Prepare for 3.6.0 release.

CHANGELOG

@@ -6,7 +6,7 @@ All notable changes to this project will be documented in this file.
 The format is based on `Keep a Changelog <http://keepachangelog.com/>`_
 and this project adheres to `Semantic Versioning <http://semver.org/>`_
 
-3.6.0 - 2022-03-31
+3.6.0 - 2022-04-05
 ------------------
 
 Added

README.rst

@@ -1,4 +1,4 @@
-WORC v3.5.0
+WORC v3.6.0
 ===========
 
 Workflow for Optimal Radiomics Classification

WORC/doc/_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: 200f1b705b4d367101e0261a187b00d0
+config: 471bd1391db5c3e45eba5232589e54ea
 tags: 645f666f9bcd5a90fca523b33c5a78b7

WORC/doc/_build/html/_modules/WORC/IOparser/config_WORC.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>WORC.IOparser.config_WORC &mdash; WORC 3.5.0 documentation</title>
+  <title>WORC.IOparser.config_WORC &mdash; WORC 3.6.0 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.5.0
+                3.6.0
               </div>
 
 
@@ -187,7 +187,7 @@ <h1>Source code for WORC.IOparser.config_WORC</h1><div class="highlight"><pre>
 
 
 <div class="viewcode-block" id="load_config"><a class="viewcode-back" href="../../../autogen/WORC.IOparser.html#WORC.IOparser.config_WORC.load_config">[docs]</a><span class="k">def</span> <span class="nf">load_config</span><span class="p">(</span><span class="n">config_file_path</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot; Parse a WORC configuration file.</span>
+    <span class="sd">&quot;&quot;&quot;Parse a WORC configuration file.</span>
 
 <span class="sd">    Arguments:</span>
 <span class="sd">        config_file_path: path to the configuration file to be parsed.</span>

WORC/doc/_build/html/_modules/WORC/IOparser/config_io_classifier.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>WORC.IOparser.config_io_classifier &mdash; WORC 3.5.0 documentation</title>
+  <title>WORC.IOparser.config_io_classifier &mdash; WORC 3.6.0 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.5.0
+                3.6.0
               </div>
 
 
@@ -165,7 +165,7 @@
   <h1>Source code for WORC.IOparser.config_io_classifier</h1><div class="highlight"><pre>
 <span></span><span class="ch">#!/usr/bin/env python</span>
 
-<span class="c1"># Copyright 2016-2021 Biomedical Imaging Group Rotterdam, Departments of</span>
+<span class="c1"># Copyright 2016-2022 Biomedical Imaging Group Rotterdam, Departments of</span>
 <span class="c1"># Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands</span>
 <span class="c1">#</span>
 <span class="c1"># Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);</span>
@@ -210,7 +210,7 @@ <h1>Source code for WORC.IOparser.config_io_classifier</h1><div class="highlight
                      <span class="s1">&#39;Resampling&#39;</span><span class="p">:</span> <span class="nb">dict</span><span class="p">(),</span> <span class="s1">&#39;Imputation&#39;</span><span class="p">:</span> <span class="nb">dict</span><span class="p">(),</span>
                      <span class="s1">&#39;Ensemble&#39;</span><span class="p">:</span> <span class="nb">dict</span><span class="p">(),</span> <span class="s1">&#39;Bootstrap&#39;</span><span class="p">:</span> <span class="nb">dict</span><span class="p">(),</span>
                      <span class="s1">&#39;FeatPreProcess&#39;</span><span class="p">:</span> <span class="nb">dict</span><span class="p">(),</span> <span class="s1">&#39;Evaluation&#39;</span><span class="p">:</span> <span class="nb">dict</span><span class="p">(),</span>
-                     <span class="s1">&#39;OneHotEncoding&#39;</span><span class="p">:</span> <span class="nb">dict</span><span class="p">()}</span>
+                     <span class="s1">&#39;OneHotEncoding&#39;</span><span class="p">:</span> <span class="nb">dict</span><span class="p">(),</span> <span class="s1">&#39;SMAC&#39;</span><span class="p">:</span> <span class="nb">dict</span><span class="p">()}</span>
 
     <span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;General&#39;</span><span class="p">][</span><span class="s1">&#39;cross_validation&#39;</span><span class="p">]</span> <span class="o">=</span>\
         <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;General&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">getboolean</span><span class="p">(</span><span class="s1">&#39;cross_validation&#39;</span><span class="p">)</span>
@@ -496,6 +496,31 @@ <h1>Source code for WORC.IOparser.config_io_classifier</h1><div class="highlight
         <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">item</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span>
          <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;Classification&#39;</span><span class="p">][</span><span class="s1">&#39;XGB_colsample_bytree&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)]</span>
 
+    <span class="c1"># Light GBM</span>
+    <span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;Classification&#39;</span><span class="p">][</span><span class="s1">&#39;LightGBM_num_leaves&#39;</span><span class="p">]</span> <span class="o">=</span>\
+        <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">item</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span>
+         <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;Classification&#39;</span><span class="p">][</span><span class="s1">&#39;LightGBM_num_leaves&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)]</span>
+
+    <span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;Classification&#39;</span><span class="p">][</span><span class="s1">&#39;LightGBM_max_depth&#39;</span><span class="p">]</span> <span class="o">=</span>\
+        <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">item</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span>
+         <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;Classification&#39;</span><span class="p">][</span><span class="s1">&#39;LightGBM_max_depth&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)]</span>
+
+    <span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;Classification&#39;</span><span class="p">][</span><span class="s1">&#39;LightGBM_min_child_samples&#39;</span><span class="p">]</span> <span class="o">=</span>\
+        <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">item</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span>
+         <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;Classification&#39;</span><span class="p">][</span><span class="s1">&#39;LightGBM_min_child_samples&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)]</span>
+
+    <span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;Classification&#39;</span><span class="p">][</span><span class="s1">&#39;LightGBM_reg_alpha&#39;</span><span class="p">]</span> <span class="o">=</span>\
+        <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">item</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span>
+         <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;Classification&#39;</span><span class="p">][</span><span class="s1">&#39;LightGBM_reg_alpha&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)]</span>
+
+    <span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;Classification&#39;</span><span class="p">][</span><span class="s1">&#39;LightGBM_reg_lambda&#39;</span><span class="p">]</span> <span class="o">=</span>\
+        <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">item</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span>
+         <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;Classification&#39;</span><span class="p">][</span><span class="s1">&#39;LightGBM_reg_lambda&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)]</span>
+
+    <span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;Classification&#39;</span><span class="p">][</span><span class="s1">&#39;LightGBM_min_child_weight&#39;</span><span class="p">]</span> <span class="o">=</span>\
+        <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">item</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span>
+         <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;Classification&#39;</span><span class="p">][</span><span class="s1">&#39;LightGBM_min_child_weight&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)]</span>
+
     <span class="c1"># Cross validation settings</span>
     <span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;CrossValidation&#39;</span><span class="p">][</span><span class="s1">&#39;Type&#39;</span><span class="p">]</span> <span class="o">=</span>\
         <span class="nb">str</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;CrossValidation&#39;</span><span class="p">][</span><span class="s1">&#39;Type&#39;</span><span class="p">])</span>
@@ -537,9 +562,26 @@ <h1>Source code for WORC.IOparser.config_io_classifier</h1><div class="highlight
     <span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;HyperOptimization&#39;</span><span class="p">][</span><span class="s1">&#39;memory&#39;</span><span class="p">]</span> <span class="o">=</span> \
         <span class="nb">str</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;HyperOptimization&#39;</span><span class="p">][</span><span class="s1">&#39;memory&#39;</span><span class="p">])</span>
 
+    <span class="c1"># Settings for SMAC</span>
+    <span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;SMAC&#39;</span><span class="p">][</span><span class="s1">&#39;use&#39;</span><span class="p">]</span> <span class="o">=</span>\
+        <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;SMAC&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">getboolean</span><span class="p">(</span><span class="s1">&#39;use&#39;</span><span class="p">)</span>
+    <span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;SMAC&#39;</span><span class="p">][</span><span class="s1">&#39;n_smac_cores&#39;</span><span class="p">]</span> <span class="o">=</span>\
+        <span class="nb">int</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;SMAC&#39;</span><span class="p">][</span><span class="s1">&#39;n_smac_cores&#39;</span><span class="p">])</span>
+    <span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;SMAC&#39;</span><span class="p">][</span><span class="s1">&#39;budget_type&#39;</span><span class="p">]</span> <span class="o">=</span>\
+        <span class="nb">str</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;SMAC&#39;</span><span class="p">][</span><span class="s1">&#39;budget_type&#39;</span><span class="p">])</span>
+    <span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;SMAC&#39;</span><span class="p">][</span><span class="s1">&#39;budget&#39;</span><span class="p">]</span> <span class="o">=</span>\
+        <span class="nb">int</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;SMAC&#39;</span><span class="p">][</span><span class="s1">&#39;budget&#39;</span><span class="p">])</span>
+    <span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;SMAC&#39;</span><span class="p">][</span><span class="s1">&#39;init_method&#39;</span><span class="p">]</span> <span class="o">=</span>\
+        <span class="nb">str</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;SMAC&#39;</span><span class="p">][</span><span class="s1">&#39;init_method&#39;</span><span class="p">])</span>
+    <span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;SMAC&#39;</span><span class="p">][</span><span class="s1">&#39;init_budget&#39;</span><span class="p">]</span> <span class="o">=</span>\
+        <span class="nb">int</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;SMAC&#39;</span><span class="p">][</span><span class="s1">&#39;init_budget&#39;</span><span class="p">])</span>
+
     <span class="c1"># Settings for ensembling</span>
-    <span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;Ensemble&#39;</span><span class="p">][</span><span class="s1">&#39;Use&#39;</span><span class="p">]</span> <span class="o">=</span>\
-        <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;Ensemble&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">getint</span><span class="p">(</span><span class="s1">&#39;Use&#39;</span><span class="p">)</span>
+    <span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;Ensemble&#39;</span><span class="p">][</span><span class="s1">&#39;Method&#39;</span><span class="p">]</span> <span class="o">=</span>\
+        <span class="nb">str</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;Ensemble&#39;</span><span class="p">][</span><span class="s1">&#39;Method&#39;</span><span class="p">])</span>
+    <span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;Ensemble&#39;</span><span class="p">][</span><span class="s1">&#39;Size&#39;</span><span class="p">]</span> <span class="o">=</span>\
+        <span class="nb">int</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;Ensemble&#39;</span><span class="p">][</span><span class="s1">&#39;Size&#39;</span><span class="p">])</span>
+        <span class="c1">#settings[&#39;Ensemble&#39;].getint(&#39;Use&#39;)</span>
 
     <span class="n">settings_dict</span><span class="p">[</span><span class="s1">&#39;Ensemble&#39;</span><span class="p">][</span><span class="s1">&#39;Metric&#39;</span><span class="p">]</span> <span class="o">=</span>\
         <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;Ensemble&#39;</span><span class="p">][</span><span class="s1">&#39;Metric&#39;</span><span class="p">]</span>

WORC/doc/_build/html/_modules/WORC/IOparser/config_preprocessing.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>WORC.IOparser.config_preprocessing &mdash; WORC 3.5.0 documentation</title>
+  <title>WORC.IOparser.config_preprocessing &mdash; WORC 3.6.0 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.5.0
+                3.6.0
               </div>
 
 

WORC/doc/_build/html/_modules/WORC/IOparser/config_segmentix.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>WORC.IOparser.config_segmentix &mdash; WORC 3.5.0 documentation</title>
+  <title>WORC.IOparser.config_segmentix &mdash; WORC 3.6.0 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.5.0
+                3.6.0
               </div>
 
 

WORC/doc/_build/html/_modules/WORC/IOparser/file_io.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>WORC.IOparser.file_io &mdash; WORC 3.5.0 documentation</title>
+  <title>WORC.IOparser.file_io &mdash; WORC 3.6.0 documentation</title>
 
 
 
@@ -62,7 +62,7 @@
 
 
               <div class="version">
-                3.5.0
+                3.6.0
               </div>