
 
@@ -14,7 +14,7 @@
 
         <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=cd3e8eb9"></script>
+        <script src="../../_static/documentation_options.js?v=25fc7194"></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>
@@ -34,7 +34,7 @@
             Pubmed Parser
           </a>
               <div class="version">
-                0.6.dev3+ga6e846d
+                0.5.2.dev1+ga7e88c8
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">

diff --git a/_modules/pubmed_parser/pubmed_oa_parser.html b/_modules/pubmed_parser/pubmed_oa_parser.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pubmed_parser.pubmed_oa_parser &mdash; Pubmed Parser 0.6.dev3+ga6e846d documentation</title>
+  <title>pubmed_parser.pubmed_oa_parser &mdash; Pubmed Parser 0.5.2.dev1+ga7e88c8 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" />
 
@@ -14,7 +14,7 @@
 
         <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=cd3e8eb9"></script>
+        <script src="../../_static/documentation_options.js?v=25fc7194"></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>
@@ -34,7 +34,7 @@
             Pubmed Parser
           </a>
               <div class="version">
-                0.6.dev3+ga6e846d
+                0.5.2.dev1+ga7e88c8
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
@@ -453,7 +453,7 @@ <h1>Source code for pubmed_parser.pubmed_oa_parser</h1><div class="highlight"><p
 
 <div class="viewcode-block" id="parse_pubmed_paragraph">
 <a class="viewcode-back" href="../../api.html#pubmed_parser.parse_pubmed_paragraph">[docs]</a>
-<span class="k">def</span> <span class="nf">parse_pubmed_paragraph</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">all_paragraph</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+<span class="k">def</span> <span class="nf">parse_pubmed_paragraph</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Give path to a given PubMed OA file, parse and return</span>
 <span class="sd">    a dictionary of all paragraphs, section that it belongs to,</span>
@@ -463,13 +463,6 @@ <h1>Source code for pubmed_parser.pubmed_oa_parser</h1><div class="highlight"><p
 <span class="sd">    ----------</span>
 <span class="sd">    path: str</span>
 <span class="sd">        A string to an XML path.</span>
-<span class="sd">    all_paragraph: bool</span>
-<span class="sd">        By default, this function will only append a paragraph if there is at least</span>
-<span class="sd">        one reference made in a paragraph (to aviod noisy parsed text).</span>
-<span class="sd">        A boolean indicating if you want to include paragraph with no references made or not</span>
-<span class="sd">        if True, include all paragraphs</span>
-<span class="sd">        if False, include only paragraphs that have references</span>
-<span class="sd">        default: False</span>
 
 <span class="sd">    Return</span>
 <span class="sd">    ------</span>
@@ -507,8 +500,8 @@ <h1>Source code for pubmed_parser.pubmed_oa_parser</h1><div class="highlight"><p
             <span class="s2">&quot;section&quot;</span><span class="p">:</span> <span class="n">section</span><span class="p">,</span>
             <span class="s2">&quot;text&quot;</span><span class="p">:</span> <span class="n">paragraph_text</span><span class="p">,</span>
         <span class="p">}</span>
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ref_ids</span><span class="p">)</span> <span class="o">&gt;=</span> <span class="mi">1</span> <span class="ow">or</span> <span class="n">all_paragraph</span><span class="p">:</span>
-            <span class="n">dict_pars</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dict_par</span><span class="p">)</span>
+
+        <span class="n">dict_pars</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dict_par</span><span class="p">)</span>
 
     <span class="k">return</span> <span class="n">dict_pars</span></div>
 

diff --git a/_modules/pubmed_parser/pubmed_web_parser.html b/_modules/pubmed_parser/pubmed_web_parser.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pubmed_parser.pubmed_web_parser &mdash; Pubmed Parser 0.6.dev3+ga6e846d documentation</title>
+  <title>pubmed_parser.pubmed_web_parser &mdash; Pubmed Parser 0.5.2.dev1+ga7e88c8 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" />
 
@@ -14,7 +14,7 @@
 
         <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=cd3e8eb9"></script>
+        <script src="../../_static/documentation_options.js?v=25fc7194"></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>
@@ -34,7 +34,7 @@
             Pubmed Parser
           </a>
               <div class="version">
-                0.6.dev3+ga6e846d
+                0.5.2.dev1+ga7e88c8
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">

diff --git a/_static/documentation_options.js b/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.6.dev3+ga6e846d',
+    VERSION: '0.5.2.dev1+ga7e88c8',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/api.html b/api.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>API Documentation &mdash; Pubmed Parser 0.6.dev3+ga6e846d documentation</title>
+  <title>API Documentation &mdash; Pubmed Parser 0.5.2.dev1+ga7e88c8 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=cd3e8eb9"></script>
+        <script src="_static/documentation_options.js?v=25fc7194"></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>
@@ -37,7 +37,7 @@
             Pubmed Parser
           </a>
               <div class="version">
-                0.6.dev3+ga6e846d
+                0.5.2.dev1+ga7e88c8
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
@@ -246,7 +246,7 @@ <h3>Return<a class="headerlink" href="#id5" title="Link to this heading"></a>
 
 <dl class="py function">
 <dt class="sig sig-object py" id="pubmed_parser.parse_pubmed_paragraph">
-<span class="sig-prename descclassname"><span class="pre">pubmed_parser.</span></span><span class="sig-name descname"><span class="pre">parse_pubmed_paragraph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">all_paragraph</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pubmed_parser/pubmed_oa_parser.html#parse_pubmed_paragraph"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pubmed_parser.parse_pubmed_paragraph" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">pubmed_parser.</span></span><span class="sig-name descname"><span class="pre">parse_pubmed_paragraph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pubmed_parser/pubmed_oa_parser.html#parse_pubmed_paragraph"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pubmed_parser.parse_pubmed_paragraph" title="Link to this definition"></a></dt>
 <dd><p>Give path to a given PubMed OA file, parse and return
 a dictionary of all paragraphs, section that it belongs to,
 and a list of reference made in each paragraph as a list of PMIDs</p>
@@ -255,13 +255,6 @@ <h3>Parameters<a class="headerlink" href="#id6" title="Link to this heading">
 <dl class="simple">
 <dt>path: str</dt><dd><p>A string to an XML path.</p>
 </dd>
-<dt>all_paragraph: bool</dt><dd><p>By default, this function will only append a paragraph if there is at least
-one reference made in a paragraph (to aviod noisy parsed text).
-A boolean indicating if you want to include paragraph with no references made or not
-if True, include all paragraphs
-if False, include only paragraphs that have references
-default: False</p>
-</dd>
 </dl>
 </section>
 <section id="id7">

diff --git a/genindex.html b/genindex.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Index &mdash; Pubmed Parser 0.6.dev3+ga6e846d documentation</title>
+  <title>Index &mdash; Pubmed Parser 0.5.2.dev1+ga7e88c8 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" />
 
@@ -14,7 +14,7 @@
 
         <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=cd3e8eb9"></script>
+        <script src="_static/documentation_options.js?v=25fc7194"></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>
@@ -34,7 +34,7 @@
             Pubmed Parser
           </a>
               <div class="version">
-                0.6.dev3+ga6e846d
+                0.5.2.dev1+ga7e88c8
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">

diff --git a/index.html b/index.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>Pubmed Parser: A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset &mdash; Pubmed Parser 0.6.dev3+ga6e846d documentation</title>
+  <title>Pubmed Parser: A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset &mdash; Pubmed Parser 0.5.2.dev1+ga7e88c8 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=cd3e8eb9"></script>
+        <script src="_static/documentation_options.js?v=25fc7194"></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>
@@ -36,7 +36,7 @@
             Pubmed Parser
           </a>
               <div class="version">
-                0.6.dev3+ga6e846d
+                0.5.2.dev1+ga7e88c8
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">

diff --git a/install.html b/install.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>Installation &mdash; Pubmed Parser 0.6.dev3+ga6e846d documentation</title>
+  <title>Installation &mdash; Pubmed Parser 0.5.2.dev1+ga7e88c8 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=cd3e8eb9"></script>
+        <script src="_static/documentation_options.js?v=25fc7194"></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>
@@ -37,7 +37,7 @@
             Pubmed Parser
           </a>
               <div class="version">
-                0.6.dev3+ga6e846d
+                0.5.2.dev1+ga7e88c8
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">

diff --git a/objects.inv b/objects.inv
diff --git a/resources.html b/resources.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>Resources &mdash; Pubmed Parser 0.6.dev3+ga6e846d documentation</title>
+  <title>Resources &mdash; Pubmed Parser 0.5.2.dev1+ga7e88c8 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=cd3e8eb9"></script>
+        <script src="_static/documentation_options.js?v=25fc7194"></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>
@@ -37,7 +37,7 @@
             Pubmed Parser
           </a>
               <div class="version">
-                0.6.dev3+ga6e846d
+                0.5.2.dev1+ga7e88c8
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">

diff --git a/search.html b/search.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Search &mdash; Pubmed Parser 0.6.dev3+ga6e846d documentation</title>
+  <title>Search &mdash; Pubmed Parser 0.5.2.dev1+ga7e88c8 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=cd3e8eb9"></script>
+        <script src="_static/documentation_options.js?v=25fc7194"></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>
@@ -37,7 +37,7 @@
             Pubmed Parser
           </a>
               <div class="version">
-                0.6.dev3+ga6e846d
+                0.5.2.dev1+ga7e88c8
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="#" method="get">