docs(master): Update docs of development line

master/_modules/niworkflows/interfaces/utility.html

@@ -588,8 +588,7 @@ <h1>Source code for niworkflows.interfaces.utility</h1><div class="highlight"><p
 <span class="sd">    &gt;&gt;&gt; addheader.inputs.in_file = &#39;data.tsv&#39;</span>
 <span class="sd">    &gt;&gt;&gt; addheader.inputs.columns = [&#39;a&#39;, &#39;b&#39;, &#39;c&#39;, &#39;d&#39;, &#39;e&#39;]</span>
 <span class="sd">    &gt;&gt;&gt; res = addheader.run()</span>
-<span class="sd">    &gt;&gt;&gt; df = pd.read_csv(res.outputs.out_file, delim_whitespace=True,</span>
-<span class="sd">    ...                  index_col=None)</span>
+<span class="sd">    &gt;&gt;&gt; df = pd.read_csv(res.outputs.out_file, sep=&#39;\s+&#39;, index_col=None)</span>
 <span class="sd">    &gt;&gt;&gt; df.columns.ravel().tolist()</span>
 <span class="sd">    [&#39;a&#39;, &#39;b&#39;, &#39;c&#39;, &#39;d&#39;, &#39;e&#39;]</span>
 
@@ -651,7 +650,7 @@ <h1>Source code for niworkflows.interfaces.utility</h1><div class="highlight"><p
 <span class="sd">    &gt;&gt;&gt; join.inputs.in_file = &#39;data.tsv&#39;</span>
 <span class="sd">    &gt;&gt;&gt; join.inputs.join_file = &#39;add.tsv&#39;</span>
 <span class="sd">    &gt;&gt;&gt; res = join.run()</span>
-<span class="sd">    &gt;&gt;&gt; df = pd.read_csv(res.outputs.out_file, delim_whitespace=True,</span>
+<span class="sd">    &gt;&gt;&gt; df = pd.read_csv(res.outputs.out_file, sep=&#39;\s+&#39;,</span>
 <span class="sd">    ...                  index_col=None, dtype=float, header=None)</span>
 <span class="sd">    &gt;&gt;&gt; df.columns.ravel().tolist() == list(range(5))</span>
 <span class="sd">    True</span>
@@ -668,8 +667,7 @@ <h1>Source code for niworkflows.interfaces.utility</h1><div class="highlight"><p
 <span class="sd">    &gt;&gt;&gt; res = join.run()</span>
 <span class="sd">    &gt;&gt;&gt; res.outputs.out_file  # doctest: +ELLIPSIS</span>
 <span class="sd">    &#39;...data_joined.tsv&#39;</span>
-<span class="sd">    &gt;&gt;&gt; df = pd.read_csv(res.outputs.out_file, delim_whitespace=True,</span>
-<span class="sd">    ...                  index_col=None)</span>
+<span class="sd">    &gt;&gt;&gt; df = pd.read_csv(res.outputs.out_file, sep=&#39;\s+&#39;, index_col=None)</span>
 <span class="sd">    &gt;&gt;&gt; df.columns.ravel().tolist()</span>
 <span class="sd">    [&#39;a&#39;, &#39;b&#39;, &#39;c&#39;, &#39;d&#39;, &#39;e&#39;]</span>
 
@@ -682,8 +680,7 @@ <h1>Source code for niworkflows.interfaces.utility</h1><div class="highlight"><p
 <span class="sd">    &gt;&gt;&gt; join.inputs.side = &#39;left&#39;</span>
 <span class="sd">    &gt;&gt;&gt; join.inputs.columns = [&#39;a&#39;, &#39;b&#39;, &#39;c&#39;, &#39;d&#39;, &#39;e&#39;]</span>
 <span class="sd">    &gt;&gt;&gt; res = join.run()</span>
-<span class="sd">    &gt;&gt;&gt; df = pd.read_csv(res.outputs.out_file, delim_whitespace=True,</span>
-<span class="sd">    ...                  index_col=None)</span>
+<span class="sd">    &gt;&gt;&gt; df = pd.read_csv(res.outputs.out_file, sep=&#39;\s+&#39;, index_col=None)</span>
 <span class="sd">    &gt;&gt;&gt; df.columns.ravel().tolist()</span>
 <span class="sd">    [&#39;a&#39;, &#39;b&#39;, &#39;c&#39;, &#39;d&#39;, &#39;e&#39;]</span>
 

master/_modules/niworkflows/viz/plots.html

@@ -1281,7 +1281,11 @@ <h1>Source code for niworkflows.viz.plots</h1><div class="highlight"><pre>
     <span class="n">gs_descending</span> <span class="o">=</span> <span class="n">gs_descending</span><span class="p">[:</span><span class="n">max_dim</span><span class="p">]</span>
     <span class="n">features</span> <span class="o">=</span> <span class="p">[</span><span class="n">p</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">corr</span><span class="o">.</span><span class="n">columns</span> <span class="k">if</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">gs_descending</span><span class="p">]</span>
     <span class="n">corr</span> <span class="o">=</span> <span class="n">corr</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">features</span><span class="p">,</span> <span class="n">features</span><span class="p">]</span>
-    <span class="n">np</span><span class="o">.</span><span class="n">fill_diagonal</span><span class="p">(</span><span class="n">corr</span><span class="o">.</span><span class="n">values</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
+
+    <span class="c1"># Modifying in-place is no longer supported</span>
+    <span class="n">corr_vals</span> <span class="o">=</span> <span class="n">corr</span><span class="o">.</span><span class="n">to_numpy</span><span class="p">(</span><span class="n">copy</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+    <span class="n">np</span><span class="o">.</span><span class="n">fill_diagonal</span><span class="p">(</span><span class="n">corr_vals</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
+    <span class="n">corr</span><span class="o">.</span><span class="n">iloc</span><span class="p">[:,</span> <span class="p">:]</span> <span class="o">=</span> <span class="n">corr_vals</span>
 
     <span class="k">if</span> <span class="n">figure</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
         <span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">15</span><span class="p">,</span> <span class="mi">5</span><span class="p">))</span>

master/api/niworkflows.interfaces.confounds.html

@@ -450,14 +450,14 @@
 indicates that the first and second exponential terms should be added.
 To retain the original terms, <code class="docutils literal notranslate"><span class="pre">1</span></code> <em>must</em> be included in the list.</p></li>
 <li><p><strong>variables</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.13)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code></a>) – List of variables for which exponential terms should be computed.</p></li>
-<li><p><strong>data</strong> (<a class="reference external" href="https://pandas.pydata.org/pandas-docs/dev/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v3.0.0.dev0+1714.gf105eefaab)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataFrame</span></code></a>) – Table of values of all observations of all variables.</p></li>
+<li><p><strong>data</strong> (<a class="reference external" href="https://pandas.pydata.org/pandas-docs/dev/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v3.0.0.dev0+1715.ge62fcb15a7)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataFrame</span></code></a>) – Table of values of all observations of all variables.</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>
 <dd class="field-even"><p><ul class="simple">
 <li><p><strong>variables_exp</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.13)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code></a>) – A list of variables to include in the final data frame after adding
 the specified exponential terms.</p></li>
-<li><p><strong>data_exp</strong> (<a class="reference external" href="https://pandas.pydata.org/pandas-docs/dev/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v3.0.0.dev0+1714.gf105eefaab)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataFrame</span></code></a>) – Table of values of all observations of all variables, including any
+<li><p><strong>data_exp</strong> (<a class="reference external" href="https://pandas.pydata.org/pandas-docs/dev/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v3.0.0.dev0+1715.ge62fcb15a7)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataFrame</span></code></a>) – Table of values of all observations of all variables, including any
 specified exponential terms.</p></li>
 </ul>
 </p>
@@ -474,13 +474,13 @@
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>expression</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code></a>) – Formula expression: either a single variable or a variable group
 paired with an operation (exponentiation or differentiation).</p></li>
-<li><p><strong>parent_data</strong> (<a class="reference external" href="https://pandas.pydata.org/pandas-docs/dev/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v3.0.0.dev0+1714.gf105eefaab)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataFrame</span></code></a>) – The source data for the model expansion.</p></li>
+<li><p><strong>parent_data</strong> (<a class="reference external" href="https://pandas.pydata.org/pandas-docs/dev/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v3.0.0.dev0+1715.ge62fcb15a7)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataFrame</span></code></a>) – The source data for the model expansion.</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>
 <dd class="field-even"><p><ul class="simple">
 <li><p><strong>variables</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.13)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code></a>) – A list of variables in the provided formula expression.</p></li>
-<li><p><strong>data</strong> (<a class="reference external" href="https://pandas.pydata.org/pandas-docs/dev/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v3.0.0.dev0+1714.gf105eefaab)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataFrame</span></code></a>) – A tabulation of all terms in the provided formula expression.</p></li>
+<li><p><strong>data</strong> (<a class="reference external" href="https://pandas.pydata.org/pandas-docs/dev/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v3.0.0.dev0+1715.ge62fcb15a7)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataFrame</span></code></a>) – A tabulation of all terms in the provided formula expression.</p></li>
 </ul>
 </p>
 </dd>
@@ -524,7 +524,7 @@
 <p>Temporal derivatives and exponential terms are computed for all terms
 in the grouping symbols that they adjoin.</p>
 </li>
-<li><p><strong>parent_data</strong> (<a class="reference external" href="https://pandas.pydata.org/pandas-docs/dev/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v3.0.0.dev0+1714.gf105eefaab)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataFrame</span></code></a>) – A tabulation of all values usable in the model formula. Each additive
+<li><p><strong>parent_data</strong> (<a class="reference external" href="https://pandas.pydata.org/pandas-docs/dev/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v3.0.0.dev0+1715.ge62fcb15a7)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataFrame</span></code></a>) – A tabulation of all values usable in the model formula. Each additive
 term in <cite>model_formula</cite> should correspond either to a variable in this
 data frame or to instructions for operating on a variable (for
 instance, computing temporal derivatives or exponential terms).</p></li>
@@ -534,7 +534,7 @@
 <dd class="field-even"><p><ul class="simple">
 <li><p><strong>variables</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.13)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code></a>) – A list of variables included in the model parsed from the provided
 formula.</p></li>
-<li><p><strong>data</strong> (<a class="reference external" href="https://pandas.pydata.org/pandas-docs/dev/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v3.0.0.dev0+1714.gf105eefaab)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataFrame</span></code></a>) – All values in the complete model.</p></li>
+<li><p><strong>data</strong> (<a class="reference external" href="https://pandas.pydata.org/pandas-docs/dev/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v3.0.0.dev0+1715.ge62fcb15a7)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataFrame</span></code></a>) – All values in the complete model.</p></li>
 </ul>
 </p>
 </dd>
@@ -548,7 +548,7 @@
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>data</strong> (<a class="reference external" href="https://pandas.pydata.org/pandas-docs/dev/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v3.0.0.dev0+1714.gf105eefaab)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataFrame</span></code></a>) – A tabulation of observations from which spike regressors should be
+<li><p><strong>data</strong> (<a class="reference external" href="https://pandas.pydata.org/pandas-docs/dev/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v3.0.0.dev0+1715.ge62fcb15a7)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataFrame</span></code></a>) – A tabulation of observations from which spike regressors should be
 estimated.</p></li>
 <li><p><strong>criteria</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.13)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">dict</span></code></a> of (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code></a>, <code class="docutils literal notranslate"><span class="pre">'&gt;'</span></code> or <code class="docutils literal notranslate"><span class="pre">'&lt;'</span></code> or <a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">float</span></code></a>)) – Criteria for generating a spike regressor. If, for a given frame, the
 value of the variable corresponding to the key exceeds the threshold
@@ -575,7 +575,7 @@
 <dd class="field-even"><p><strong>data</strong> – The input DataFrame with a column for each spike regressor.</p>
 </dd>
 <dt class="field-odd">Return type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://pandas.pydata.org/pandas-docs/dev/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v3.0.0.dev0+1714.gf105eefaab)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataFrame</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://pandas.pydata.org/pandas-docs/dev/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v3.0.0.dev0+1715.ge62fcb15a7)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataFrame</span></code></a></p>
 </dd>
 </dl>
 <p class="rubric">References</p>
@@ -601,14 +601,14 @@
 To retain the original terms, <code class="docutils literal notranslate"><span class="pre">0</span></code> <em>must</em> be included in the list.</p></li>
 <li><p><strong>variables</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.13)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code></a>) – List of variables for which temporal derivative terms should be
 computed.</p></li>
-<li><p><strong>data</strong> (<a class="reference external" href="https://pandas.pydata.org/pandas-docs/dev/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v3.0.0.dev0+1714.gf105eefaab)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataFrame</span></code></a>) – Table of values of all observations of all variables.</p></li>
+<li><p><strong>data</strong> (<a class="reference external" href="https://pandas.pydata.org/pandas-docs/dev/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v3.0.0.dev0+1715.ge62fcb15a7)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataFrame</span></code></a>) – Table of values of all observations of all variables.</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>
 <dd class="field-even"><p><ul class="simple">
 <li><p><strong>variables_deriv</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.13)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code></a>) – A list of variables to include in the final data frame after adding
 the specified derivative terms.</p></li>
-<li><p><strong>data_deriv</strong> (<a class="reference external" href="https://pandas.pydata.org/pandas-docs/dev/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v3.0.0.dev0+1714.gf105eefaab)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataFrame</span></code></a>) – Table of values of all observations of all variables, including any
+<li><p><strong>data_deriv</strong> (<a class="reference external" href="https://pandas.pydata.org/pandas-docs/dev/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v3.0.0.dev0+1715.ge62fcb15a7)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataFrame</span></code></a>) – Table of values of all observations of all variables, including any
 specified derivative terms.</p></li>
 </ul>
 </p>