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pyscal · Nov 28, 2023 · b403836 · b403836
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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: 6768baffdf00506d3cf9439b6ca2ec83
+config: 9bfb6f3cb120dcbe9edf1109593c0075
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/_images/6ea5f2ca981d5ab4cf0c54ab9dda44dc8112e4a91a445f3af2ad652d54b703fa.svg b/_images/6ea5f2ca981d5ab4cf0c54ab9dda44dc8112e4a91a445f3af2ad652d54b703fa.svg
diff --git a/_images/8d51af6b5f3d2a00358f046e37e467d23ad13f99bc3c47ce0d41c5c9dcbfa3a8.svg b/_images/8d51af6b5f3d2a00358f046e37e467d23ad13f99bc3c47ce0d41c5c9dcbfa3a8.svg
diff --git a/_images/adf515a694539a755814d39a2b5ca23eb645a84d8b572622487ce597992695b0.svg b/_images/adf515a694539a755814d39a2b5ca23eb645a84d8b572622487ce597992695b0.svg
diff --git a/_images/e9b1a505b6c437fdc80c4c8445e01d22d4fc71b3ddf465392aa422c37c86fd75.svg b/_images/e9b1a505b6c437fdc80c4c8445e01d22d4fc71b3ddf465392aa422c37c86fd75.svg
diff --git a/_static/basic.css b/_static/basic.css
@@ -236,6 +236,16 @@ div.body p, div.body dd, div.body li, div.body blockquote {
 a.headerlink {
     visibility: hidden;
 }
+a.brackets:before,
+span.brackets > a:before{
+    content: "[";
+}
+
+a.brackets:after,
+span.brackets > a:after {
+    content: "]";
+}
+
 
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
@@ -324,17 +334,11 @@ aside.sidebar {
 p.sidebar-title {
     font-weight: bold;
 }
-nav.contents,
-aside.topic,
-
 div.admonition, div.topic, blockquote {
     clear: left;
 }
 
 /* -- topics ---------------------------------------------------------------- */
-nav.contents,
-aside.topic,
-
 div.topic {
     border: 1px solid #ccc;
     padding: 7px;
@@ -373,19 +377,13 @@ div.body p.centered {
 
 div.sidebar > :last-child,
 aside.sidebar > :last-child,
-nav.contents > :last-child,
-aside.topic > :last-child,
-
 div.topic > :last-child,
 div.admonition > :last-child {
     margin-bottom: 0;
 }
 
 div.sidebar::after,
 aside.sidebar::after,
-nav.contents::after,
-aside.topic::after,
-
 div.topic::after,
 div.admonition::after,
 blockquote::after {

diff --git a/docs/acknowledgements.html b/docs/acknowledgements.html
@@ -7,7 +7,7 @@
 
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
     <title>Acknowledgements &#8212; pyscal-rdf</title>
 

diff --git a/docs/examples.html b/docs/examples.html
@@ -7,7 +7,7 @@
 
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
     <title>Examples &#8212; pyscal-rdf</title>
 

diff --git a/docs/extending.html b/docs/extending.html
@@ -7,7 +7,7 @@
 
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
     <title>Support &#8212; pyscal-rdf</title>
 

diff --git a/docs/gettingstarted.html b/docs/gettingstarted.html
@@ -7,7 +7,7 @@
 
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
     <title>Installation &#8212; pyscal-rdf</title>
 

diff --git a/docs/intro.html b/docs/intro.html
@@ -7,7 +7,7 @@
 
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
     <title>pyscal-rdf &#8212; pyscal-rdf</title>
 
@@ -404,7 +404,7 @@ <h1>pyscal-rdf<a class="headerlink" href="#pyscal-rdf" title="Permalink to this
 <span class="g g-Whitespace">      </span><span class="mi">1</span> <span class="n">struct</span> <span class="o">=</span> <span class="n">graph</span><span class="o">.</span><span class="n">create</span><span class="o">.</span><span class="n">lattice</span><span class="o">.</span><span class="n">l12</span><span class="p">(</span><span class="n">element</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;Ni&#39;</span><span class="p">,</span> <span class="s1">&#39;Al&#39;</span><span class="p">])</span>
 <span class="ne">----&gt; </span><span class="mi">2</span> <span class="n">struct</span><span class="o">.</span><span class="n">show</span><span class="o">.</span><span class="n">all</span><span class="p">()</span>
 
-<span class="nn">File /usr/share/miniconda/envs/test/lib/python3.8/site-packages/pyscal3/operations/visualize.py:333,</span> in <span class="ni">plot_simple</span><span class="nt">(sys, colors, radius, opacity)</span>
+<span class="nn">File /usr/share/miniconda/envs/test/lib/python3.11/site-packages/pyscal3/operations/visualize.py:333,</span> in <span class="ni">plot_simple</span><span class="nt">(sys, colors, radius, opacity)</span>
 <span class="g g-Whitespace">    </span><span class="mi">331</span> <span class="n">box</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">box</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
 <span class="g g-Whitespace">    </span><span class="mi">332</span> <span class="n">origin</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">])</span>
 <span class="ne">--&gt; </span><span class="mi">333</span> <span class="n">traces</span> <span class="o">=</span> <span class="n">create_box_plot</span><span class="p">(</span><span class="n">box</span><span class="p">,</span> <span class="n">origin</span><span class="p">)</span>
@@ -416,7 +416,7 @@ <h1>pyscal-rdf<a class="headerlink" href="#pyscal-rdf" title="Permalink to this
 <span class="g g-Whitespace">    </span><span class="mi">350</span>         <span class="p">)</span>
 <span class="g g-Whitespace">    </span><span class="mi">351</span>     <span class="p">)</span>
 
-<span class="nn">File /usr/share/miniconda/envs/test/lib/python3.8/site-packages/pyscal3/operations/visualize.py:44,</span> in <span class="ni">create_box_plot</span><span class="nt">(box, origin)</span>
+<span class="nn">File /usr/share/miniconda/envs/test/lib/python3.11/site-packages/pyscal3/operations/visualize.py:44,</span> in <span class="ni">create_box_plot</span><span class="nt">(box, origin)</span>
 <span class="g g-Whitespace">     </span><span class="mi">42</span> <span class="n">traces</span> <span class="o">=</span> <span class="p">[]</span>
 <span class="g g-Whitespace">     </span><span class="mi">43</span> <span class="k">for</span> <span class="n">face</span> <span class="ow">in</span> <span class="n">faces</span><span class="p">:</span>
 <span class="ne">---&gt; </span><span class="mi">44</span>     <span class="n">trace</span> <span class="o">=</span> <span class="n">go</span><span class="o">.</span><span class="n">Scatter3d</span><span class="p">(</span>
@@ -431,7 +431,7 @@ <h1>pyscal-rdf<a class="headerlink" href="#pyscal-rdf" title="Permalink to this
 <span class="g g-Whitespace">     </span><span class="mi">53</span>     <span class="n">traces</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">trace</span><span class="p">)</span>
 <span class="g g-Whitespace">     </span><span class="mi">54</span> <span class="k">return</span> <span class="n">traces</span>
 
-<span class="ne">UnboundLocalError</span>: local variable &#39;go&#39; referenced before assignment
+<span class="ne">UnboundLocalError</span>: cannot access local variable &#39;go&#39; where it is not associated with a value
 </pre></div>
 </div>
 </div>

diff --git a/docs/license.html b/docs/license.html
@@ -7,7 +7,7 @@
 
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
     <title>License &#8212; pyscal-rdf</title>
 

diff --git a/examples/01_getting_started.html b/examples/01_getting_started.html
@@ -7,7 +7,7 @@
 
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
     <title>Getting started &#8212; pyscal-rdf</title>
 
@@ -436,7 +436,7 @@ <h2>Creation of structures<a class="headerlink" href="#creation-of-structures" t
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../_images/adf515a694539a755814d39a2b5ca23eb645a84d8b572622487ce597992695b0.svg" src="../_images/adf515a694539a755814d39a2b5ca23eb645a84d8b572622487ce597992695b0.svg" /></div>
+<img alt="../_images/6ea5f2ca981d5ab4cf0c54ab9dda44dc8112e4a91a445f3af2ad652d54b703fa.svg" src="../_images/6ea5f2ca981d5ab4cf0c54ab9dda44dc8112e4a91a445f3af2ad652d54b703fa.svg" /></div>
 </div>
 <p>Now a Si diamond structure</p>
 <div class="cell docutils container">
@@ -462,7 +462,7 @@ <h2>Creation of structures<a class="headerlink" href="#creation-of-structures" t
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../_images/e9b1a505b6c437fdc80c4c8445e01d22d4fc71b3ddf465392aa422c37c86fd75.svg" src="../_images/e9b1a505b6c437fdc80c4c8445e01d22d4fc71b3ddf465392aa422c37c86fd75.svg" /></div>
+<img alt="../_images/8d51af6b5f3d2a00358f046e37e467d23ad13f99bc3c47ce0d41c5c9dcbfa3a8.svg" src="../_images/8d51af6b5f3d2a00358f046e37e467d23ad13f99bc3c47ce0d41c5c9dcbfa3a8.svg" /></div>
 </div>
 <p>We can save the graph and reload it as needed</p>
 </section>

diff --git a/examples/02_grain_boundaries.html b/examples/02_grain_boundaries.html
@@ -7,7 +7,7 @@
 
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
     <title>Creating Grain Boundaries &#8212; pyscal-rdf</title>
 
@@ -443,7 +443,7 @@ <h1>Creating Grain Boundaries<a class="headerlink" href="#creating-grain-boundar
 <span class="n">Cell</span> <span class="n">In</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span> <span class="n">line</span> <span class="mi">1</span>
 <span class="ne">----&gt; </span><span class="mi">1</span> <span class="n">struct_gb_1</span><span class="o">.</span><span class="n">show</span><span class="o">.</span><span class="n">all</span><span class="p">()</span>
 
-<span class="nn">File /usr/share/miniconda/envs/test/lib/python3.8/site-packages/pyscal3/operations/visualize.py:333,</span> in <span class="ni">plot_simple</span><span class="nt">(sys, colors, radius, opacity)</span>
+<span class="nn">File /usr/share/miniconda/envs/test/lib/python3.11/site-packages/pyscal3/operations/visualize.py:333,</span> in <span class="ni">plot_simple</span><span class="nt">(sys, colors, radius, opacity)</span>
 <span class="g g-Whitespace">    </span><span class="mi">331</span> <span class="n">box</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">box</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
 <span class="g g-Whitespace">    </span><span class="mi">332</span> <span class="n">origin</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">])</span>
 <span class="ne">--&gt; </span><span class="mi">333</span> <span class="n">traces</span> <span class="o">=</span> <span class="n">create_box_plot</span><span class="p">(</span><span class="n">box</span><span class="p">,</span> <span class="n">origin</span><span class="p">)</span>
@@ -455,7 +455,7 @@ <h1>Creating Grain Boundaries<a class="headerlink" href="#creating-grain-boundar
 <span class="g g-Whitespace">    </span><span class="mi">350</span>         <span class="p">)</span>
 <span class="g g-Whitespace">    </span><span class="mi">351</span>     <span class="p">)</span>
 
-<span class="nn">File /usr/share/miniconda/envs/test/lib/python3.8/site-packages/pyscal3/operations/visualize.py:44,</span> in <span class="ni">create_box_plot</span><span class="nt">(box, origin)</span>
+<span class="nn">File /usr/share/miniconda/envs/test/lib/python3.11/site-packages/pyscal3/operations/visualize.py:44,</span> in <span class="ni">create_box_plot</span><span class="nt">(box, origin)</span>
 <span class="g g-Whitespace">     </span><span class="mi">42</span> <span class="n">traces</span> <span class="o">=</span> <span class="p">[]</span>
 <span class="g g-Whitespace">     </span><span class="mi">43</span> <span class="k">for</span> <span class="n">face</span> <span class="ow">in</span> <span class="n">faces</span><span class="p">:</span>
 <span class="ne">---&gt; </span><span class="mi">44</span>     <span class="n">trace</span> <span class="o">=</span> <span class="n">go</span><span class="o">.</span><span class="n">Scatter3d</span><span class="p">(</span>
@@ -470,7 +470,7 @@ <h1>Creating Grain Boundaries<a class="headerlink" href="#creating-grain-boundar
 <span class="g g-Whitespace">     </span><span class="mi">53</span>     <span class="n">traces</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">trace</span><span class="p">)</span>
 <span class="g g-Whitespace">     </span><span class="mi">54</span> <span class="k">return</span> <span class="n">traces</span>
 
-<span class="ne">UnboundLocalError</span>: local variable &#39;go&#39; referenced before assignment
+<span class="ne">UnboundLocalError</span>: cannot access local variable &#39;go&#39; where it is not associated with a value
 </pre></div>
 </div>
 </div>

diff --git a/reports/docs/intro.err.log b/reports/docs/intro.err.log
@@ -1,17 +1,20 @@
 Traceback (most recent call last):
-  File "/usr/share/miniconda/envs/test/lib/python3.8/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+  File "/usr/share/miniconda/envs/test/lib/python3.11/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
     executenb(
-  File "/usr/share/miniconda/envs/test/lib/python3.8/site-packages/nbclient/client.py", line 1305, in execute
+  File "/usr/share/miniconda/envs/test/lib/python3.11/site-packages/nbclient/client.py", line 1305, in execute
     return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
-  File "/usr/share/miniconda/envs/test/lib/python3.8/site-packages/jupyter_core/utils/__init__.py", line 173, in wrapped
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/usr/share/miniconda/envs/test/lib/python3.11/site-packages/jupyter_core/utils/__init__.py", line 173, in wrapped
     return loop.run_until_complete(inner)
-  File "/usr/share/miniconda/envs/test/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/usr/share/miniconda/envs/test/lib/python3.11/asyncio/base_events.py", line 653, in run_until_complete
     return future.result()
-  File "/usr/share/miniconda/envs/test/lib/python3.8/site-packages/nbclient/client.py", line 705, in async_execute
+           ^^^^^^^^^^^^^^^
+  File "/usr/share/miniconda/envs/test/lib/python3.11/site-packages/nbclient/client.py", line 705, in async_execute
     await self.async_execute_cell(
-  File "/usr/share/miniconda/envs/test/lib/python3.8/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+  File "/usr/share/miniconda/envs/test/lib/python3.11/site-packages/nbclient/client.py", line 1058, in async_execute_cell
     await self._check_raise_for_error(cell, cell_index, exec_reply)
-  File "/usr/share/miniconda/envs/test/lib/python3.8/site-packages/nbclient/client.py", line 914, in _check_raise_for_error
+  File "/usr/share/miniconda/envs/test/lib/python3.11/site-packages/nbclient/client.py", line 914, in _check_raise_for_error
     raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
 nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
 ------------------
@@ -30,7 +33,7 @@ Cell [0;32mIn[4], line 2[0m
 [1;32m      1[0m struct [38;5;241m=[39m graph[38;5;241m.[39mcreate[38;5;241m.[39mlattice[38;5;241m.[39ml12(element[38;5;241m=[39m[[38;5;124m'[39m[38;5;124mNi[39m[38;5;124m'[39m, [38;5;124m'[39m[38;5;124mAl[39m[38;5;124m'[39m])
 [0;32m----> 2[0m [43mstruct[49m[38;5;241;43m.[39;49m[43mshow[49m[38;5;241;43m.[39;49m[43mall[49m[43m([49m[43m)[49m
 
-File [0;32m/usr/share/miniconda/envs/test/lib/python3.8/site-packages/pyscal3/operations/visualize.py:333[0m, in [0;36mplot_simple[0;34m(sys, colors, radius, opacity)[0m
+File [0;32m/usr/share/miniconda/envs/test/lib/python3.11/site-packages/pyscal3/operations/visualize.py:333[0m, in [0;36mplot_simple[0;34m(sys, colors, radius, opacity)[0m
 [1;32m    331[0m box [38;5;241m=[39m sys[38;5;241m.[39mbox[38;5;241m.[39mcopy()
 [1;32m    332[0m origin [38;5;241m=[39m np[38;5;241m.[39marray([[38;5;241m0[39m,[38;5;241m0[39m,[38;5;241m0[39m])
 [0;32m--> 333[0m traces [38;5;241m=[39m [43mcreate_box_plot[49m[43m([49m[43mbox[49m[43m,[49m[43m [49m[43morigin[49m[43m)[49m
@@ -42,7 +45,7 @@ File [0;32m/usr/share/miniconda/envs/test/lib/python3.8/site-packages/pyscal3/o
 [1;32m    350[0m         )
 [1;32m    351[0m     )
 
-File [0;32m/usr/share/miniconda/envs/test/lib/python3.8/site-packages/pyscal3/operations/visualize.py:44[0m, in [0;36mcreate_box_plot[0;34m(box, origin)[0m
+File [0;32m/usr/share/miniconda/envs/test/lib/python3.11/site-packages/pyscal3/operations/visualize.py:44[0m, in [0;36mcreate_box_plot[0;34m(box, origin)[0m
 [1;32m     42[0m traces [38;5;241m=[39m []
 [1;32m     43[0m [38;5;28;01mfor[39;00m face [38;5;129;01min[39;00m faces:
 [0;32m---> 44[0m     trace [38;5;241m=[39m [43mgo[49m[38;5;241m.[39mScatter3d(
@@ -57,5 +60,5 @@ File [0;32m/usr/share/miniconda/envs/test/lib/python3.8/site-packages/pyscal3/o
 [1;32m     53[0m     traces[38;5;241m.[39mappend(trace)
 [1;32m     54[0m [38;5;28;01mreturn[39;00m traces
 
-[0;31mUnboundLocalError[0m: local variable 'go' referenced before assignment
+[0;31mUnboundLocalError[0m: cannot access local variable 'go' where it is not associated with a value