📝 Update FROM base from default to blank (#326)

docs/nightly/_modules/index.html

@@ -395,6 +395,8 @@ <h1>All modules for which code is available</h1>
 <li><a href="CPAC/timeseries/timeseries_analysis">CPAC.timeseries.timeseries_analysis</a></li>
 <li><a href="CPAC/utils/bids_utils">CPAC.utils.bids_utils</a></li>
 <li><a href="CPAC/utils/configuration/configuration">CPAC.utils.configuration.configuration</a></li>
+<li><a href="CPAC/utils/configuration/diff">CPAC.utils.configuration.diff</a></li>
+<li><a href="CPAC/utils/configuration/yaml_template">CPAC.utils.configuration.yaml_template</a></li>
 <li><a href="CPAC/utils/create_flame_model_files">CPAC.utils.create_flame_model_files</a></li>
 <li><a href="CPAC/utils/create_fsl_flame_preset">CPAC.utils.create_fsl_flame_preset</a></li>
 <li><a href="CPAC/utils/create_group_analysis_info_files">CPAC.utils.create_group_analysis_info_files</a></li>

docs/nightly/developer/pipeline.html

@@ -486,7 +486,7 @@ <h1>Pipeline Development<a class="headerlink" href="#pipeline-development" title
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>resource_idx</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-class docutils literal notranslate"><span class="pre">str</span></code></a>)</p></li>
-<li><p><strong>cfg</strong> (<a class="reference internal" href="utils#CPAC.utils.configuration.Configuration" title="CPAC.utils.configuration.Configuration"><code class="xref py py-class docutils literal notranslate"><span class="pre">CPAC.utils.configuration.Configuration</span></code></a>)</p></li>
+<li><p><strong>cfg</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">CPAC.utils.configuration.Configuration</span></code>)</p></li>
 <li><p><strong>json_info</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-class docutils literal notranslate"><span class="pre">dict</span></code></a>)</p></li>
 <li><p><strong>out_dct</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-class docutils literal notranslate"><span class="pre">dict</span></code></a>)</p></li>
 </ul>

docs/nightly/developer/workflows/alff.html

@@ -376,7 +376,7 @@
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>wf</strong> (<a class="reference external" href="https://nipype.readthedocs.io/en/1.8.6/api/generated/nipype.pipeline.engine.workflows.html#nipype.pipeline.engine.workflows.Workflow" title="(in nipype v1.8.6)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Workflow</span></code></a>)</p></li>
-<li><p><strong>cfg</strong> (<a class="reference internal" href="../utils#CPAC.utils.configuration.Configuration" title="CPAC.utils.configuration.Configuration"><code class="xref py py-class docutils literal notranslate"><span class="pre">Configuration</span></code></a>)</p></li>
+<li><p><strong>cfg</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">Configuration</span></code>)</p></li>
 <li><p><strong>strat_pool</strong></p></li>
 <li><p><strong>pipe_num</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>)</p></li>
 <li><p><strong>opt</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-class docutils literal notranslate"><span class="pre">str</span></code></a>, <em>optional</em>)</p></li>
@@ -400,7 +400,7 @@
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>wf</strong> (<a class="reference external" href="https://nipype.readthedocs.io/en/1.8.6/api/generated/nipype.pipeline.engine.workflows.html#nipype.pipeline.engine.workflows.Workflow" title="(in nipype v1.8.6)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Workflow</span></code></a>)</p></li>
-<li><p><strong>cfg</strong> (<a class="reference internal" href="../utils#CPAC.utils.configuration.Configuration" title="CPAC.utils.configuration.Configuration"><code class="xref py py-class docutils literal notranslate"><span class="pre">Configuration</span></code></a>)</p></li>
+<li><p><strong>cfg</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">Configuration</span></code>)</p></li>
 <li><p><strong>strat_pool</strong></p></li>
 <li><p><strong>pipe_num</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>)</p></li>
 <li><p><strong>opt</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-class docutils literal notranslate"><span class="pre">str</span></code></a>, <em>optional</em>)</p></li>

docs/nightly/developer/workflows/cpac_pipeline.html

@@ -370,7 +370,7 @@
 <span id="cpac-pipeline"></span><h1>C-PAC Pipeline Construction<a class="headerlink" href="#c-pac-pipeline-construction" title="Link to this heading">¶</a></h1>
 <section id="configuration-object">
 <h2>Configuration Object<a class="headerlink" href="#configuration-object" title="Link to this heading">¶</a></h2>
-<p>The ‘c’ variable in cpac_pipeline.py is a <a class="reference external" href="https://github.com/FCP-INDI/C-PAC/blob/main/CPAC/utils/configuration.py">Configuration object</a>, which is an abstract representation used to store the options for the pipeline configuration YAML after it is read in by C-PAC.  Each attribute of the Configuration object is a key from the YAML file, with values mirroring the YAML.</p>
+<p>The ‘c’ variable in cpac_pipeline.py is a <a class="reference internal" href="../utils#CPAC.utils.configuration.configuration.Configuration" title="CPAC.utils.configuration.configuration.Configuration"><code class="xref py py-class docutils literal notranslate"><span class="pre">Configuration</span></code></a> object, which is an abstract representation used to store the options for the pipeline configuration YAML after it is read in by C-PAC.  Each attribute of the Configuration object is a key from the YAML file, with values mirroring the YAML.</p>
 </section>
 <section id="strategy-object">
 <h2>Strategy Object<a class="headerlink" href="#strategy-object" title="Link to this heading">¶</a></h2>