docs(master): Update docs of development line

nipreps · Jan 10, 2025 · 9124e47 · 9124e47
1 parent 903338b
commit 9124e47
Show file tree

Hide file tree

Showing 38 changed files with 24 additions and 23 deletions.
diff --git a/master/_images/niworkflows-anat-ants-1.png b/master/_images/niworkflows-anat-ants-1.png
diff --git a/master/_images/niworkflows-anat-ants-2.png b/master/_images/niworkflows-anat-ants-2.png
diff --git a/master/_images/niworkflows-anat-ants-3.png b/master/_images/niworkflows-anat-ants-3.png
diff --git a/master/_images/niworkflows-anat-coregistration-1.png b/master/_images/niworkflows-anat-coregistration-1.png
diff --git a/master/_images/niworkflows-anat-freesurfer-1.png b/master/_images/niworkflows-anat-freesurfer-1.png
diff --git a/master/_images/niworkflows-anat-skullstrip-1.png b/master/_images/niworkflows-anat-skullstrip-1.png
diff --git a/master/_images/niworkflows-func-util-1.png b/master/_images/niworkflows-func-util-1.png
diff --git a/master/_images/niworkflows-func-util-2.png b/master/_images/niworkflows-func-util-2.png
diff --git a/master/_images/niworkflows-func-util-3.png b/master/_images/niworkflows-func-util-3.png
diff --git a/master/_images/niworkflows-workflows-epi-refmap-1.png b/master/_images/niworkflows-workflows-epi-refmap-1.png
diff --git a/master/_modules/niworkflows/interfaces/bids.html b/master/_modules/niworkflows/interfaces/bids.html
@@ -602,12 +602,13 @@ <h1>Source code for niworkflows.interfaces.bids</h1><div class="highlight"><pre>
     <span class="n">_require_funcs</span> <span class="o">=</span> <span class="kc">True</span>
 
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-        <span class="n">anat_only</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;anat_only&#39;</span><span class="p">)</span>
+        <span class="n">anat_only</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;anat_only&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
         <span class="n">anat_derivatives</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;anat_derivatives&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+        <span class="n">require_t1w</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;require_t1w&#39;</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
         <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
         <span class="k">if</span> <span class="n">anat_only</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_require_funcs</span> <span class="o">=</span> <span class="ow">not</span> <span class="n">anat_only</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_require_t1w</span> <span class="o">=</span> <span class="n">anat_derivatives</span> <span class="ow">is</span> <span class="kc">None</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_require_t1w</span> <span class="o">=</span> <span class="n">require_t1w</span> <span class="ow">and</span> <span class="n">anat_derivatives</span> <span class="ow">is</span> <span class="kc">None</span>
 
     <span class="k">def</span> <span class="nf">_run_interface</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">runtime</span><span class="p">):</span>
         <span class="n">bids_dict</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">inputs</span><span class="o">.</span><span class="n">subject_data</span>

diff --git a/master/_static/pygments.css b/master/_static/pygments.css
@@ -106,17 +106,17 @@ body[data-theme="dark"] .highlight .cp { color: #ff3a3a; font-weight: bold } /*
 body[data-theme="dark"] .highlight .cpf { color: #ababab; font-style: italic } /* Comment.PreprocFile */
 body[data-theme="dark"] .highlight .c1 { color: #ababab; font-style: italic } /* Comment.Single */
 body[data-theme="dark"] .highlight .cs { color: #e50808; font-weight: bold; background-color: #520000 } /* Comment.Special */
-body[data-theme="dark"] .highlight .gd { color: #ff3a3a } /* Generic.Deleted */
+body[data-theme="dark"] .highlight .gd { color: #d22323 } /* Generic.Deleted */
 body[data-theme="dark"] .highlight .ge { color: #d0d0d0; font-style: italic } /* Generic.Emph */
 body[data-theme="dark"] .highlight .ges { color: #d0d0d0; font-weight: bold; font-style: italic } /* Generic.EmphStrong */
-body[data-theme="dark"] .highlight .gr { color: #ff3a3a } /* Generic.Error */
+body[data-theme="dark"] .highlight .gr { color: #d22323 } /* Generic.Error */
 body[data-theme="dark"] .highlight .gh { color: #ffffff; font-weight: bold } /* Generic.Heading */
 body[data-theme="dark"] .highlight .gi { color: #589819 } /* Generic.Inserted */
 body[data-theme="dark"] .highlight .go { color: #cccccc } /* Generic.Output */
 body[data-theme="dark"] .highlight .gp { color: #aaaaaa } /* Generic.Prompt */
 body[data-theme="dark"] .highlight .gs { color: #d0d0d0; font-weight: bold } /* Generic.Strong */
 body[data-theme="dark"] .highlight .gu { color: #ffffff; text-decoration: underline } /* Generic.Subheading */
-body[data-theme="dark"] .highlight .gt { color: #ff3a3a } /* Generic.Traceback */
+body[data-theme="dark"] .highlight .gt { color: #d22323 } /* Generic.Traceback */
 body[data-theme="dark"] .highlight .kc { color: #6ebf26; font-weight: bold } /* Keyword.Constant */
 body[data-theme="dark"] .highlight .kd { color: #6ebf26; font-weight: bold } /* Keyword.Declaration */
 body[data-theme="dark"] .highlight .kn { color: #6ebf26; font-weight: bold } /* Keyword.Namespace */
@@ -192,17 +192,17 @@ body:not([data-theme="light"]) .highlight .cp { color: #ff3a3a; font-weight: bol
 body:not([data-theme="light"]) .highlight .cpf { color: #ababab; font-style: italic } /* Comment.PreprocFile */
 body:not([data-theme="light"]) .highlight .c1 { color: #ababab; font-style: italic } /* Comment.Single */
 body:not([data-theme="light"]) .highlight .cs { color: #e50808; font-weight: bold; background-color: #520000 } /* Comment.Special */
-body:not([data-theme="light"]) .highlight .gd { color: #ff3a3a } /* Generic.Deleted */
+body:not([data-theme="light"]) .highlight .gd { color: #d22323 } /* Generic.Deleted */
 body:not([data-theme="light"]) .highlight .ge { color: #d0d0d0; font-style: italic } /* Generic.Emph */
 body:not([data-theme="light"]) .highlight .ges { color: #d0d0d0; font-weight: bold; font-style: italic } /* Generic.EmphStrong */
-body:not([data-theme="light"]) .highlight .gr { color: #ff3a3a } /* Generic.Error */
+body:not([data-theme="light"]) .highlight .gr { color: #d22323 } /* Generic.Error */
 body:not([data-theme="light"]) .highlight .gh { color: #ffffff; font-weight: bold } /* Generic.Heading */
 body:not([data-theme="light"]) .highlight .gi { color: #589819 } /* Generic.Inserted */
 body:not([data-theme="light"]) .highlight .go { color: #cccccc } /* Generic.Output */
 body:not([data-theme="light"]) .highlight .gp { color: #aaaaaa } /* Generic.Prompt */
 body:not([data-theme="light"]) .highlight .gs { color: #d0d0d0; font-weight: bold } /* Generic.Strong */
 body:not([data-theme="light"]) .highlight .gu { color: #ffffff; text-decoration: underline } /* Generic.Subheading */
-body:not([data-theme="light"]) .highlight .gt { color: #ff3a3a } /* Generic.Traceback */
+body:not([data-theme="light"]) .highlight .gt { color: #d22323 } /* Generic.Traceback */
 body:not([data-theme="light"]) .highlight .kc { color: #6ebf26; font-weight: bold } /* Keyword.Constant */
 body:not([data-theme="light"]) .highlight .kd { color: #6ebf26; font-weight: bold } /* Keyword.Declaration */
 body:not([data-theme="light"]) .highlight .kn { color: #6ebf26; font-weight: bold } /* Keyword.Namespace */

diff --git a/master/api/niworkflows-anat-ants-1.pdf b/master/api/niworkflows-anat-ants-1.pdf
diff --git a/master/api/niworkflows-anat-ants-1.png b/master/api/niworkflows-anat-ants-1.png
diff --git a/master/api/niworkflows-anat-ants-2.pdf b/master/api/niworkflows-anat-ants-2.pdf
diff --git a/master/api/niworkflows-anat-ants-2.png b/master/api/niworkflows-anat-ants-2.png
diff --git a/master/api/niworkflows-anat-ants-3.pdf b/master/api/niworkflows-anat-ants-3.pdf
diff --git a/master/api/niworkflows-anat-ants-3.png b/master/api/niworkflows-anat-ants-3.png
diff --git a/master/api/niworkflows-anat-coregistration-1.pdf b/master/api/niworkflows-anat-coregistration-1.pdf
diff --git a/master/api/niworkflows-anat-coregistration-1.png b/master/api/niworkflows-anat-coregistration-1.png
diff --git a/master/api/niworkflows-anat-freesurfer-1.pdf b/master/api/niworkflows-anat-freesurfer-1.pdf
diff --git a/master/api/niworkflows-anat-freesurfer-1.png b/master/api/niworkflows-anat-freesurfer-1.png
diff --git a/master/api/niworkflows-anat-skullstrip-1.pdf b/master/api/niworkflows-anat-skullstrip-1.pdf
diff --git a/master/api/niworkflows-anat-skullstrip-1.png b/master/api/niworkflows-anat-skullstrip-1.png
diff --git a/master/api/niworkflows-func-util-1.pdf b/master/api/niworkflows-func-util-1.pdf
diff --git a/master/api/niworkflows-func-util-1.png b/master/api/niworkflows-func-util-1.png
diff --git a/master/api/niworkflows-func-util-2.pdf b/master/api/niworkflows-func-util-2.pdf
diff --git a/master/api/niworkflows-func-util-2.png b/master/api/niworkflows-func-util-2.png
diff --git a/master/api/niworkflows-func-util-3.pdf b/master/api/niworkflows-func-util-3.pdf
diff --git a/master/api/niworkflows-func-util-3.png b/master/api/niworkflows-func-util-3.png
diff --git a/master/api/niworkflows-workflows-epi-refmap-1.pdf b/master/api/niworkflows-workflows-epi-refmap-1.pdf
diff --git a/master/api/niworkflows-workflows-epi-refmap-1.png b/master/api/niworkflows-workflows-epi-refmap-1.png
diff --git a/master/api/niworkflows.data.html b/master/api/niworkflows.data.html
@@ -371,7 +371,7 @@
 
 <dl class="py method">
 <dt class="sig sig-object py" id="niworkflows.data.load.readable">
-<span class="sig-prename descclassname"><span class="pre">load.</span></span><span class="sig-name descname"><span class="pre">readable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">segments</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">Traversable</span></span></span><a class="headerlink" href="#niworkflows.data.load.readable" title="Link to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">load.</span></span><span class="sig-name descname"><span class="pre">readable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">segments</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/importlib.resources.abc.html#importlib.resources.abc.Traversable" title="(in Python v3.13)"><span class="pre">Traversable</span></a></span></span><a class="headerlink" href="#niworkflows.data.load.readable" title="Link to this definition">¶</a></dt>
 <dd><p>Provide read access to a resource through a Path-like interface.</p>
 <p>This file may or may not exist on the filesystem, and may be
 efficiently used for read operations, including directory traversal.</p>