Add tutorial with alphabetic subnames

breimanntools · Sep 22, 2023 · 5bd90c6 · 5bd90c6
1 parent 8e4b762
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diff --git a/aaanalysis/data_loader/__pycache__/data_loader.cpython-39.pyc b/aaanalysis/data_loader/__pycache__/data_loader.cpython-39.pyc
diff --git a/aaanalysis/data_loader/data_loader.py b/aaanalysis/data_loader/data_loader.py
@@ -203,7 +203,7 @@ def load_dataset(name: str = "INFO",
 
     See Also
     --------
-    * Step-by-step guide in the `data loading tutorial <tutorial2_data_loader.html>`_.
+    * Step-by-step guide in the `data loading tutorial <tutorial2a_data_loader.html>`_.
     * Overview of all benchmarks in :ref:`t1_overview_benchmarks`.
 
     """

diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/generated/aaanalysis.load_dataset.doctree b/docs/build/doctrees/generated/aaanalysis.load_dataset.doctree
diff --git a/docs/build/doctrees/generated/tutorial2a_data_loader.doctree b/docs/build/doctrees/generated/tutorial2a_data_loader.doctree
diff --git a/docs/build/doctrees/tutorials.doctree b/docs/build/doctrees/tutorials.doctree
diff --git a/docs/build/html/_images/output_10_0.png b/docs/build/html/_images/output_10_0.png
diff --git a/docs/build/html/_images/output_11_0.png b/docs/build/html/_images/output_11_0.png
diff --git a/docs/build/html/_images/output_12_0.png b/docs/build/html/_images/output_12_0.png
diff --git a/docs/build/html/_images/output_13_0.png b/docs/build/html/_images/output_13_0.png
diff --git a/docs/build/html/_images/output_9_0.png b/docs/build/html/_images/output_9_0.png
diff --git a/...l/_images/social_previews/summary_generated_tutorial2a_data_loader_17a0722e.png b/...l/_images/social_previews/summary_generated_tutorial2a_data_loader_17a0722e.png
diff --git a/...ource/generated/tutorial2_data_loader.rst → .../generated/tutorial2a_data_loader.rst.txt b/...ource/generated/tutorial2_data_loader.rst → .../generated/tutorial2a_data_loader.rst.txt
@@ -282,9 +282,11 @@ The protein sequences can have varying length:
     import seaborn as sns
     # Utility AAanalysis function for publication ready plots
     aa.plot_settings(font_scale=1.2) 
+    df_seq = aa.load_dataset(name="SEQ_CAPSID", n=100)
     list_seq_lens = df_seq["sequence"].apply(len)
     sns.histplot(list_seq_lens, binwidth=50)
     sns.despine()
+    plt.xlim(0, 1500)
     plt.show()
 
 
@@ -302,6 +304,7 @@ parameters:
     aa.plot_settings(font_scale=1.2)  # Utility AAanalysis function for publication ready plots
     sns.histplot(list_seq_lens, binwidth=50)
     sns.despine()
+    plt.xlim(0, 1500)
     plt.show()
 
 

diff --git a/docs/build/html/_sources/tutorials.rst.txt b/docs/build/html/_sources/tutorials.rst.txt
@@ -20,4 +20,4 @@ Further Tutorials
 .. toctree::
    :maxdepth: 1
 
-   generated/tutorial2_data_loader
+   generated/tutorial2a_data_loader
diff --git a/docs/build/html/api.html b/docs/build/html/api.html
@@ -42,7 +42,7 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="aaanalysis.load_dataset" href="generated/aaanalysis.load_dataset.html" />
-    <link rel="prev" title="Data loading" href="generated/tutorial2_data_loader.html" /> 
+    <link rel="prev" title="Data loading" href="generated/tutorial2a_data_loader.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -223,7 +223,7 @@ <h2>Plot Utilities<a class="headerlink" href="#plot-utilities" title="Permalink
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="generated/tutorial2_data_loader.html" class="btn btn-neutral float-left" title="Data loading" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="generated/tutorial2a_data_loader.html" class="btn btn-neutral float-left" title="Data loading" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
         <a href="generated/aaanalysis.load_dataset.html" class="btn btn-neutral float-right" title="aaanalysis.load_dataset" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 

diff --git a/docs/build/html/generated/aaanalysis.load_dataset.html b/docs/build/html/generated/aaanalysis.load_dataset.html
@@ -177,7 +177,7 @@ <h1>aaanalysis.load_dataset<a class="headerlink" href="#aaanalysis-load-dataset"
 <div class="admonition seealso">
 <p class="admonition-title">See also</p>
 <ul class="simple">
-<li><p>Step-by-step guide in the <a class="reference external" href="tutorial2_data_loader.html">data loading tutorial</a>.</p></li>
+<li><p>Step-by-step guide in the <a class="reference external" href="tutorial2a_data_loader.html">data loading tutorial</a>.</p></li>
 <li><p>Overview of all benchmarks in <a class="reference internal" href="../index/tables.html#t1-overview-benchmarks"><span class="std std-ref">Protein Benchmark Datasets</span></a>.</p></li>
 </ul>
 </div>

diff --git a/docs/build/html/generated/tutorial2_data_loader.html b/docs/build/html/generated/tutorial2_data_loader.html
@@ -9,7 +9,7 @@
 <meta property="og:description" content="This is a tutorial on loading of protein and amino acid scale datasets. Loading of protein benchmarks: Load the overview table of protein benchmark datasets using the default settings: The benchmar..." />
 <meta property="og:image:width" content="1146" />
 <meta property="og:image:height" content="600" />
-<meta property="og:image" content="/None" />
+<meta property="og:image" content="/_images/social_previews/summary_generated_tutorial2_data_loader_17a0722e.png" />
 <meta property="og:image:alt" content="This is a tutorial on loading of protein and amino acid scale datasets. Loading of protein benchmarks: Load the overview table of protein benchmark datasets..." />
 <meta name="description" content="This is a tutorial on loading of protein and amino acid scale datasets. Loading of protein benchmarks: Load the overview table of protein benchmark datasets using the default settings: The benchmar..." />
 <meta name="twitter:card" content="summary_large_image" />
@@ -40,9 +40,7 @@
         <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
-    <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="API" href="../api.html" />
-    <link rel="prev" title="Tutorials" href="../tutorials.html" /> 
+    <link rel="search" title="Search" href="../search.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -75,15 +73,8 @@
 <li class="toctree-l1"><a class="reference internal" href="../index/CONTRIBUTING_COPY.html">Contributing</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">EXAMPLES</span></p>
-<ul class="current">
-<li class="toctree-l1 current"><a class="reference internal" href="../tutorials.html">Tutorials</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="../tutorials.html#quick-start">Quick start</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="../tutorials.html#further-tutorials">Further Tutorials</a><ul class="current">
-<li class="toctree-l3 current"><a class="current reference internal" href="#">Data loading</a></li>
-</ul>
-</li>
-</ul>
-</li>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../tutorials.html">Tutorials</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">REFERENCES</span></p>
 <ul>
@@ -108,7 +99,6 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="../tutorials.html">Tutorials</a></li>
       <li class="breadcrumb-item active">Data loading</li>
       <li class="wy-breadcrumbs-aside">
               <a href="https://github.com/breimanntools/aaanalysis/blob/master/generated/tutorial2_data_loader.rst" class="fa fa-github"> Edit on GitHub</a>
@@ -902,10 +892,7 @@ <h2>Loading of protein benchmarks: Positive-Unlabeled (PU) datasets<a class="hea
 
            </div>
           </div>
-          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="../tutorials.html" class="btn btn-neutral float-left" title="Tutorials" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="../api.html" class="btn btn-neutral float-right" title="API" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
-    </div>
+          <footer>
 
   <hr/>