Deploying to gh-pages from @ e87d85a 🚀

pydna-group · Oct 3, 2024 · 9b8cf60 · 9b8cf60
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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: 195022872e99b13eb20f9f8e9ecf0ea1
+config: aed188ca1e3e2f26c04c0f0c2965274d
 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; pydna 0.0.0.post1+3220013 documentation</title>
+  <title>Overview: module code &mdash; pydna 0.0.0.post1+e87d85a 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=cf305423"></script>
+        <script src="../_static/documentation_options.js?v=749bf11f"></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>

diff --git a/_modules/pydna.html b/_modules/pydna.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna &mdash; pydna 0.0.0.post1+3220013 documentation</title>
+  <title>pydna &mdash; pydna 0.0.0.post1+e87d85a 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=cf305423"></script>
+        <script src="../_static/documentation_options.js?v=749bf11f"></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>
@@ -223,7 +223,7 @@ <h1>Source code for pydna</h1><div class="highlight"><pre>
 <span class="n">__maintainer__</span> <span class="o">=</span> <span class="s2">&quot;Björn Johansson&quot;</span>
 <span class="n">__email__</span> <span class="o">=</span> <span class="s2">&quot;[email protected]&quot;</span>
 <span class="n">__status__</span> <span class="o">=</span> <span class="s2">&quot;Development&quot;</span>  <span class="c1"># &quot;Production&quot; #&quot;Prototype&quot;</span>
-<span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;0.0.0-post.1+3220013&quot;</span>
+<span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;0.0.0-post.1+e87d85a&quot;</span>
 
 
 <span class="c1"># create config directory</span>

diff --git a/_modules/pydna/amplicon.html b/_modules/pydna/amplicon.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna.amplicon &mdash; pydna 0.0.0.post1+3220013 documentation</title>
+  <title>pydna.amplicon &mdash; pydna 0.0.0.post1+e87d85a 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=cf305423"></script>
+        <script src="../../_static/documentation_options.js?v=749bf11f"></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>

diff --git a/_modules/pydna/amplify.html b/_modules/pydna/amplify.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna.amplify &mdash; pydna 0.0.0.post1+3220013 documentation</title>
+  <title>pydna.amplify &mdash; pydna 0.0.0.post1+e87d85a 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=cf305423"></script>
+        <script src="../../_static/documentation_options.js?v=749bf11f"></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>
@@ -91,7 +91,7 @@ <h1>Source code for pydna.amplify</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">pydna.utils</span> <span class="kn">import</span> <span class="n">flatten</span> <span class="k">as</span> <span class="n">_flatten</span>
 
 <span class="c1"># from pydna.utils import memorize as _memorize</span>
-<span class="kn">from</span> <span class="nn">pydna.utils</span> <span class="kn">import</span> <span class="n">rc</span> <span class="k">as</span> <span class="n">_rc</span>
+<span class="kn">from</span> <span class="nn">pydna.utils</span> <span class="kn">import</span> <span class="n">rc</span> <span class="k">as</span> <span class="n">_rc</span><span class="p">,</span> <span class="n">shift_feature</span> <span class="k">as</span> <span class="n">_shift_feature</span>
 <span class="kn">from</span> <span class="nn">pydna.amplicon</span> <span class="kn">import</span> <span class="n">Amplicon</span> <span class="k">as</span> <span class="n">_Amplicon</span>
 <span class="kn">from</span> <span class="nn">pydna.primer</span> <span class="kn">import</span> <span class="n">Primer</span> <span class="k">as</span> <span class="n">_Primer</span>
 <span class="kn">from</span> <span class="nn">pydna.seqrecord</span> <span class="kn">import</span> <span class="n">SeqRecord</span> <span class="k">as</span> <span class="n">_SeqRecord</span>
@@ -427,6 +427,8 @@ <h1>Source code for pydna.amplify</h1><div class="highlight"><pre>
                     <span class="n">feats</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span>
                         <span class="n">fp</span><span class="o">.</span><span class="n">position</span> <span class="o">-</span> <span class="n">fp</span><span class="o">.</span><span class="n">_fp</span> <span class="p">:</span> <span class="n">rp</span><span class="o">.</span><span class="n">position</span> <span class="o">+</span> <span class="n">rp</span><span class="o">.</span><span class="n">_fp</span>
                     <span class="p">]</span><span class="o">.</span><span class="n">features</span>  <span class="c1"># Save features covered by primers</span>
+                    <span class="n">shift_amount</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">fp</span><span class="o">.</span><span class="n">tail</span><span class="p">)</span>
+                    <span class="n">feats</span> <span class="o">=</span> <span class="p">[</span><span class="n">_shift_feature</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">shift_amount</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span> <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">feats</span><span class="p">]</span>
                     <span class="n">tpl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span>
                 <span class="k">else</span><span class="p">:</span>
                     <span class="k">continue</span>

diff --git a/_modules/pydna/assembly.html b/_modules/pydna/assembly.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna.assembly &mdash; pydna 0.0.0.post1+3220013 documentation</title>
+  <title>pydna.assembly &mdash; pydna 0.0.0.post1+e87d85a 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=cf305423"></script>
+        <script src="../../_static/documentation_options.js?v=749bf11f"></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>

diff --git a/_modules/pydna/common_sub_strings.html b/_modules/pydna/common_sub_strings.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna.common_sub_strings &mdash; pydna 0.0.0.post1+3220013 documentation</title>
+  <title>pydna.common_sub_strings &mdash; pydna 0.0.0.post1+e87d85a 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=cf305423"></script>
+        <script src="../../_static/documentation_options.js?v=749bf11f"></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>

diff --git a/_modules/pydna/contig.html b/_modules/pydna/contig.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna.contig &mdash; pydna 0.0.0.post1+3220013 documentation</title>
+  <title>pydna.contig &mdash; pydna 0.0.0.post1+e87d85a 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=cf305423"></script>
+        <script src="../../_static/documentation_options.js?v=749bf11f"></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>

diff --git a/_modules/pydna/design.html b/_modules/pydna/design.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna.design &mdash; pydna 0.0.0.post1+3220013 documentation</title>
+  <title>pydna.design &mdash; pydna 0.0.0.post1+e87d85a 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=cf305423"></script>
+        <script src="../../_static/documentation_options.js?v=749bf11f"></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>

diff --git a/_modules/pydna/dseq.html b/_modules/pydna/dseq.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna.dseq &mdash; pydna 0.0.0.post1+3220013 documentation</title>
+  <title>pydna.dseq &mdash; pydna 0.0.0.post1+e87d85a 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=cf305423"></script>
+        <script src="../../_static/documentation_options.js?v=749bf11f"></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>

diff --git a/_modules/pydna/dseqrecord.html b/_modules/pydna/dseqrecord.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna.dseqrecord &mdash; pydna 0.0.0.post1+3220013 documentation</title>
+  <title>pydna.dseqrecord &mdash; pydna 0.0.0.post1+e87d85a 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=cf305423"></script>
+        <script src="../../_static/documentation_options.js?v=749bf11f"></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>

diff --git a/_modules/pydna/editor.html b/_modules/pydna/editor.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna.editor &mdash; pydna 0.0.0.post1+3220013 documentation</title>
+  <title>pydna.editor &mdash; pydna 0.0.0.post1+e87d85a 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=cf305423"></script>
+        <script src="../../_static/documentation_options.js?v=749bf11f"></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>

diff --git a/_modules/pydna/gel.html b/_modules/pydna/gel.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna.gel &mdash; pydna 0.0.0.post1+3220013 documentation</title>
+  <title>pydna.gel &mdash; pydna 0.0.0.post1+e87d85a 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=cf305423"></script>
+        <script src="../../_static/documentation_options.js?v=749bf11f"></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>

diff --git a/_modules/pydna/genbank.html b/_modules/pydna/genbank.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna.genbank &mdash; pydna 0.0.0.post1+3220013 documentation</title>
+  <title>pydna.genbank &mdash; pydna 0.0.0.post1+e87d85a 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=cf305423"></script>
+        <script src="../../_static/documentation_options.js?v=749bf11f"></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>

diff --git a/_modules/pydna/genbankfile.html b/_modules/pydna/genbankfile.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna.genbankfile &mdash; pydna 0.0.0.post1+3220013 documentation</title>
+  <title>pydna.genbankfile &mdash; pydna 0.0.0.post1+e87d85a 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=cf305423"></script>
+        <script src="../../_static/documentation_options.js?v=749bf11f"></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>

diff --git a/_modules/pydna/genbankfixer.html b/_modules/pydna/genbankfixer.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>pydna.genbankfixer &mdash; pydna 0.0.0.post1+3220013 documentation</title>
+  <title>pydna.genbankfixer &mdash; pydna 0.0.0.post1+e87d85a 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=cf305423"></script>
+        <script src="../../_static/documentation_options.js?v=749bf11f"></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>