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LondonBiofoundry · Sep 25, 2021 · a72bc1a · a72bc1a
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diff --git a/docs/_modules/basicsynbio/cam/echo_instructions.html b/docs/_modules/basicsynbio/cam/echo_instructions.html
@@ -59,7 +59,7 @@ <h1>Source code for basicsynbio.cam.echo_instructions</h1><div class="highlight"
     <span class="n">buffer_well</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;A1&quot;</span><span class="p">,</span>
     <span class="n">water_well</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;B1&quot;</span><span class="p">,</span>
     <span class="n">alternate_well</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
-    <span class="n">assemblies_per_clip</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">28</span><span class="p">,</span>
+    <span class="n">assemblies_per_clip</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">20</span><span class="p">,</span>
     <span class="n">clips_plate_size</span><span class="p">:</span> <span class="n">Literal</span><span class="p">[</span><span class="mi">6</span><span class="p">,</span> <span class="mi">24</span><span class="p">,</span> <span class="mi">96</span><span class="p">,</span> <span class="mi">384</span><span class="p">,</span> <span class="mi">1536</span><span class="p">]</span> <span class="o">=</span> <span class="mi">384</span><span class="p">,</span>
     <span class="n">assemblies_plate_size</span><span class="p">:</span> <span class="n">Literal</span><span class="p">[</span><span class="mi">6</span><span class="p">,</span> <span class="mi">24</span><span class="p">,</span> <span class="mi">96</span><span class="p">,</span> <span class="mi">384</span><span class="p">,</span> <span class="mi">1536</span><span class="p">]</span> <span class="o">=</span> <span class="mi">96</span><span class="p">,</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>

diff --git a/docs/_modules/basicsynbio/cam/main.html b/docs/_modules/basicsynbio/cam/main.html
@@ -298,6 +298,7 @@ <h1>Source code for basicsynbio.cam.main</h1><div class="highlight"><pre>
             <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">index</span><span class="p">):</span> <span class="p">{</span>
                 <span class="s2">&quot;id&quot;</span><span class="p">:</span> <span class="n">value</span><span class="p">[</span><span class="s2">&quot;linker&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">id</span><span class="p">,</span>
                 <span class="s2">&quot;linker_class&quot;</span><span class="p">:</span> <span class="nb">str</span><span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="n">value</span><span class="p">[</span><span class="s2">&quot;linker&quot;</span><span class="p">])),</span>
+                <span class="s2">&quot;name&quot;</span><span class="p">:</span> <span class="n">value</span><span class="p">[</span><span class="s2">&quot;linker&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
                 <span class="s2">&quot;sequence&quot;</span><span class="p">:</span> <span class="nb">str</span><span class="p">(</span><span class="n">value</span><span class="p">[</span><span class="s2">&quot;linker&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">seq</span><span class="p">),</span>
                 <span class="s2">&quot;prefix_id&quot;</span><span class="p">:</span> <span class="n">value</span><span class="p">[</span><span class="s2">&quot;linker&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">prefix_id</span><span class="p">,</span>
                 <span class="s2">&quot;suffix_id&quot;</span><span class="p">:</span> <span class="n">value</span><span class="p">[</span><span class="s2">&quot;linker&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">suffix_id</span><span class="p">,</span>
@@ -459,10 +460,16 @@ <h1>Source code for basicsynbio.cam.main</h1><div class="highlight"><pre>
         <span class="n">unique_linkers</span> <span class="o">=</span> <span class="p">{}</span>
         <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">dictionary</span><span class="p">[</span><span class="s2">&quot;unique_linkers&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
             <span class="k">if</span> <span class="n">re</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">&quot;.*BasicLinker&quot;</span><span class="p">,</span> <span class="n">value</span><span class="p">[</span><span class="s2">&quot;linker_class&quot;</span><span class="p">]):</span>
-                <span class="n">unique_linker</span> <span class="o">=</span> <span class="n">BasicLinker</span><span class="p">(</span><span class="n">seq</span><span class="o">=</span><span class="n">Seq</span><span class="p">(</span><span class="n">value</span><span class="p">[</span><span class="s2">&quot;sequence&quot;</span><span class="p">]),</span> <span class="nb">id</span><span class="o">=</span><span class="n">value</span><span class="p">[</span><span class="s2">&quot;id&quot;</span><span class="p">])</span>
+                <span class="n">unique_linker</span> <span class="o">=</span> <span class="n">BasicLinker</span><span class="p">(</span>
+                    <span class="n">seq</span><span class="o">=</span><span class="n">Seq</span><span class="p">(</span><span class="n">value</span><span class="p">[</span><span class="s2">&quot;sequence&quot;</span><span class="p">]),</span>
+                    <span class="nb">id</span><span class="o">=</span><span class="n">value</span><span class="p">[</span><span class="s2">&quot;id&quot;</span><span class="p">],</span>
+                    <span class="n">name</span><span class="o">=</span><span class="n">value</span><span class="p">[</span><span class="s2">&quot;name&quot;</span><span class="p">],</span>
+                <span class="p">)</span>
             <span class="k">elif</span> <span class="n">re</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">&quot;.*BasicUTRRBSLinker&quot;</span><span class="p">,</span> <span class="n">value</span><span class="p">[</span><span class="s2">&quot;linker_class&quot;</span><span class="p">]):</span>
                 <span class="n">unique_linker</span> <span class="o">=</span> <span class="n">BasicUTRRBSLinker</span><span class="p">(</span>
-                    <span class="n">seq</span><span class="o">=</span><span class="n">Seq</span><span class="p">(</span><span class="n">value</span><span class="p">[</span><span class="s2">&quot;sequence&quot;</span><span class="p">]),</span> <span class="nb">id</span><span class="o">=</span><span class="n">value</span><span class="p">[</span><span class="s2">&quot;id&quot;</span><span class="p">]</span>
+                    <span class="n">seq</span><span class="o">=</span><span class="n">Seq</span><span class="p">(</span><span class="n">value</span><span class="p">[</span><span class="s2">&quot;sequence&quot;</span><span class="p">]),</span>
+                    <span class="nb">id</span><span class="o">=</span><span class="n">value</span><span class="p">[</span><span class="s2">&quot;id&quot;</span><span class="p">],</span>
+                    <span class="n">name</span><span class="o">=</span><span class="n">value</span><span class="p">[</span><span class="s2">&quot;name&quot;</span><span class="p">],</span>
                 <span class="p">)</span>
             <span class="k">else</span><span class="p">:</span>
                 <span class="k">raise</span> <span class="n">LinkerException</span><span class="p">(</span>

diff --git a/docs/_modules/basicsynbio/cam/pdf_instructions.html b/docs/_modules/basicsynbio/cam/pdf_instructions.html
@@ -78,8 +78,8 @@ <h1>Source code for basicsynbio.cam.pdf_instructions</h1><div class="highlight">
 
 <span class="sd">    Args:</span>
 <span class="sd">        basic_build: BasicBuild object the pdf lab instructions are written for.</span>
-<span class="sd">        path (optional): path to zipped folder of csv files. If none defaults to</span>
-<span class="sd">            working directory with a time stamped name, output csvs is created.</span>
+<span class="sd">        path (optional): path to pdf file. If none defaults to</span>
+<span class="sd">            working directory with a time stamped name.</span>
 <span class="sd">        assemblies_per_clip (optional): number of assemblies each purified clip reaction can support.</span>
 
 <span class="sd">    Returns:</span>
@@ -158,7 +158,7 @@ <h1>Source code for basicsynbio.cam.pdf_instructions</h1><div class="highlight">
     <span class="k">if</span> <span class="n">path</span> <span class="o">==</span> <span class="kc">None</span><span class="p">:</span>
         <span class="n">now</span> <span class="o">=</span> <span class="n">datetime</span><span class="o">.</span><span class="n">now</span><span class="p">()</span>
         <span class="n">pdf_filename</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span>
-            <span class="n">Path</span><span class="o">.</span><span class="n">cwd</span><span class="p">()</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">&quot;Echo_Instructions_</span><span class="si">{</span><span class="n">now</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%d</span><span class="s1">-%m-%Y_%H.%M.%S&#39;</span><span class="p">)</span><span class="si">}</span><span class="s2">.zip&quot;</span>
+            <span class="n">Path</span><span class="o">.</span><span class="n">cwd</span><span class="p">()</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">&quot;Manual_instructions_</span><span class="si">{</span><span class="n">now</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%d</span><span class="s1">-%m-%Y_%H.%M.%S&#39;</span><span class="p">)</span><span class="si">}</span><span class="s2">.pdf&quot;</span>
         <span class="p">)</span>
     <span class="k">else</span><span class="p">:</span>
         <span class="n">pdf_filename</span> <span class="o">=</span> <span class="n">path</span>
@@ -279,12 +279,6 @@ <h1>Source code for basicsynbio.cam.pdf_instructions</h1><div class="highlight">
         <span class="p">)</span>
     <span class="p">)</span>
     <span class="n">elems</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Spacer</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mf">0.4</span> <span class="o">*</span> <span class="n">cm</span><span class="p">))</span>
-    <span class="n">elems</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
-        <span class="n">Paragraph</span><span class="p">(</span>
-            <span class="s2">&quot;We recommend the above up each clip can be used in up to 28 assemblies.&quot;</span><span class="p">,</span>
-            <span class="n">styles</span><span class="p">[</span><span class="s2">&quot;BodyText&quot;</span><span class="p">],</span>
-        <span class="p">)</span>
-    <span class="p">)</span>
     <span class="n">elems</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Spacer</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mf">0.4</span> <span class="o">*</span> <span class="n">cm</span><span class="p">))</span>
     <span class="n">elems</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
         <span class="n">Paragraph</span><span class="p">(</span>