docs(master): Update docs of development line

master/api/niworkflows.engine.workflows.html

@@ -343,7 +343,7 @@
 <dl class="py class">
 <dt class="sig sig-object py" id="niworkflows.engine.workflows.LiterateWorkflow">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">niworkflows.engine.workflows.</span></span><span class="sig-name descname"><span class="pre">LiterateWorkflow</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">base_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/niworkflows/engine/workflows.html#LiterateWorkflow"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#niworkflows.engine.workflows.LiterateWorkflow" title="Link to this definition">¶</a></dt>
-<dd><p>Bases: <a class="reference external" href="https://nipype.readthedocs.io/en/latest/api/generated/nipype.pipeline.engine.workflows.html#nipype.pipeline.engine.workflows.Workflow" title="(in nipype v1.8.7.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Workflow</span></code></a></p>
+<dd><p>Bases: <a class="reference external" href="https://nipype.readthedocs.io/en/latest/api/generated/nipype.pipeline.engine.workflows.html#nipype.pipeline.engine.workflows.Workflow" title="(in nipype v1.9.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Workflow</span></code></a></p>
 <p>Controls the setup and execution of a pipeline of processes.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="niworkflows.engine.workflows.LiterateWorkflow.visit_desc">

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+1611.g2a1ca9da29)"><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+1618.g1908f2eb96)"><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+1611.g2a1ca9da29)"><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+1618.g1908f2eb96)"><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+1611.g2a1ca9da29)"><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+1618.g1908f2eb96)"><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+1611.g2a1ca9da29)"><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+1618.g1908f2eb96)"><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+1611.g2a1ca9da29)"><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+1618.g1908f2eb96)"><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+1611.g2a1ca9da29)"><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+1618.g1908f2eb96)"><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+1611.g2a1ca9da29)"><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+1618.g1908f2eb96)"><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+1611.g2a1ca9da29)"><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+1618.g1908f2eb96)"><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+1611.g2a1ca9da29)"><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+1618.g1908f2eb96)"><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+1611.g2a1ca9da29)"><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+1618.g1908f2eb96)"><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>

master/api/niworkflows.interfaces.fixes.html

@@ -372,9 +372,9 @@
 (Nipype <strong>default</strong> value: <code class="docutils literal notranslate"><span class="pre">False</span></code>)</p></li>
 <li><p><strong>input_image_type</strong> (<em>0 or 1 or 2 or 3</em>) – Option specifying the input image type of scalar (default), vector, tensor, or time series.
 Maps to a command-line argument: <code class="code docutils literal notranslate"><span class="pre">--input-image-type</span> <span class="pre">%d</span></code>.</p></li>
-<li><p><strong>interpolation</strong> (<em>‘Linear’ or ‘NearestNeighbor’ or ‘CosineWindowedSinc’ or ‘WelchWindowedSinc’ or ‘HammingWindowedSinc’ or ‘LanczosWindowedSinc’ or ‘MultiLabel’ or ‘Gaussian’ or ‘BSpline’</em>) – Maps to a command-line argument: <code class="code docutils literal notranslate"><span class="pre">%s</span></code>.
+<li><p><strong>interpolation</strong> (<em>‘Linear’ or ‘NearestNeighbor’ or ‘CosineWindowedSinc’ or ‘WelchWindowedSinc’ or ‘HammingWindowedSinc’ or ‘LanczosWindowedSinc’ or ‘MultiLabel’ or ‘Gaussian’ or ‘BSpline’ or ‘GenericLabel’</em>) – Maps to a command-line argument: <code class="code docutils literal notranslate"><span class="pre">%s</span></code>.
 (Nipype <strong>default</strong> value: <code class="docutils literal notranslate"><span class="pre">Linear</span></code>)</p></li>
-<li><p><strong>interpolation_parameters</strong> (<em>a tuple of the form: (an integer) or a tuple of the form: (a float, a float)</em>)</p></li>
+<li><p><strong>interpolation_parameters</strong> (<em>a tuple of the form: (an integer) or a tuple of the form: (a float, a float) or a tuple of the form: (a string)</em>)</p></li>
 <li><p><strong>invert_transform_flags</strong> (<em>a list of items which are a boolean</em>)</p></li>
 <li><p><strong>num_threads</strong> (<em>an integer</em>) – Number of ITK threads to use.
 (Nipype <strong>default</strong> value: <code class="docutils literal notranslate"><span class="pre">1</span></code>)</p></li>

master/api/niworkflows.interfaces.freesurfer.html

@@ -947,7 +947,7 @@
 Maps to a command-line argument: <code class="code docutils literal notranslate"><span class="pre">--fixtp</span></code>.</p></li>
 <li><p><strong>in_intensity_scales</strong> (<em>a list of items which are a pathlike object or string representing an existing file</em>) – Use initial intensity scales.
 Maps to a command-line argument: <code class="code docutils literal notranslate"><span class="pre">--iscalein</span> <span class="pre">%s</span></code>.</p></li>
-<li><p><strong>initial_timepoint</strong> (<em>an integer</em>) – Use TP# for spacial init (default random), 0: no init.
+<li><p><strong>initial_timepoint</strong> (<em>an integer</em>) – Use TP# for special init (default random), 0: no init.
 Maps to a command-line argument: <code class="code docutils literal notranslate"><span class="pre">--inittp</span> <span class="pre">%d</span></code>.</p></li>
 <li><p><strong>initial_transforms</strong> (<em>a list of items which are a pathlike object or string representing an existing file</em>) – Use initial transforms (lta) on source.
 Maps to a command-line argument: <code class="code docutils literal notranslate"><span class="pre">--ixforms</span> <span class="pre">%s</span></code>.</p></li>

master/api/niworkflows.interfaces.header.html

@@ -373,7 +373,7 @@
 <dl class="py attribute">
 <dt class="sig sig-object py" id="niworkflows.interfaces.header.CopyXForm.output_spec">
 <span class="sig-name descname"><span class="pre">output_spec</span></span><a class="headerlink" href="#niworkflows.interfaces.header.CopyXForm.output_spec" title="Link to this definition">¶</a></dt>
-<dd><p>alias of <a class="reference external" href="https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.base.specs.html#nipype.interfaces.base.specs.DynamicTraitedSpec" title="(in nipype v1.8.7.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">DynamicTraitedSpec</span></code></a></p>
+<dd><p>alias of <a class="reference external" href="https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.base.specs.html#nipype.interfaces.base.specs.DynamicTraitedSpec" title="(in nipype v1.9.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">DynamicTraitedSpec</span></code></a></p>
 </dd></dl>
 
 </dd></dl>