Set references in data_loader (one is broken) and refs in tables.rst

.readthedocs.yaml

@@ -24,6 +24,7 @@ submodules:
   include:
      - "tutorials"
 
-formats:
-  - htmlzip
-  - epub
+#formats: disabled during development
+#  - htmlzip
+#  - epub
+#  - pdf (run into error when created by RTD)

aaanalysis/data_loader/data_loader.py

@@ -153,7 +153,7 @@ def load_dataset(name: str = "INFO",
     Load protein benchmarking datasets.
 
     The benchmarks are categorized into amino acid ('AA'), domain ('DOM'), and sequence ('SEQ') level
-    datasets. Use default settings (``name='INFO'``) for an overview table. Detailed analysis is in .
+    datasets. Use default settings (``name='INFO'``) for an overview table. Detailed analysis is in [Breimann23a]_.
 
     Parameters
     ----------
@@ -186,8 +186,8 @@ def load_dataset(name: str = "INFO",
 
     See Also
     --------
-    * Overview of all benchmarks in .
-    * Detailed usage tutorial in the .
+    * Overview of all benchmarks in  :ref:`1_overview_benchmarks`.
+    * Detailed step-by-step guide in the `data loader tutorial <tutorials/tutorial2_data_loader.ipynb>`_.
 
     Examples
     --------

docs/build/html/_sources/index/tables.rst.txt

@@ -79,7 +79,7 @@ and unlabeled (2) data samples, as indicated by appending '_PU' to the dataset n
      - 184900
      - PROSPERous
      - Prediction of caspase-3 cleavage site
-     - Song18
+     - :ref:`Song18 <Song18>`
      - 1 (adjacent to cleavage site), 0 (not adjacent to cleavage site)
    * - Amino acid
      - AA_FURIN
@@ -89,7 +89,7 @@ and unlabeled (2) data samples, as indicated by appending '_PU' to the dataset n
      - 58840
      - PROSPERous
      - Prediction of furin cleavage site
-     - Song18
+     - :ref:`Song18 <Song18>`
      - 1 (adjacent to cleavage site), 0 (not adjacent to cleavage site)
    * - Amino acid
      - AA_LDR
@@ -99,7 +99,7 @@ and unlabeled (2) data samples, as indicated by appending '_PU' to the dataset n
      - 82779
      - IDP-Seq2Seq
      - Prediction of long intrinsically disordered regions (LDR)
-     - Tang20
+     - :ref:`Tang20 <Tang20>`
      - 1 (disordered), 0 (ordered)
    * - Amino acid
      - AA_MMP2
@@ -109,7 +109,7 @@ and unlabeled (2) data samples, as indicated by appending '_PU' to the dataset n
      - 310560
      - PROSPERous
      - Prediction of Matrix metallopeptidase-2 (MMP2) cleavage site
-     - Song18
+     - :ref:`Song18 <Song18>`
      - 1 (adjacent to cleavage site), 0 (not adjacent to cleavage site)
    * - Amino acid
      - AA_RNABIND
@@ -119,7 +119,7 @@ and unlabeled (2) data samples, as indicated by appending '_PU' to the dataset n
      - 48509
      - GMKSVM-RU
      - Prediction of RNA-binding protein residues (RBP60 dataset)
-     - Yang21
+     - :ref:`Yang21 <Yang21>`
      - 1 (binding), 0 (non-binding)
    * - Amino acid
      - AA_SA
@@ -129,7 +129,7 @@ and unlabeled (2) data samples, as indicated by appending '_PU' to the dataset n
      - 84523
      - PROSPERous
      - Prediction of solvent accessibility (SA) of residue (AA_CASPASE3 data set)
-     - Song18
+     - :ref:`Song18 <Song18>`
      - 1 (exposed/accessible), 0 (buried/non-accessible)
    * - Sequence
      - SEQ_AMYLO
@@ -139,7 +139,7 @@ and unlabeled (2) data samples, as indicated by appending '_PU' to the dataset n
      - 903
      - ReRF-Pred
      - Prediction of amyloidognenic regions
-     - Teng21
+     - :ref:`Teng21 <Teng21>`
      - 1 (amyloidogenic), 0 (non-amyloidogenic)
    * - Sequence
      - SEQ_CAPSID
@@ -149,7 +149,7 @@ and unlabeled (2) data samples, as indicated by appending '_PU' to the dataset n
      - 4071
      - VIRALpro
      - Prediction of capdsid proteins
-     - Galiez16
+     - :ref:`Galiez16 <Galiez16>`
      - 1 (capsid protein), 0 (non-capsid protein)
    * - Sequence
      - SEQ_DISULFIDE
@@ -159,7 +159,7 @@ and unlabeled (2) data samples, as indicated by appending '_PU' to the dataset n
      - 1650
      - Dipro
      - Prediction of disulfide bridges in sequences
-     - Cheng06
+     - :ref:`Cheng06 <Cheng06>`
      - 1 (sequence with SS bond), 0 (sequence without SS bond)
    * - Sequence
      - SEQ_LOCATION
@@ -169,7 +169,7 @@ and unlabeled (2) data samples, as indicated by appending '_PU' to the dataset n
      - 790
      - nan
      - Prediction of subcellular location of protein (cytoplasm vs plasma membrane)
-     - Shen19
+     - :ref:`Shen19 <Shen19>`
      - 1 (protein in cytoplasm), 0 (protein in plasma membrane) 
    * - Sequence
      - SEQ_SOLUBLE
@@ -179,7 +179,7 @@ and unlabeled (2) data samples, as indicated by appending '_PU' to the dataset n
      - 8704
      - SOLpro
      - Prediction of soluble and insoluble proteins
-     - Magnan09
+     - :ref:`Magnan09 <Magnan09>`
      - 1 (soluble), 0 (insoluble)
    * - Sequence
      - SEQ_TAIL
@@ -189,7 +189,7 @@ and unlabeled (2) data samples, as indicated by appending '_PU' to the dataset n
      - 4094
      - VIRALpro
      - Prediction of tail proteins
-     - Galiez16
+     - :ref:`Galiez16 <Galiez16>`
      - 1 (tail protein), 0 (non-tail protein)
    * - Domain
      - DOM_GSEC
@@ -199,7 +199,7 @@ and unlabeled (2) data samples, as indicated by appending '_PU' to the dataset n
      - 63
      - nan
      - Prediction of gamma-secretase substrates
-     - Breimann23c
+     - :ref:`Breimann23c <Breimann23c>`
      - 1 (substrate), 0 (non-substrate)
    * - Domain
      - DOM_GSEC_PU
@@ -209,7 +209,7 @@ and unlabeled (2) data samples, as indicated by appending '_PU' to the dataset n
      - 0
      - nan
      - Prediction of gamma-secretase substrates (PU dataset)
-     - Breimann23c
+     - :ref:`Breimann23c <Breimann23c>`
      - 1 (substrate), 2 (unknown substrate status)
 
 
@@ -230,25 +230,25 @@ Various amino acid scale datasets are provided.
    * - scales
      - Amino acid scales (min-max normalized)
      - 586
-     - Breimann23b
+     - :ref:`Breimann23b <Breimann23b>`
    * - scales_raw
      - Amino acid scales (raw values)
      - 586
-     - Kawashima08
+     - :ref:`Kawashima08 <Kawashima08>`
    * - scales_classification
      - Classification of scales (Aaontology)
      - 586
-     - Breimann23b
+     - :ref:`Breimann23b <Breimann23b>`
    * - scales_pc
      - Principal component (PC) compressed scales
      - 20
-     - Breimann23a
+     - :ref:`Breimann23a <Breimann23a>`
    * - top60
      - Top 60 scale subsets
      - 60
-     - Breimann23a
+     - :ref:`Breimann23a <Breimann23a>`
    * - top60_eval
      - Evaluation of top 60 scale subsets
      - 60
-     - Breimann23a
+     - :ref:`Breimann23a <Breimann23a>`
 

docs/build/html/generated/aaanalysis.CPPPlot.html

@@ -302,7 +302,7 @@ <h1>aaanalysis.CPPPlot<a class="headerlink" href="#aaanalysis-cppplot" title="Pe
 <div class="admonition-examples admonition">
 <p class="admonition-title">Examples</p>
 <p>Plot CPP feature heatmap:</p>
-<p>(<a class="reference download internal" download="" href="../_downloads/4381eb917ab8b66dc7d40d07eb8d2a87/aaanalysis-CPPPlot-1.py"><code class="xref download docutils literal notranslate"><span class="pre">Source</span> <span class="pre">code</span></code></a>)</p>
+<p>(<a class="reference download internal" download="" href="../_downloads/fe02006031f96dc9a3a8b158e5899dae/aaanalysis-CPPPlot-1.py"><code class="xref download docutils literal notranslate"><span class="pre">Source</span> <span class="pre">code</span></code></a>)</p>
 </div>
 </dd></dl>
 

docs/build/html/generated/aaanalysis.load_dataset.html

@@ -128,7 +128,7 @@ <h1>aaanalysis.load_dataset<a class="headerlink" href="#aaanalysis-load-dataset"
 <span class="sig-prename descclassname"><span class="pre">aaanalysis.</span></span><span class="sig-name descname"><span class="pre">load_dataset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'INFO'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">random</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">non_canonical_aa</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'remove'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_len</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_len</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">aa_window_size</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/breimanntools/aaanalysis/tree/master/aaanalysis/data_loader/data_loader.py#L144-L237"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#aaanalysis.load_dataset" title="Permalink to this definition"></a></dt>
 <dd><p>Load protein benchmarking datasets.</p>
 <p>The benchmarks are categorized into amino acid (‘AA’), domain (‘DOM’), and sequence (‘SEQ’) level
-datasets. Use default settings (<code class="docutils literal notranslate"><span class="pre">name='INFO'</span></code>) for an overview table. Detailed analysis is in .</p>
+datasets. Use default settings (<code class="docutils literal notranslate"><span class="pre">name='INFO'</span></code>) for an overview table. Detailed analysis is in <a class="reference internal" href="../index/references.html#breimann23a" id="id1"><span>[Breimann23a]</span></a>.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
@@ -157,8 +157,8 @@ <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>Overview of all benchmarks in .</p></li>
-<li><p>Detailed usage tutorial in the .</p></li>
+<li><p>Overview of all benchmarks in  <span class="xref std std-ref">1_overview_benchmarks</span>.</p></li>
+<li><p>Detailed step-by-step guide in the <a class="reference external" href="tutorials/tutorial2_data_loader.ipynb">data loader tutorial</a>.</p></li>
 </ul>
 </div>
 <div class="admonition-examples admonition">

docs/build/html/index/tables.html

@@ -197,7 +197,7 @@ <h2><a class="toc-backref" href="#id2" role="doc-backlink">Protein Benchmark Dat
 <td><p>184900</p></td>
 <td><p>PROSPERous</p></td>
 <td><p>Prediction of caspase-3 cleavage site</p></td>
-<td><p>Song18</p></td>
+<td><p><a class="reference internal" href="references.html#song18"><span class="std std-ref">Song18</span></a></p></td>
 <td><p>1 (adjacent to cleavage site), 0 (not adjacent to cleavage site)</p></td>
 </tr>
 <tr class="row-odd"><td><p>Amino acid</p></td>
@@ -208,7 +208,7 @@ <h2><a class="toc-backref" href="#id2" role="doc-backlink">Protein Benchmark Dat
 <td><p>58840</p></td>
 <td><p>PROSPERous</p></td>
 <td><p>Prediction of furin cleavage site</p></td>
-<td><p>Song18</p></td>
+<td><p><a class="reference internal" href="references.html#song18"><span class="std std-ref">Song18</span></a></p></td>
 <td><p>1 (adjacent to cleavage site), 0 (not adjacent to cleavage site)</p></td>
 </tr>
 <tr class="row-even"><td><p>Amino acid</p></td>
@@ -219,7 +219,7 @@ <h2><a class="toc-backref" href="#id2" role="doc-backlink">Protein Benchmark Dat
 <td><p>82779</p></td>
 <td><p>IDP-Seq2Seq</p></td>
 <td><p>Prediction of long intrinsically disordered regions (LDR)</p></td>
-<td><p>Tang20</p></td>
+<td><p><a class="reference internal" href="references.html#tang20"><span class="std std-ref">Tang20</span></a></p></td>
 <td><p>1 (disordered), 0 (ordered)</p></td>
 </tr>
 <tr class="row-odd"><td><p>Amino acid</p></td>
@@ -230,7 +230,7 @@ <h2><a class="toc-backref" href="#id2" role="doc-backlink">Protein Benchmark Dat
 <td><p>310560</p></td>
 <td><p>PROSPERous</p></td>
 <td><p>Prediction of Matrix metallopeptidase-2 (MMP2) cleavage site</p></td>
-<td><p>Song18</p></td>
+<td><p><a class="reference internal" href="references.html#song18"><span class="std std-ref">Song18</span></a></p></td>
 <td><p>1 (adjacent to cleavage site), 0 (not adjacent to cleavage site)</p></td>
 </tr>
 <tr class="row-even"><td><p>Amino acid</p></td>
@@ -241,7 +241,7 @@ <h2><a class="toc-backref" href="#id2" role="doc-backlink">Protein Benchmark Dat
 <td><p>48509</p></td>
 <td><p>GMKSVM-RU</p></td>
 <td><p>Prediction of RNA-binding protein residues (RBP60 dataset)</p></td>
-<td><p>Yang21</p></td>
+<td><p><a class="reference internal" href="references.html#yang21"><span class="std std-ref">Yang21</span></a></p></td>
 <td><p>1 (binding), 0 (non-binding)</p></td>
 </tr>
 <tr class="row-odd"><td><p>Amino acid</p></td>
@@ -252,7 +252,7 @@ <h2><a class="toc-backref" href="#id2" role="doc-backlink">Protein Benchmark Dat
 <td><p>84523</p></td>
 <td><p>PROSPERous</p></td>
 <td><p>Prediction of solvent accessibility (SA) of residue (AA_CASPASE3 data set)</p></td>
-<td><p>Song18</p></td>
+<td><p><a class="reference internal" href="references.html#song18"><span class="std std-ref">Song18</span></a></p></td>
 <td><p>1 (exposed/accessible), 0 (buried/non-accessible)</p></td>
 </tr>
 <tr class="row-even"><td><p>Sequence</p></td>
@@ -263,7 +263,7 @@ <h2><a class="toc-backref" href="#id2" role="doc-backlink">Protein Benchmark Dat
 <td><p>903</p></td>
 <td><p>ReRF-Pred</p></td>
 <td><p>Prediction of amyloidognenic regions</p></td>
-<td><p>Teng21</p></td>
+<td><p><a class="reference internal" href="references.html#teng21"><span class="std std-ref">Teng21</span></a></p></td>
 <td><p>1 (amyloidogenic), 0 (non-amyloidogenic)</p></td>
 </tr>
 <tr class="row-odd"><td><p>Sequence</p></td>
@@ -274,7 +274,7 @@ <h2><a class="toc-backref" href="#id2" role="doc-backlink">Protein Benchmark Dat
 <td><p>4071</p></td>
 <td><p>VIRALpro</p></td>
 <td><p>Prediction of capdsid proteins</p></td>
-<td><p>Galiez16</p></td>
+<td><p><a class="reference internal" href="references.html#galiez16"><span class="std std-ref">Galiez16</span></a></p></td>
 <td><p>1 (capsid protein), 0 (non-capsid protein)</p></td>
 </tr>
 <tr class="row-even"><td><p>Sequence</p></td>
@@ -285,7 +285,7 @@ <h2><a class="toc-backref" href="#id2" role="doc-backlink">Protein Benchmark Dat
 <td><p>1650</p></td>
 <td><p>Dipro</p></td>
 <td><p>Prediction of disulfide bridges in sequences</p></td>
-<td><p>Cheng06</p></td>
+<td><p><a class="reference internal" href="references.html#cheng06"><span class="std std-ref">Cheng06</span></a></p></td>
 <td><p>1 (sequence with SS bond), 0 (sequence without SS bond)</p></td>
 </tr>
 <tr class="row-odd"><td><p>Sequence</p></td>
@@ -296,7 +296,7 @@ <h2><a class="toc-backref" href="#id2" role="doc-backlink">Protein Benchmark Dat
 <td><p>790</p></td>
 <td><p>nan</p></td>
 <td><p>Prediction of subcellular location of protein (cytoplasm vs plasma membrane)</p></td>
-<td><p>Shen19</p></td>
+<td><p><a class="reference internal" href="references.html#shen19"><span class="std std-ref">Shen19</span></a></p></td>
 <td><p>1 (protein in cytoplasm), 0 (protein in plasma membrane)</p></td>
 </tr>
 <tr class="row-even"><td><p>Sequence</p></td>
@@ -307,7 +307,7 @@ <h2><a class="toc-backref" href="#id2" role="doc-backlink">Protein Benchmark Dat
 <td><p>8704</p></td>
 <td><p>SOLpro</p></td>
 <td><p>Prediction of soluble and insoluble proteins</p></td>
-<td><p>Magnan09</p></td>
+<td><p><a class="reference internal" href="references.html#magnan09"><span class="std std-ref">Magnan09</span></a></p></td>
 <td><p>1 (soluble), 0 (insoluble)</p></td>
 </tr>
 <tr class="row-odd"><td><p>Sequence</p></td>
@@ -318,7 +318,7 @@ <h2><a class="toc-backref" href="#id2" role="doc-backlink">Protein Benchmark Dat
 <td><p>4094</p></td>
 <td><p>VIRALpro</p></td>
 <td><p>Prediction of tail proteins</p></td>
-<td><p>Galiez16</p></td>
+<td><p><a class="reference internal" href="references.html#galiez16"><span class="std std-ref">Galiez16</span></a></p></td>
 <td><p>1 (tail protein), 0 (non-tail protein)</p></td>
 </tr>
 <tr class="row-even"><td><p>Domain</p></td>
@@ -329,7 +329,7 @@ <h2><a class="toc-backref" href="#id2" role="doc-backlink">Protein Benchmark Dat
 <td><p>63</p></td>
 <td><p>nan</p></td>
 <td><p>Prediction of gamma-secretase substrates</p></td>
-<td><p>Breimann23c</p></td>
+<td><p><a class="reference internal" href="references.html#breimann23c"><span class="std std-ref">Breimann23c</span></a></p></td>
 <td><p>1 (substrate), 0 (non-substrate)</p></td>
 </tr>
 <tr class="row-odd"><td><p>Domain</p></td>
@@ -340,7 +340,7 @@ <h2><a class="toc-backref" href="#id2" role="doc-backlink">Protein Benchmark Dat
 <td><p>0</p></td>
 <td><p>nan</p></td>
 <td><p>Prediction of gamma-secretase substrates (PU dataset)</p></td>
-<td><p>Breimann23c</p></td>
+<td><p><a class="reference internal" href="references.html#breimann23c"><span class="std std-ref">Breimann23c</span></a></p></td>
 <td><p>1 (substrate), 2 (unknown substrate status)</p></td>
 </tr>
 </tbody>
@@ -367,32 +367,32 @@ <h2><a class="toc-backref" href="#id3" role="doc-backlink">Amino Acid Scale Data
 <tr class="row-even"><td><p>scales</p></td>
 <td><p>Amino acid scales (min-max normalized)</p></td>
 <td><p>586</p></td>
-<td><p>Breimann23b</p></td>
+<td><p><a class="reference internal" href="references.html#breimann23b"><span class="std std-ref">Breimann23b</span></a></p></td>
 </tr>
 <tr class="row-odd"><td><p>scales_raw</p></td>
 <td><p>Amino acid scales (raw values)</p></td>
 <td><p>586</p></td>
-<td><p>Kawashima08</p></td>
+<td><p><a class="reference internal" href="references.html#kawashima08"><span class="std std-ref">Kawashima08</span></a></p></td>
 </tr>
 <tr class="row-even"><td><p>scales_classification</p></td>
 <td><p>Classification of scales (Aaontology)</p></td>
 <td><p>586</p></td>
-<td><p>Breimann23b</p></td>
+<td><p><a class="reference internal" href="references.html#breimann23b"><span class="std std-ref">Breimann23b</span></a></p></td>
 </tr>
 <tr class="row-odd"><td><p>scales_pc</p></td>
 <td><p>Principal component (PC) compressed scales</p></td>
 <td><p>20</p></td>
-<td><p>Breimann23a</p></td>
+<td><p><a class="reference internal" href="references.html#breimann23a"><span class="std std-ref">Breimann23a</span></a></p></td>
 </tr>
 <tr class="row-even"><td><p>top60</p></td>
 <td><p>Top 60 scale subsets</p></td>
 <td><p>60</p></td>
-<td><p>Breimann23a</p></td>
+<td><p><a class="reference internal" href="references.html#breimann23a"><span class="std std-ref">Breimann23a</span></a></p></td>
 </tr>
 <tr class="row-odd"><td><p>top60_eval</p></td>
 <td><p>Evaluation of top 60 scale subsets</p></td>
 <td><p>60</p></td>
-<td><p>Breimann23a</p></td>
+<td><p><a class="reference internal" href="references.html#breimann23a"><span class="std std-ref">Breimann23a</span></a></p></td>
 </tr>
 </tbody>
 </table>