Automated update f3690dae2f4e13fc8d767c236210d3553d2c7feb

Author: Sphinx

dev/Tutorial/chapter_introduction.html

@@ -291,15 +291,11 @@ <h2>Frequently Asked Questions (FAQ)<a class="headerlink" href="#frequently-aske
 </li>
 <li><div class="line-block">
 <div class="line"><em>Where is the latest version of this document?</em></div>
-<div class="line">If you download a Biopython source code archive, it will include
-the relevant version in both HTML and PDF formats. The latest
-published version of this document (updated at each release) is
-online:</div>
+<div class="line">The latest published version of this document (updated at each
+release) is online at <a class="reference external" href="https://biopython.org/docs/latest/">https://biopython.org/docs/latest/</a> with
+<a class="reference external" href="https://biopython.org/docs/dev/">https://biopython.org/docs/dev/</a> for the documentation being worked
+on for the next release.</div>
 </div>
-<ul class="simple">
-<li><p><a class="reference external" href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">http://biopython.org/DIST/docs/tutorial/Tutorial.html</a></p></li>
-<li><p><a class="reference external" href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">http://biopython.org/DIST/docs/tutorial/Tutorial.pdf</a></p></li>
-</ul>
 </li>
 <li><div class="line-block">
 <div class="line"><em>What is wrong with my sequence comparisons?</em></div>

dev/api/Bio.AlignIO.html

@@ -300,11 +300,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 in a PHYLIP file containing one or more alignments using Bio.AlignIO, or you
 can read in the sequences within these alignments using Bio.SeqIO.</p>
 <p>Bio.AlignIO is also documented at <a class="reference external" href="http://biopython.org/wiki/AlignIO">http://biopython.org/wiki/AlignIO</a> and by
-a whole chapter in our tutorial:</p>
-<ul class="simple">
-<li><p><a class="reference external" href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">HTML Tutorial</a></p></li>
-<li><p><a class="reference external" href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF Tutorial</a></p></li>
-</ul>
+a whole chapter in our <a class="reference external" href="https://biopython.org/docs/latest/Tutorial/index.html">Tutorial</a>:</p>
 <section id="input">
 <h3>Input<a class="headerlink" href="#input" title="Link to this heading"></a></h3>
 <p>For the typical special case when your file or handle contains one and only

dev/api/Bio.Entrez.html

@@ -252,9 +252,8 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 in this case a remote network connection, and provides methods like
 <code class="docutils literal notranslate"><span class="pre">.read()</span></code> or offers iteration over the contents line by line. See
 also “What the heck is a handle?” in the Biopython Tutorial and
-Cookbook: <a class="reference external" href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">http://biopython.org/DIST/docs/tutorial/Tutorial.html</a>
-<a class="reference external" href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">http://biopython.org/DIST/docs/tutorial/Tutorial.pdf</a>
-The handle returned by these functions can be either in text mode or
+Cookbook: <a class="reference external" href="https://biopython.org/docs/latest/Tutorial/index.html">https://biopython.org/docs/latest/Tutorial/index.html</a></p>
+<p>The handle returned by these functions can be either in text mode or
 in binary mode, depending on the data requested and the results
 returned by NCBI Entrez. Typically, XML data will be in binary mode
 while other data will be in text mode, as required by the downstream

dev/api/Bio.Seq.html

@@ -100,13 +100,7 @@
   <section id="module-Bio.Seq">
 <span id="bio-seq-module"></span><h1>Bio.Seq module<a class="headerlink" href="#module-Bio.Seq" title="Link to this heading"></a></h1>
 <p>Provide objects to represent biological sequences.</p>
-<dl class="simple">
-<dt>See also the <a class="reference external" href="http://biopython.org/wiki/Seq">Seq</a> wiki and the chapter in our tutorial:</dt><dd><ul class="simple">
-<li><p><a class="reference external" href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">HTML Tutorial</a></p></li>
-<li><p><a class="reference external" href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF Tutorial</a></p></li>
-</ul>
-</dd>
-</dl>
+<p>See also the <a class="reference external" href="http://biopython.org/wiki/Seq">Seq</a> wiki and the chapter in our <a class="reference external" href="https://biopython.org/docs/latest/Tutorial/index.html">Tutorial</a>.</p>
 <dl class="py class">
 <dt class="sig sig-object py" id="Bio.Seq.SequenceDataAbstractBaseClass">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">Bio.Seq.</span></span><span class="sig-name descname"><span class="pre">SequenceDataAbstractBaseClass</span></span><a class="headerlink" href="#Bio.Seq.SequenceDataAbstractBaseClass" title="Link to this definition"></a></dt>

dev/api/Bio.SeqIO.html

@@ -771,13 +771,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 <section id="module-Bio.SeqIO">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-Bio.SeqIO" title="Link to this heading"></a></h2>
 <p>Sequence input/output as SeqRecord objects.</p>
-<p>Bio.SeqIO is also documented at <a class="reference external" href="http://biopython.org/wiki/SeqIO">SeqIO</a> and by a whole chapter in our tutorial:</p>
-<blockquote>
-<div><ul class="simple">
-<li><p><a class="reference external" href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">HTML Tutorial</a></p></li>
-<li><p><a class="reference external" href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF Tutorial</a></p></li>
-</ul>
-</div></blockquote>
+<p>Bio.SeqIO is also documented at <a class="reference external" href="http://biopython.org/wiki/SeqIO">SeqIO</a> and by a whole chapter in our <a class="reference external" href="https://biopython.org/docs/latest/Tutorial/index.html">Tutorial</a>:</p>
 <section id="input">
 <h3>Input<a class="headerlink" href="#input" title="Link to this heading"></a></h3>
 <p>The main function is Bio.SeqIO.parse(…) which takes an input file handle