add ref to in contribution section of docs

docs/_modules/basicsynbio/cam/main.html

@@ -32,51 +32,22 @@
           <div class="body" role="main">
 
   <h1>Source code for basicsynbio.cam.main</h1><div class="highlight"><pre>
-<span></span><span class="sd">&quot;&quot;&quot;Module contains a collection of objects for computer assisted manufacturing</span>
-<span class="sd">within the BASIC DNA assembly framework.&quot;&quot;&quot;</span>
+<span></span><span class="sd">&quot;&quot;&quot;Module contains key objects for computer assisted manufacturing (CAM)</span>
+<span class="sd">within the BASIC DNA assembly framework.</span>
+<span class="sd">&quot;&quot;&quot;</span>
 
-<span class="kn">from</span> <span class="nn">Bio.SeqUtils</span> <span class="kn">import</span> <span class="n">molecular_weight</span>
 <span class="kn">from</span> <span class="nn">Bio.Seq</span> <span class="kn">import</span> <span class="n">Seq</span>
-<span class="kn">from</span> <span class="nn">Bio.SeqRecord</span> <span class="kn">import</span> <span class="n">SeqRecord</span>
 <span class="kn">from</span> <span class="nn">basicsynbio.main</span> <span class="kn">import</span> <span class="p">(</span>
     <span class="n">BasicAssembly</span><span class="p">,</span>
     <span class="n">BasicLinker</span><span class="p">,</span>
     <span class="n">BasicPart</span><span class="p">,</span>
     <span class="n">BasicUTRRBSLinker</span><span class="p">,</span>
-    <span class="n">ClipReaction</span><span class="p">,</span>
     <span class="n">LinkerException</span><span class="p">,</span>
 <span class="p">)</span>
-<span class="kn">import</span> <span class="nn">csv</span>
-<span class="kn">from</span> <span class="nn">dataclasses</span> <span class="kn">import</span> <span class="n">dataclass</span>
-<span class="kn">from</span> <span class="nn">datetime</span> <span class="kn">import</span> <span class="n">datetime</span>
 <span class="kn">from</span> <span class="nn">collections</span> <span class="kn">import</span> <span class="n">OrderedDict</span><span class="p">,</span> <span class="n">Counter</span>
-<span class="kn">import</span> <span class="nn">hashlib</span>
 <span class="kn">import</span> <span class="nn">json</span>
-<span class="kn">import</span> <span class="nn">os</span>
-<span class="kn">from</span> <span class="nn">pathlib</span> <span class="kn">import</span> <span class="n">Path</span>
-<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span><span class="p">,</span> <span class="n">Dict</span><span class="p">,</span> <span class="n">Generator</span>
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Dict</span><span class="p">,</span> <span class="n">Generator</span>
 <span class="kn">import</span> <span class="nn">re</span>
-<span class="kn">import</span> <span class="nn">zipfile</span>
-
-
-<div class="viewcode-block" id="new_part_resuspension"><a class="viewcode-back" href="../../../api.html#basicsynbio.cam.main.new_part_resuspension">[docs]</a><span class="k">def</span> <span class="nf">new_part_resuspension</span><span class="p">(</span>
-    <span class="n">part</span><span class="p">:</span> <span class="n">BasicPart</span><span class="p">,</span> <span class="n">mass</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span> <span class="n">double_stranded</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span>
-<span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">float</span><span class="p">:</span>
-    <span class="sd">&quot;&quot;&quot;Returns the volume of resuspension buffer (µL) required for a 75 nM</span>
-<span class="sd">    solution of part, equivalent to 75 fmol/µL.</span>
-
-<span class="sd">    Args:</span>
-<span class="sd">        part: BasicPart object.</span>
-<span class="sd">        mass: mass of synthesised part (ng).</span>
-<span class="sd">        double_stranded (optional): True (default) indicates part is dsDNA.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="k">return</span> <span class="p">(</span>
-        <span class="p">(</span><span class="n">mass</span> <span class="o">*</span> <span class="mi">10</span> <span class="o">**</span> <span class="o">-</span><span class="mi">9</span><span class="p">)</span>
-        <span class="o">/</span> <span class="n">molecular_weight</span><span class="p">(</span><span class="n">part</span><span class="o">.</span><span class="n">seq</span><span class="p">,</span> <span class="n">double_stranded</span><span class="o">=</span><span class="n">double_stranded</span><span class="p">)</span>
-        <span class="o">*</span> <span class="mi">1</span>
-        <span class="o">/</span> <span class="p">(</span><span class="mf">75e-9</span><span class="p">)</span>
-        <span class="o">*</span> <span class="mi">10</span> <span class="o">**</span> <span class="mi">6</span>
-    <span class="p">)</span></div>
 
 
 <div class="viewcode-block" id="BasicBuild"><a class="viewcode-back" href="../../../api.html#basicsynbio.cam.main.BasicBuild">[docs]</a><span class="k">class</span> <span class="nc">BasicBuild</span><span class="p">:</span>
@@ -482,30 +453,6 @@ <h1>Source code for basicsynbio.cam.main</h1><div class="highlight"><pre>
 
 <div class="viewcode-block" id="BuildException"><a class="viewcode-back" href="../../../api.html#basicsynbio.cam.main.BuildException">[docs]</a><span class="k">class</span> <span class="nc">BuildException</span><span class="p">(</span><span class="ne">Exception</span><span class="p">):</span>
     <span class="k">pass</span></div>
-
-
-<div class="viewcode-block" id="seqrecord_hexdigest"><a class="viewcode-back" href="../../../api.html#basicsynbio.cam.main.seqrecord_hexdigest">[docs]</a><span class="k">def</span> <span class="nf">seqrecord_hexdigest</span><span class="p">(</span><span class="n">seqrecord_obj</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="n">SeqRecord</span><span class="p">,</span> <span class="n">BasicPart</span><span class="p">,</span> <span class="n">BasicLinker</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
-    <span class="sd">&quot;&quot;&quot;Returns an MD5 hash of a Bio.SeqRecord.SeqRecord-like object, using</span>
-<span class="sd">    relevant attributes.</span>
-
-<span class="sd">    Note:</span>
-<span class="sd">        Care should be taken when using the return value of this function as an identifier/hash for seqrecord_obj given these objects are mutable.</span>
-
-<span class="sd">    Args:</span>
-<span class="sd">        seqrecord_obj: Bio.SeqRecord.SeqRecord-like object, containing relevant</span>
-<span class="sd">            attributes</span>
-
-<span class="sd">    Returns:</span>
-<span class="sd">        MD5 hash</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="n">seqrec_hash</span> <span class="o">=</span> <span class="n">hashlib</span><span class="o">.</span><span class="n">md5</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">seqrecord_obj</span><span class="o">.</span><span class="n">seq</span><span class="p">)</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s2">&quot;UTF-8&quot;</span><span class="p">))</span>
-    <span class="n">bytes_objs</span> <span class="o">=</span> <span class="p">[</span>
-        <span class="nb">getattr</span><span class="p">(</span><span class="n">seqrecord_obj</span><span class="p">,</span> <span class="n">attribute</span><span class="p">)</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s2">&quot;UTF-8&quot;</span><span class="p">)</span>
-        <span class="k">for</span> <span class="n">attribute</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;name&quot;</span><span class="p">,</span> <span class="s2">&quot;description&quot;</span><span class="p">]</span>
-    <span class="p">]</span>
-    <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">bytes_objs</span><span class="p">:</span>
-        <span class="n">seqrec_hash</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
-    <span class="k">return</span> <span class="n">seqrec_hash</span><span class="o">.</span><span class="n">hexdigest</span><span class="p">()</span></div>
 </pre></div>
 
           </div>

docs/_sources/contributing.rst.txt

@@ -62,7 +62,9 @@ General Guidelines
 * Code should be formatted using `black`_.
 * New code should have associated tests written using `pytest`_.
 * Update the documentation if required. The documentation is formatted using `Sphinx`_ and as such all files must be written in reST.
-* Update GitHub pages by running ``make github`` in the */docsource* directory.
+* Update GitHub pages by running ``make github`` in the */docsource* directory. This implements GitHub Pages as described by `Anne Gentle`_.
+
+.. _Anne Gentle: https://www.docslikecode.com/articles/github-pages-python-sphinx/
 
 Guidelines for docstrings
 ^^^^^^^^^^^^^^^^^^^^^^^^^

docs/api.html

@@ -492,7 +492,7 @@ <h1>API reference<a class="headerlink" href="#api-reference" title="Permalink to
 </div>
 <div class="section" id="module-basicsynbio.cam.main">
 <span id="cam-main-py"></span><h2>cam.main.py<a class="headerlink" href="#module-basicsynbio.cam.main" title="Permalink to this headline">¶</a></h2>
-<p>Module contains a collection of objects for computer assisted manufacturing
+<p>Module contains key objects for computer assisted manufacturing (CAM)
 within the BASIC DNA assembly framework.</p>
 <dl class="py class">
 <dt id="basicsynbio.cam.main.BasicBuild">
@@ -729,42 +729,6 @@ <h1>API reference<a class="headerlink" href="#api-reference" title="Permalink to
 <em class="property">exception </em><code class="sig-prename descclassname">basicsynbio.cam.main.</code><code class="sig-name descname">BuildException</code><a class="reference internal" href="_modules/basicsynbio/cam/main.html#BuildException"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#basicsynbio.cam.main.BuildException" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
-<dl class="py function">
-<dt id="basicsynbio.cam.main.new_part_resuspension">
-<code class="sig-prename descclassname">basicsynbio.cam.main.</code><code class="sig-name descname">new_part_resuspension</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">part</span><span class="p">:</span> <span class="n"><a class="reference internal" href="#basicsynbio.main.BasicPart" title="basicsynbio.main.BasicPart">basicsynbio.main.BasicPart</a></span></em>, <em class="sig-param"><span class="n">mass</span><span class="p">:</span> <span class="n">float</span></em>, <em class="sig-param"><span class="n">double_stranded</span><span class="p">:</span> <span class="n">bool</span> <span class="o">=</span> <span class="default_value">True</span></em><span class="sig-paren">)</span> &#x2192; float<a class="reference internal" href="_modules/basicsynbio/cam/main.html#new_part_resuspension"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#basicsynbio.cam.main.new_part_resuspension" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns the volume of resuspension buffer (µL) required for a 75 nM
-solution of part, equivalent to 75 fmol/µL.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>part</strong> – BasicPart object.</p></li>
-<li><p><strong>mass</strong> – mass of synthesised part (ng).</p></li>
-<li><p><strong>double_stranded</strong> (<em>optional</em>) – True (default) indicates part is dsDNA.</p></li>
-</ul>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py function">
-<dt id="basicsynbio.cam.main.seqrecord_hexdigest">
-<code class="sig-prename descclassname">basicsynbio.cam.main.</code><code class="sig-name descname">seqrecord_hexdigest</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">seqrecord_obj</span><span class="p">:</span> <span class="n">Union<span class="p">[</span>Bio.SeqRecord.SeqRecord<span class="p">, </span><a class="reference internal" href="#basicsynbio.main.BasicPart" title="basicsynbio.main.BasicPart">basicsynbio.main.BasicPart</a><span class="p">, </span><a class="reference internal" href="#basicsynbio.main.BasicLinker" title="basicsynbio.main.BasicLinker">basicsynbio.main.BasicLinker</a><span class="p">]</span></span></em><span class="sig-paren">)</span> &#x2192; str<a class="reference internal" href="_modules/basicsynbio/cam/main.html#seqrecord_hexdigest"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#basicsynbio.cam.main.seqrecord_hexdigest" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns an MD5 hash of a Bio.SeqRecord.SeqRecord-like object, using
-relevant attributes.</p>
-<div class="admonition note">
-<p class="admonition-title">Note</p>
-<p>Care should be taken when using the return value of this function as an identifier/hash for seqrecord_obj given these objects are mutable.</p>
-</div>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>seqrecord_obj</strong> – Bio.SeqRecord.SeqRecord-like object, containing relevant
-attributes</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>MD5 hash</p>
-</dd>
-</dl>
-</dd></dl>
-
 </div>
 <div class="section" id="module-basicsynbio.decorators">
 <span id="decorators-py"></span><h2>decorators.py<a class="headerlink" href="#module-basicsynbio.decorators" title="Permalink to this headline">¶</a></h2>

docs/contributing.html

@@ -105,7 +105,7 @@ <h3>General Guidelines<a class="headerlink" href="#general-guidelines" title="Pe
 <li><p>Code should be formatted using <a class="reference external" href="https://github.com/psf/black">black</a>.</p></li>
 <li><p>New code should have associated tests written using <a class="reference external" href="https://docs.pytest.org/en/stable/">pytest</a>.</p></li>
 <li><p>Update the documentation if required. The documentation is formatted using <a class="reference external" href="https://www.sphinx-doc.org/en/master/usage/quickstart.html">Sphinx</a> and as such all files must be written in reST.</p></li>
-<li><p>Update GitHub pages by running <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">github</span></code> in the <em>/docsource</em> directory.</p></li>
+<li><p>Update GitHub pages by running <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">github</span></code> in the <em>/docsource</em> directory. This implements GitHub Pages as described by <a class="reference external" href="https://www.docslikecode.com/articles/github-pages-python-sphinx/">Anne Gentle</a>.</p></li>
 </ul>
 </div>
 <div class="section" id="guidelines-for-docstrings">

docs/genindex.html

@@ -264,10 +264,6 @@ <h2 id="N">N</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api.html#basicsynbio.main.BasicLinker.name">name (basicsynbio.main.BasicLinker attribute)</a>
-</li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api.html#basicsynbio.cam.main.new_part_resuspension">new_part_resuspension() (in module basicsynbio.cam.main)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -330,8 +326,6 @@ <h2 id="S">S</h2>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api.html#basicsynbio.main.seqrec2part">seqrec2part() (in module basicsynbio.main)</a>
-</li>
-      <li><a href="api.html#basicsynbio.cam.main.seqrecord_hexdigest">seqrecord_hexdigest() (in module basicsynbio.cam.main)</a>
 </li>
       <li><a href="api.html#basicsynbio.main.BasicLinker.suffix_id">suffix_id (basicsynbio.main.BasicLinker attribute)</a>
 </li>