fix issues for github workflow #push

.github/workflows/deploy.yml

@@ -56,6 +56,7 @@ jobs:
           source ~/.bashrc
           conda activate book
           pip install -r requirements.txt
+          pip install -e .
 
       - name: Build the book
         shell: bash -l {0}

book/_build/html/.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: cf28b2445aa898147aa7536b45e45564
+config: 09f9591df36fba7b867082d637863797
 tags: 645f666f9bcd5a90fca523b33c5a78b7

book/_build/html/content/1_Abstract.html

@@ -34,7 +34,7 @@
     <link rel="stylesheet" type="text/css" href="../_static/styles/sphinx-book-theme.css?v=a3416100" />
     <link rel="stylesheet" type="text/css" href="../_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
-    <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+    <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
     <link rel="stylesheet" type="text/css" href="../_static/sphinx-thebe.css?v=4fa983c6" />
     <link rel="stylesheet" type="text/css" href="../_static/sphinx-design.min.css?v=95c83b7e" />
     <link rel="stylesheet" type="text/css" href="../_static/theme.css?v=24b9ed36" />

book/_build/html/content/4_AFM_and_XRD.html

@@ -34,7 +34,7 @@
     <link rel="stylesheet" type="text/css" href="../_static/styles/sphinx-book-theme.css?v=a3416100" />
     <link rel="stylesheet" type="text/css" href="../_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
-    <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+    <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
     <link rel="stylesheet" type="text/css" href="../_static/sphinx-thebe.css?v=4fa983c6" />
     <link rel="stylesheet" type="text/css" href="../_static/sphinx-design.min.css?v=95c83b7e" />
     <link rel="stylesheet" type="text/css" href="../_static/theme.css?v=24b9ed36" />
@@ -454,48 +454,7 @@ <h2>Sample 1 - treated_213nm<a class="headerlink" href="#sample-1-treated-213nm"
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output traceback highlight-ipythontb notranslate"><div class="highlight"><pre><span></span><span class="gt">---------------------------------------------------------------------------</span>
-<span class="ne">FileNotFoundError</span><span class="g g-Whitespace">                         </span>Traceback (most recent call last)
-<span class="n">Cell</span> <span class="n">In</span><span class="p">[</span><span class="mi">2</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">img2</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">loadtxt</span><span class="p">(</span><span class="s1">&#39;../data/AFM/treated_213nm-film.txt&#39;</span><span class="p">)[:</span><span class="mi">256</span><span class="p">]</span>
-<span class="g g-Whitespace">      </span><span class="mi">2</span> <span class="n">scalebar_dict</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;image_size&#39;</span><span class="p">:</span> <span class="mi">2008</span><span class="p">,</span> <span class="s1">&#39;scale_size&#39;</span><span class="p">:</span> <span class="mi">500</span><span class="p">,</span> <span class="s1">&#39;units&#39;</span><span class="p">:</span> <span class="s1">&#39;nm&#39;</span><span class="p">}</span>
-<span class="g g-Whitespace">      </span><span class="mi">3</span> <span class="n">visualize_afm_image</span><span class="p">(</span><span class="n">img2</span><span class="p">,</span> <span class="n">colorbar_range</span><span class="o">=</span><span class="p">[</span><span class="o">-</span><span class="mf">4e-10</span><span class="p">,</span> <span class="mf">4e-10</span><span class="p">],</span> <span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">6</span><span class="p">,</span><span class="mi">4</span><span class="p">),</span> <span class="n">scalebar_dict</span><span class="o">=</span><span class="n">scalebar_dict</span><span class="p">,)</span>
-
-<span class="nn">File ~/miniconda3/envs/delete_test/lib/python3.11/site-packages/numpy/lib/npyio.py:1373,</span> in <span class="ni">loadtxt</span><span class="nt">(fname, dtype, comments, delimiter, converters, skiprows, usecols, unpack, ndmin, encoding, max_rows, quotechar, like)</span>
-<span class="g g-Whitespace">   </span><span class="mi">1370</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">delimiter</span><span class="p">,</span> <span class="nb">bytes</span><span class="p">):</span>
-<span class="g g-Whitespace">   </span><span class="mi">1371</span>     <span class="n">delimiter</span> <span class="o">=</span> <span class="n">delimiter</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;latin1&#39;</span><span class="p">)</span>
-<span class="ne">-&gt; </span><span class="mi">1373</span> <span class="n">arr</span> <span class="o">=</span> <span class="n">_read</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="n">dtype</span><span class="p">,</span> <span class="n">comment</span><span class="o">=</span><span class="n">comment</span><span class="p">,</span> <span class="n">delimiter</span><span class="o">=</span><span class="n">delimiter</span><span class="p">,</span>
-<span class="g g-Whitespace">   </span><span class="mi">1374</span>             <span class="n">converters</span><span class="o">=</span><span class="n">converters</span><span class="p">,</span> <span class="n">skiplines</span><span class="o">=</span><span class="n">skiprows</span><span class="p">,</span> <span class="n">usecols</span><span class="o">=</span><span class="n">usecols</span><span class="p">,</span>
-<span class="g g-Whitespace">   </span><span class="mi">1375</span>             <span class="n">unpack</span><span class="o">=</span><span class="n">unpack</span><span class="p">,</span> <span class="n">ndmin</span><span class="o">=</span><span class="n">ndmin</span><span class="p">,</span> <span class="n">encoding</span><span class="o">=</span><span class="n">encoding</span><span class="p">,</span>
-<span class="g g-Whitespace">   </span><span class="mi">1376</span>             <span class="n">max_rows</span><span class="o">=</span><span class="n">max_rows</span><span class="p">,</span> <span class="n">quote</span><span class="o">=</span><span class="n">quotechar</span><span class="p">)</span>
-<span class="g g-Whitespace">   </span><span class="mi">1378</span> <span class="k">return</span> <span class="n">arr</span>
-
-<span class="nn">File ~/miniconda3/envs/delete_test/lib/python3.11/site-packages/numpy/lib/npyio.py:992,</span> in <span class="ni">_read</span><span class="nt">(fname, delimiter, comment, quote, imaginary_unit, usecols, skiplines, max_rows, converters, ndmin, unpack, dtype, encoding)</span>
-<span class="g g-Whitespace">    </span><span class="mi">990</span>     <span class="n">fname</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">fspath</span><span class="p">(</span><span class="n">fname</span><span class="p">)</span>
-<span class="g g-Whitespace">    </span><span class="mi">991</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
-<span class="ne">--&gt; </span><span class="mi">992</span>     <span class="n">fh</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">lib</span><span class="o">.</span><span class="n">_datasource</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="s1">&#39;rt&#39;</span><span class="p">,</span> <span class="n">encoding</span><span class="o">=</span><span class="n">encoding</span><span class="p">)</span>
-<span class="g g-Whitespace">    </span><span class="mi">993</span>     <span class="k">if</span> <span class="n">encoding</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
-<span class="g g-Whitespace">    </span><span class="mi">994</span>         <span class="n">encoding</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">fh</span><span class="p">,</span> <span class="s1">&#39;encoding&#39;</span><span class="p">,</span> <span class="s1">&#39;latin1&#39;</span><span class="p">)</span>
-
-<span class="nn">File ~/miniconda3/envs/delete_test/lib/python3.11/site-packages/numpy/lib/_datasource.py:193,</span> in <span class="ni">open</span><span class="nt">(path, mode, destpath, encoding, newline)</span>
-<span class="g g-Whitespace">    </span><span class="mi">156</span><span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="g g-Whitespace">    </span><span class="mi">157</span><span class="sd"> Open `path` with `mode` and return the file object.</span>
-<span class="g g-Whitespace">    </span><span class="mi">158</span><span class="sd"> </span>
-<span class="sd">   (...)</span>
-<span class="g g-Whitespace">    </span><span class="mi">189</span><span class="sd"> </span>
-<span class="g g-Whitespace">    </span><span class="mi">190</span><span class="sd"> &quot;&quot;&quot;</span>
-<span class="g g-Whitespace">    </span><span class="mi">192</span> <span class="n">ds</span> <span class="o">=</span> <span class="n">DataSource</span><span class="p">(</span><span class="n">destpath</span><span class="p">)</span>
-<span class="ne">--&gt; </span><span class="mi">193</span> <span class="k">return</span> <span class="n">ds</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">mode</span><span class="p">,</span> <span class="n">encoding</span><span class="o">=</span><span class="n">encoding</span><span class="p">,</span> <span class="n">newline</span><span class="o">=</span><span class="n">newline</span><span class="p">)</span>
-
-<span class="nn">File ~/miniconda3/envs/delete_test/lib/python3.11/site-packages/numpy/lib/_datasource.py:533,</span> in <span class="ni">DataSource.open</span><span class="nt">(self, path, mode, encoding, newline)</span>
-<span class="g g-Whitespace">    </span><span class="mi">530</span>     <span class="k">return</span> <span class="n">_file_openers</span><span class="p">[</span><span class="n">ext</span><span class="p">](</span><span class="n">found</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="n">mode</span><span class="p">,</span>
-<span class="g g-Whitespace">    </span><span class="mi">531</span>                               <span class="n">encoding</span><span class="o">=</span><span class="n">encoding</span><span class="p">,</span> <span class="n">newline</span><span class="o">=</span><span class="n">newline</span><span class="p">)</span>
-<span class="g g-Whitespace">    </span><span class="mi">532</span> <span class="k">else</span><span class="p">:</span>
-<span class="ne">--&gt; </span><span class="mi">533</span>     <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">path</span><span class="si">}</span><span class="s2"> not found.&quot;</span><span class="p">)</span>
-
-<span class="ne">FileNotFoundError</span>: ../data/AFM/treated_213nm-film.txt not found.
-</pre></div>
-</div>
+<img alt="../_images/a470631f77313aca2cf8b8caff8258dff3ba645e1d8ac2bf9c7072b83e5ffc96.png" src="../_images/a470631f77313aca2cf8b8caff8258dff3ba645e1d8ac2bf9c7072b83e5ffc96.png" />
 </div>
 </div>
 <div class="cell docutils container">
@@ -637,7 +596,9 @@ <h2>Summary of XRD and RSM<a class="headerlink" href="#summary-of-xrd-and-rsm" t
 </div>
 <div class="cell_output docutils container">
 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>../Figures/2.AFM_XRD/S2-XRD_RSM.png
-../Figures/2.AFM_XRD/S2-XRD_RSM.svg
+</pre></div>
+</div>
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>../Figures/2.AFM_XRD/S2-XRD_RSM.svg
 </pre></div>
 </div>
 <img alt="../_images/3e6458b83243f6fe68b93ae91ea1c4bbcceae308d9c3c92efa025b179e17e3a4.png" src="../_images/3e6458b83243f6fe68b93ae91ea1c4bbcceae308d9c3c92efa025b179e17e3a4.png" />