docs(master): Update docs of development line

master/_modules/niworkflows/interfaces/bids.html

@@ -1117,7 +1117,7 @@ <h1>Source code for niworkflows.interfaces.bids</h1><div class="highlight"><pre>
                 <span class="n">_copy_any</span><span class="p">(</span><span class="n">in_file</span><span class="p">,</span> <span class="n">out_file</span><span class="p">)</span>
 
             <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">inputs</span><span class="o">.</span><span class="n">metadata</span><span class="p">:</span>
-                <span class="n">sidecar</span> <span class="o">=</span> <span class="n">out_file</span><span class="o">.</span><span class="n">parent</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">out_file</span><span class="o">.</span><span class="n">name</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="w"> </span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="si">}</span><span class="s2">.json&quot;</span>
+                <span class="n">sidecar</span> <span class="o">=</span> <span class="n">out_file</span><span class="o">.</span><span class="n">parent</span> <span class="o">/</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">out_file</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;.&quot;</span><span class="p">,</span><span class="w"> </span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="si">}</span><span class="s1">.json&#39;</span>
                 <span class="n">sidecar</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">missing_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
                 <span class="n">sidecar</span><span class="o">.</span><span class="n">write_text</span><span class="p">(</span><span class="n">dumps</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">inputs</span><span class="o">.</span><span class="n">metadata</span><span class="p">,</span> <span class="n">indent</span><span class="o">=</span><span class="mi">2</span><span class="p">))</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">_results</span><span class="p">[</span><span class="s1">&#39;out_meta&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">sidecar</span><span class="p">))</span>
@@ -1583,7 +1583,7 @@ <h1>Source code for niworkflows.interfaces.bids</h1><div class="highlight"><pre>
                 <span class="p">{</span><span class="n">k</span><span class="p">:</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">inputs</span><span class="p">,</span> <span class="n">k</span><span class="p">)</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">meta_fields</span> <span class="k">if</span> <span class="n">k</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_static_traits</span><span class="p">}</span>
             <span class="p">)</span>
             <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_metadata</span><span class="p">:</span>
-                <span class="n">sidecar</span> <span class="o">=</span> <span class="n">out_file</span><span class="o">.</span><span class="n">parent</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">out_file</span><span class="o">.</span><span class="n">name</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="w"> </span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="si">}</span><span class="s2">.json&quot;</span>
+                <span class="n">sidecar</span> <span class="o">=</span> <span class="n">out_file</span><span class="o">.</span><span class="n">parent</span> <span class="o">/</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">out_file</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;.&quot;</span><span class="p">,</span><span class="w"> </span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="si">}</span><span class="s1">.json&#39;</span>
                 <span class="n">unlink</span><span class="p">(</span><span class="n">sidecar</span><span class="p">,</span> <span class="n">missing_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
                 <span class="n">sidecar</span><span class="o">.</span><span class="n">write_text</span><span class="p">(</span><span class="n">dumps</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_metadata</span><span class="p">,</span> <span class="n">sort_keys</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">indent</span><span class="o">=</span><span class="mi">2</span><span class="p">))</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">_results</span><span class="p">[</span><span class="s1">&#39;out_meta&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">sidecar</span><span class="p">)</span>
@@ -1836,8 +1836,8 @@ <h1>Source code for niworkflows.interfaces.bids</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">xyz</span><span class="si">}</span><span class="s1"> mm^3&#39;</span>
 
     <span class="k">return</span> <span class="p">(</span>
-        <span class="sa">f</span><span class="s2">&quot;Template </span><span class="si">{</span><span class="n">space</span><span class="si">}</span><span class="s2"> (</span><span class="si">{</span><span class="n">_fmt_xyz</span><span class="p">(</span><span class="n">res_meta</span><span class="p">[</span><span class="s1">&#39;zooms&#39;</span><span class="p">])</span><span class="si">}</span><span class="s2">),&quot;</span>
-        <span class="sa">f</span><span class="s2">&quot; curated by TemplateFlow </span><span class="si">{</span><span class="n">tf</span><span class="o">.</span><span class="n">__version__</span><span class="si">}</span><span class="s2">&quot;</span>
+        <span class="sa">f</span><span class="s1">&#39;Template </span><span class="si">{</span><span class="n">space</span><span class="si">}</span><span class="s1"> (</span><span class="si">{</span><span class="n">_fmt_xyz</span><span class="p">(</span><span class="n">res_meta</span><span class="p">[</span><span class="s2">&quot;zooms&quot;</span><span class="p">])</span><span class="si">}</span><span class="s1">),&#39;</span>
+        <span class="sa">f</span><span class="s1">&#39; curated by TemplateFlow </span><span class="si">{</span><span class="n">tf</span><span class="o">.</span><span class="n">__version__</span><span class="si">}</span><span class="s1">&#39;</span>
     <span class="p">)</span>
 </pre></div>
         </article>

master/_modules/niworkflows/interfaces/confounds.html

@@ -514,8 +514,7 @@ <h1>Source code for niworkflows.interfaces.confounds</h1><div class="highlight">
     <span class="n">concatenate</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">True</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="s1">&#39;Indicates whether to concatenate spikes to existing confounds &#39;</span>
-        <span class="s1">&#39;or return spikes only&#39;</span><span class="p">,</span>
+        <span class="n">desc</span><span class="o">=</span><span class="s1">&#39;Indicates whether to concatenate spikes to existing confounds or return spikes only&#39;</span><span class="p">,</span>
     <span class="p">)</span>
     <span class="n">output_format</span> <span class="o">=</span> <span class="n">traits</span><span class="o">.</span><span class="n">Enum</span><span class="p">(</span>
         <span class="s1">&#39;spikes&#39;</span><span class="p">,</span> <span class="s1">&#39;mask&#39;</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="s1">&#39;Format of output (spikes or mask)&#39;</span>

master/_modules/niworkflows/interfaces/images.html

@@ -1057,8 +1057,7 @@ <h1>Source code for niworkflows.interfaces.images</h1><div class="highlight"><pr
         <span class="c1"># This check assumes all input masks have same dimensions</span>
         <span class="k">if</span> <span class="n">img</span><span class="o">.</span><span class="n">shape</span><span class="p">[:</span><span class="mi">3</span><span class="p">]</span> <span class="o">!=</span> <span class="n">mask_imgs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span><span class="p">[:</span><span class="mi">3</span><span class="p">]:</span>
             <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span>
-                <span class="s1">&#39;Input image and mask should be of &#39;</span>
-                <span class="s1">&#39;same dimensions before running SignalExtraction&#39;</span>
+                <span class="s1">&#39;Input image and mask should be of same dimensions before running SignalExtraction&#39;</span>
             <span class="p">)</span>
         <span class="c1"># Load the mask.</span>
         <span class="c1"># If mask is a list, each mask is treated as its own ROI/parcel</span>

master/_modules/niworkflows/interfaces/itk.html

@@ -426,8 +426,7 @@ <h1>Source code for niworkflows.interfaces.itk</h1><div class="highlight"><pre>
     <span class="n">input_image</span> <span class="o">=</span> <span class="n">InputMultiObject</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="s1">&#39;input time-series as a list of volumes after splitting&#39;</span>
-        <span class="s1">&#39; through the fourth dimension&#39;</span><span class="p">,</span>
+        <span class="n">desc</span><span class="o">=</span><span class="s1">&#39;input time-series as a list of volumes after splitting through the fourth dimension&#39;</span><span class="p">,</span>
     <span class="p">)</span>
     <span class="n">num_threads</span> <span class="o">=</span> <span class="n">traits</span><span class="o">.</span><span class="n">Int</span><span class="p">(</span><span class="mi">1</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">nohash</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="s1">&#39;number of parallel processes&#39;</span><span class="p">)</span>
     <span class="n">save_cmd</span> <span class="o">=</span> <span class="n">traits</span><span class="o">.</span><span class="n">Bool</span><span class="p">(</span>

master/_modules/niworkflows/interfaces/nibabel.html

@@ -525,7 +525,7 @@ <h1>Source code for niworkflows.interfaces.nibabel</h1><div class="highlight"><p
         <span class="n">img</span> <span class="o">=</span> <span class="n">nb</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">in_file</span><span class="p">)</span>
         <span class="n">extra_dims</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">dim</span> <span class="k">for</span> <span class="n">dim</span> <span class="ow">in</span> <span class="n">img</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">3</span><span class="p">:]</span> <span class="k">if</span> <span class="n">dim</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">)</span> <span class="ow">or</span> <span class="p">(</span><span class="mi">1</span><span class="p">,)</span>
         <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">extra_dims</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">1</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Invalid shape </span><span class="si">{</span><span class="s1">&#39;x&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">s</span><span class="p">)</span><span class="w"> </span><span class="k">for</span><span class="w"> </span><span class="n">s</span><span class="w"> </span><span class="ow">in</span><span class="w"> </span><span class="n">img</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Invalid shape </span><span class="si">{</span><span class="s2">&quot;x&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">s</span><span class="p">)</span><span class="w"> </span><span class="k">for</span><span class="w"> </span><span class="n">s</span><span class="w"> </span><span class="ow">in</span><span class="w"> </span><span class="n">img</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
         <span class="n">img</span> <span class="o">=</span> <span class="n">img</span><span class="o">.</span><span class="vm">__class__</span><span class="p">(</span>
             <span class="n">img</span><span class="o">.</span><span class="n">dataobj</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="n">img</span><span class="o">.</span><span class="n">shape</span><span class="p">[:</span><span class="mi">3</span><span class="p">]</span> <span class="o">+</span> <span class="n">extra_dims</span><span class="p">),</span> <span class="n">img</span><span class="o">.</span><span class="n">affine</span><span class="p">,</span> <span class="n">img</span><span class="o">.</span><span class="n">header</span>
         <span class="p">)</span>

master/_modules/niworkflows/interfaces/surf.html

@@ -529,7 +529,7 @@ <h1>Source code for niworkflows.interfaces.surf</h1><div class="highlight"><pre>
         <span class="n">in_file</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">inputs</span><span class="o">.</span><span class="n">in_file</span><span class="p">)</span>
         <span class="n">extension</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">in_file</span><span class="o">.</span><span class="n">suffixes</span><span class="p">[</span><span class="o">-</span><span class="p">((</span><span class="n">in_file</span><span class="o">.</span><span class="n">suffixes</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;.gz&#39;</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="p">:])</span>
         <span class="n">info</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_pattern</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">in_file</span><span class="o">.</span><span class="n">name</span><span class="p">[:</span> <span class="o">-</span><span class="nb">len</span><span class="p">(</span><span class="n">extension</span><span class="p">)])</span><span class="o">.</span><span class="n">groupdict</span><span class="p">()</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_results</span><span class="p">[</span><span class="s1">&#39;extension&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">info</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;extprefix&#39;</span><span class="p">,</span><span class="w"> </span><span class="kc">None</span><span class="p">)</span><span class="w"> </span><span class="ow">or</span><span class="w"> </span><span class="s1">&#39;&#39;</span><span class="si">}{</span><span class="n">extension</span><span class="si">}</span><span class="s2">&quot;</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_results</span><span class="p">[</span><span class="s1">&#39;extension&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">info</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s2">&quot;extprefix&quot;</span><span class="p">,</span><span class="w"> </span><span class="kc">None</span><span class="p">)</span><span class="w"> </span><span class="ow">or</span><span class="w"> </span><span class="s2">&quot;&quot;</span><span class="si">}{</span><span class="n">extension</span><span class="si">}</span><span class="s1">&#39;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_results</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">info</span><span class="p">)</span>
         <span class="k">if</span> <span class="s1">&#39;hemi&#39;</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_results</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_results</span><span class="p">[</span><span class="s1">&#39;hemi&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_results</span><span class="p">[</span><span class="s1">&#39;hemi&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>