docs(master): Update docs of development line

master/_modules/niworkflows/interfaces/confounds.html

@@ -311,6 +311,7 @@ <h1>Source code for niworkflows.interfaces.confounds</h1><div class="highlight">
 <span class="kn">import</span> <span class="nn">os</span>
 <span class="kn">import</span> <span class="nn">re</span>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+<span class="kn">import</span> <span class="nn">operator</span>
 <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
 <span class="kn">from</span> <span class="nn">functools</span> <span class="kn">import</span> <span class="n">reduce</span>
 <span class="kn">from</span> <span class="nn">collections</span> <span class="kn">import</span> <span class="n">deque</span><span class="p">,</span> <span class="n">OrderedDict</span>
@@ -447,7 +448,7 @@ <h1>Source code for niworkflows.interfaces.confounds</h1><div class="highlight">
     <span class="n">dvars_thresh</span> <span class="o">=</span> <span class="n">traits</span><span class="o">.</span><span class="n">Float</span><span class="p">(</span>
         <span class="mf">1.5</span><span class="p">,</span>
         <span class="n">usedefault</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
-        <span class="n">desc</span><span class="o">=</span><span class="s2">&quot;Minimum standardised DVARS threshold for flagging a frame as &quot;</span> <span class="s2">&quot;a spike.&quot;</span><span class="p">,</span>
+        <span class="n">desc</span><span class="o">=</span><span class="s2">&quot;Minimum standardised DVARS threshold for flagging a frame as a spike.&quot;</span><span class="p">,</span>
     <span class="p">)</span>
     <span class="n">header_prefix</span> <span class="o">=</span> <span class="n">traits</span><span class="o">.</span><span class="n">Str</span><span class="p">(</span>
         <span class="s2">&quot;motion_outlier&quot;</span><span class="p">,</span>
@@ -458,7 +459,7 @@ <h1>Source code for niworkflows.interfaces.confounds</h1><div class="highlight">
         <span class="n">traits</span><span class="o">.</span><span class="n">Int</span><span class="p">,</span>
         <span class="n">value</span><span class="o">=</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
         <span class="n">usedefault</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
-        <span class="n">desc</span><span class="o">=</span><span class="s2">&quot;Relative indices of lagging frames to flag for &quot;</span> <span class="s2">&quot;each flagged frame&quot;</span><span class="p">,</span>
+        <span class="n">desc</span><span class="o">=</span><span class="s2">&quot;Relative indices of lagging frames to flag for each flagged frame&quot;</span><span class="p">,</span>
     <span class="p">)</span>
     <span class="n">minimum_contiguous</span> <span class="o">=</span> <span class="n">traits</span><span class="o">.</span><span class="n">Either</span><span class="p">(</span>
         <span class="kc">None</span><span class="p">,</span>
@@ -593,7 +594,7 @@ <h1>Source code for niworkflows.interfaces.confounds</h1><div class="highlight">
             <span class="n">mask</span><span class="p">[</span><span class="n">metric</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">metric</span><span class="p">]</span> <span class="o">&lt;</span> <span class="n">threshold</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span>
         <span class="k">elif</span> <span class="n">criterion</span> <span class="o">==</span> <span class="s2">&quot;&gt;&quot;</span><span class="p">:</span>
             <span class="n">mask</span><span class="p">[</span><span class="n">metric</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">metric</span><span class="p">]</span> <span class="o">&gt;</span> <span class="n">threshold</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span>
-    <span class="n">mask</span> <span class="o">=</span> <span class="n">reduce</span><span class="p">((</span><span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">:</span> <span class="n">x</span> <span class="o">|</span> <span class="n">y</span><span class="p">),</span> <span class="n">mask</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
+    <span class="n">mask</span> <span class="o">=</span> <span class="n">reduce</span><span class="p">(</span><span class="n">operator</span><span class="o">.</span><span class="n">or_</span><span class="p">,</span> <span class="n">mask</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
 
     <span class="k">for</span> <span class="n">lag</span> <span class="ow">in</span> <span class="n">lags</span><span class="p">:</span>
         <span class="n">mask</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([</span><span class="n">m</span> <span class="o">+</span> <span class="n">lag</span> <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="n">mask</span><span class="p">])</span> <span class="o">|</span> <span class="n">mask</span>
@@ -663,7 +664,7 @@ <h1>Source code for niworkflows.interfaces.confounds</h1><div class="highlight">
         <span class="n">variables_deriv</span><span class="p">[</span><span class="n">o</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;</span><span class="si">{}</span><span class="s2">_derivative</span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="n">o</span><span class="p">)</span> <span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">variables</span><span class="p">]</span>
         <span class="n">data_deriv</span><span class="p">[</span><span class="n">o</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">tile</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">,</span> <span class="n">data</span><span class="p">[</span><span class="n">variables</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span>
         <span class="n">data_deriv</span><span class="p">[</span><span class="n">o</span><span class="p">][</span><span class="n">o</span><span class="p">:,</span> <span class="p">:]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">diff</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">variables</span><span class="p">],</span> <span class="n">n</span><span class="o">=</span><span class="n">o</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-    <span class="n">variables_deriv</span> <span class="o">=</span> <span class="n">reduce</span><span class="p">((</span><span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">:</span> <span class="n">x</span> <span class="o">+</span> <span class="n">y</span><span class="p">),</span> <span class="n">variables_deriv</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
+    <span class="n">variables_deriv</span> <span class="o">=</span> <span class="n">reduce</span><span class="p">(</span><span class="n">operator</span><span class="o">.</span><span class="n">add</span><span class="p">,</span> <span class="n">variables_deriv</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
     <span class="n">data_deriv</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
         <span class="n">columns</span><span class="o">=</span><span class="n">variables_deriv</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">([</span><span class="o">*</span><span class="n">data_deriv</span><span class="o">.</span><span class="n">values</span><span class="p">()],</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
     <span class="p">)</span>
@@ -708,7 +709,7 @@ <h1>Source code for niworkflows.interfaces.confounds</h1><div class="highlight">
     <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">order</span><span class="p">:</span>
         <span class="n">variables_exp</span><span class="p">[</span><span class="n">o</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;</span><span class="si">{}</span><span class="s2">_power</span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="n">o</span><span class="p">)</span> <span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">variables</span><span class="p">]</span>
         <span class="n">data_exp</span><span class="p">[</span><span class="n">o</span><span class="p">]</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="n">variables</span><span class="p">]</span> <span class="o">**</span> <span class="n">o</span>
-    <span class="n">variables_exp</span> <span class="o">=</span> <span class="n">reduce</span><span class="p">((</span><span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">:</span> <span class="n">x</span> <span class="o">+</span> <span class="n">y</span><span class="p">),</span> <span class="n">variables_exp</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
+    <span class="n">variables_exp</span> <span class="o">=</span> <span class="n">reduce</span><span class="p">(</span><span class="n">operator</span><span class="o">.</span><span class="n">add</span><span class="p">,</span> <span class="n">variables_exp</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
     <span class="n">data_exp</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
         <span class="n">columns</span><span class="o">=</span><span class="n">variables_exp</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">([</span><span class="o">*</span><span class="n">data_exp</span><span class="o">.</span><span class="n">values</span><span class="p">()],</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
     <span class="p">)</span>
@@ -878,7 +879,7 @@ <h1>Source code for niworkflows.interfaces.confounds</h1><div class="highlight">
             <span class="n">var</span><span class="p">[</span><span class="n">col</span><span class="p">]</span><span class="o">.</span><span class="n">appendleft</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
         <span class="k">else</span><span class="p">:</span>
             <span class="n">var</span><span class="p">[</span><span class="n">col</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
-    <span class="n">unscrambled</span> <span class="o">=</span> <span class="n">reduce</span><span class="p">((</span><span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">:</span> <span class="n">x</span> <span class="o">+</span> <span class="n">y</span><span class="p">),</span> <span class="n">var</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
+    <span class="n">unscrambled</span> <span class="o">=</span> <span class="n">reduce</span><span class="p">(</span><span class="n">operator</span><span class="o">.</span><span class="n">add</span><span class="p">,</span> <span class="n">var</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
     <span class="k">return</span> <span class="n">data</span><span class="p">[[</span><span class="o">*</span><span class="n">unscrambled</span><span class="p">]]</span>
 
 
@@ -959,7 +960,7 @@ <h1>Source code for niworkflows.interfaces.confounds</h1><div class="highlight">
             <span class="p">(</span><span class="n">variables</span><span class="p">[</span><span class="n">expression</span><span class="p">],</span> <span class="n">data</span><span class="p">[</span><span class="n">expression</span><span class="p">])</span> <span class="o">=</span> <span class="n">parse_expression</span><span class="p">(</span>
                 <span class="n">expression</span><span class="p">,</span> <span class="n">parent_data</span>
             <span class="p">)</span>
-    <span class="n">variables</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">reduce</span><span class="p">((</span><span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">:</span> <span class="n">x</span> <span class="o">+</span> <span class="n">y</span><span class="p">),</span> <span class="n">variables</span><span class="o">.</span><span class="n">values</span><span class="p">())))</span>
+    <span class="n">variables</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">reduce</span><span class="p">(</span><span class="n">operator</span><span class="o">.</span><span class="n">add</span><span class="p">,</span> <span class="n">variables</span><span class="o">.</span><span class="n">values</span><span class="p">())))</span>
     <span class="n">data</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">((</span><span class="n">data</span><span class="o">.</span><span class="n">values</span><span class="p">()),</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
 
     <span class="k">if</span> <span class="n">unscramble</span><span class="p">:</span>

master/_modules/niworkflows/interfaces/header.html

@@ -681,7 +681,7 @@ <h1>Source code for niworkflows.interfaces.header</h1><div class="highlight"><pr
     <span class="n">max_32bit</span> <span class="o">=</span> <span class="n">traits</span><span class="o">.</span><span class="n">Bool</span><span class="p">(</span>
         <span class="kc">False</span><span class="p">,</span>
         <span class="n">usedefault</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
-        <span class="n">desc</span><span class="o">=</span><span class="s2">&quot;cast data to float32 if higher &quot;</span> <span class="s2">&quot;precision is encountered&quot;</span><span class="p">,</span>
+        <span class="n">desc</span><span class="o">=</span><span class="s2">&quot;cast data to float32 if higher precision is encountered&quot;</span><span class="p">,</span>
     <span class="p">)</span>
 
 

master/_modules/niworkflows/interfaces/images.html

@@ -980,7 +980,7 @@ <h1>Source code for niworkflows.interfaces.images</h1><div class="highlight"><pr
         <span class="s2">&quot;signals.tsv&quot;</span><span class="p">,</span>
         <span class="n">usedefault</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
         <span class="n">exists</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
-        <span class="n">desc</span><span class="o">=</span><span class="s2">&quot;The name of the file to output to. &quot;</span> <span class="s2">&quot;signals.tsv by default&quot;</span><span class="p">,</span>
+        <span class="n">desc</span><span class="o">=</span><span class="s2">&quot;The name of the file to output to. signals.tsv by default&quot;</span><span class="p">,</span>
     <span class="p">)</span>
 
 

master/_modules/niworkflows/interfaces/plotting.html

@@ -410,7 +410,7 @@ <h1>Source code for niworkflows.interfaces.plotting</h1><div class="highlight"><
     <span class="n">metadata_files</span> <span class="o">=</span> <span class="n">traits</span><span class="o">.</span><span class="n">List</span><span class="p">(</span>
         <span class="n">File</span><span class="p">(</span><span class="n">exists</span><span class="o">=</span><span class="kc">True</span><span class="p">),</span>
         <span class="n">mandatory</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
-        <span class="n">desc</span><span class="o">=</span><span class="s2">&quot;List of files containing component &quot;</span> <span class="s2">&quot;metadata&quot;</span><span class="p">,</span>
+        <span class="n">desc</span><span class="o">=</span><span class="s2">&quot;List of files containing component metadata&quot;</span><span class="p">,</span>
     <span class="p">)</span>
     <span class="n">metadata_sources</span> <span class="o">=</span> <span class="n">traits</span><span class="o">.</span><span class="n">List</span><span class="p">(</span>
         <span class="n">traits</span><span class="o">.</span><span class="n">Str</span><span class="p">,</span>
@@ -423,7 +423,7 @@ <h1>Source code for niworkflows.interfaces.plotting</h1><div class="highlight"><
         <span class="n">traits</span><span class="o">.</span><span class="n">Float</span><span class="p">(</span><span class="mf">0.7</span><span class="p">),</span>
         <span class="n">traits</span><span class="o">.</span><span class="n">Float</span><span class="p">(</span><span class="mf">0.9</span><span class="p">),</span>
         <span class="n">usedefault</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
-        <span class="n">desc</span><span class="o">=</span><span class="s2">&quot;Levels of explained variance to include in &quot;</span> <span class="s2">&quot;plot&quot;</span><span class="p">,</span>
+        <span class="n">desc</span><span class="o">=</span><span class="s2">&quot;Levels of explained variance to include in plot&quot;</span><span class="p">,</span>
     <span class="p">)</span>
     <span class="n">out_file</span> <span class="o">=</span> <span class="n">traits</span><span class="o">.</span><span class="n">Either</span><span class="p">(</span>
         <span class="kc">None</span><span class="p">,</span> <span class="n">File</span><span class="p">,</span> <span class="n">value</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">usedefault</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="s2">&quot;Path to save plot&quot;</span>