auto: deploy new website

Author: nipreps-bot

apps/docker/index.html

@@ -1334,7 +1334,7 @@ <h3 id="application-specific-options">Application-specific options<a class="head
 command line follows the interface defined by the specific
 <em>BIDS App</em> (for instance,
 <a href="https://fmriprep.readthedocs.io/en/latest/usage.html"><em>fMRIPrep</em></a>
-or <a href="https://mriqc.readthedocs.io/en/latest/running.html#command-line-interface"><em>MRIQC</em></a>).</p>
+or <a href="https://mriqc.readthedocs.io/en/latest/usage.html#a-bids-apps-command-line-interface"><em>MRIQC</em></a>).</p>
 <p>The first section of a call consists of arguments specific to <em>Docker</em>,
 which configure the execution of the container:</p>
 <div class="highlight"><pre><span></span><code><span class="hll">$<span class="w"> </span>docker<span class="w"> </span>run<span class="w"> </span>-ti<span class="w"> </span>--rm<span class="w"> </span><span class="se">\</span>

apps/framework/index.html

@@ -1033,7 +1033,7 @@ <h2 id="what-is-bids">What is BIDS?<a class="headerlink" href="#what-is-bids" ti
 brain datasets, including MRI.
 The common naming convention and folder structure allow researchers to easily reuse BIDS datasets, re-apply analysis protocols, and run standardized automatic data preprocessing pipelines (and particularly, BIDS Apps).
 The <a href="https://github.com/bids-standard/bids-starter-kit">BIDS starter-kit</a> contains a wide collection of educational resources.
-Validity of the structure can be assessed with the online <a href="https://bids-standard.github.io/bidsvalidator/">BIDS-Validator</a>.
+Validity of the structure can be assessed with the online <a href="https://bids-standard.github.io/bids-validator/">BIDS-Validator</a>.
 The tree of a typical, valid (<em>BIDS-compliant</em>) dataset is shown below:</p>
 <div class="highlight"><pre><span></span><code>ds000003/
  ├─ CHANGES

apps/singularity/index.html

@@ -1155,7 +1155,7 @@ <h2 id="running-a-singularity-image">Running a Singularity Image<a class="header
 <span class="w">    </span>--participant-label<span class="w"> </span>label
 </code></pre></div>
 <h2 id="handling-environment-variables">Handling environment variables<a class="headerlink" href="#handling-environment-variables" title="Permanent link">&para;</a></h2>
-<p>Singularity by default <a href="https://github.com/singularityware/singularity/issues/445">exposes all environment variables from the host inside the container</a>.
+<p>Singularity by default <a href="https://github.com/apptainer/singularity/issues/445">exposes all environment variables from the host inside the container</a>.
 Because of this, your host libraries (e.g., <a href="https://nipype.readthedocs.io">NiPype</a> or a Python environment) could be accidentally used instead of the ones inside the
 container. To avoid such a situation, we strongly <strong>recommend</strong> using the
 <code>--cleanenv</code> argument in all scenarios. For example:</p>

assets/ORN-Workshop/index.html

@@ -259,7 +259,7 @@
           highlightLines: true,
           countIncrementalSlides: false,
           highlightSpans: true,
-          sourceUrl: 'https://raw.githubusercontent.com/nipreps/nipreps.github.io/mkdocs/docs/assets/ORN-Workshop/presentation.md',
+          sourceUrl: 'presentation.md',
           ratio: '16:9'
       });
     </script>

assets/ORN-Workshop/presentation/index.html

@@ -968,7 +968,7 @@ <h1 id="workflows">Workflows<a class="headerlink" href="#workflows" title="Perma
 <br />
 <br /></p>
 <p align="center">
-<img src="../nipreps-qr.svg" width="70%" />
+<object type="text/xml+svg" data="https://raw.githubusercontent.com/nipreps/identity/refs/heads/main/nipreps-general/qr-code.svg" style="width: 70%"></object>
 </p>
 <p><br /></p>
 <p align="center">
@@ -988,7 +988,7 @@ <h1 id="workflows_1">Workflows<a class="headerlink" href="#workflows_1" title="P
 <br />
 <br /></p>
 <p align="center">
-<img src="../nipreps-qr.svg" width="70%" />
+<object type="text/xml+svg" data="https://raw.githubusercontent.com/nipreps/identity/refs/heads/main/nipreps-general/qr-code.svg" style="width: 70%"></object>
 </p>
 <p><br /></p>
 <p align="center">
@@ -1039,7 +1039,7 @@ <h3 id="-evaluation-what-is-it-unique-about-the-workflow-wrt-existing-alternativ
 <hr />
 <h2 id="the-garden-of-forking-paths">The garden of forking paths<a class="headerlink" href="#the-garden-of-forking-paths" title="Permanent link">&para;</a></h2>
 <p align="center">
-<img src="assets/narps.png" width="800px" alt="NARPS Paper" />
+<img src="../assets/narps.png" width="800px" alt="NARPS Paper" />
 </p>
 
 <p>(Botvinik-Nezer et al., 2020)</p>
@@ -1050,7 +1050,7 @@ <h3 id="fmriprep-produces-analysis-ready-data-from-diverse-data">fMRIPrep produc
 <ul>
 <li>minimal requirements (<a href="https://bids-standard.github.io/bids-validator/">BIDS-compliant</a>);</li>
 <li><em>agnostic</em> to downstream steps of the workflow</li>
-<li>produces <a href="https://bids-specification.readthedocs.io/en/derivatives/05-derivatives/01-introduction.html">BIDS-Derivatives</a>;</li>
+<li>produces <a href="https://bids-specification.readthedocs.io/en/stable/derivatives/introduction.html">BIDS-Derivatives</a>;</li>
 <li>robust against inhomogeneity of data across studies</li>
 </ul>
 <p>???</p>
@@ -1120,7 +1120,7 @@ <h2 id="why">Why?<a class="headerlink" href="#why" title="Permanent link">&para;
 <hr />
 <h2 id="key-aspect-credit-all-direct-contributors">Key aspect: credit all direct contributors<a class="headerlink" href="#key-aspect-credit-all-direct-contributors" title="Permanent link">&para;</a></h2>
 <p align="center">
-<img src="assets/fmriprep-authors.png" width="700px" alt="fMRIPrep authors" />
+<img src="../assets/fmriprep-authors.png" width="700px" alt="fMRIPrep authors" />
 </p>
 
 <p>--</p>

assets/bhd2020/index.html

@@ -259,7 +259,7 @@
           highlightLines: true,
           countIncrementalSlides: false,
           highlightSpans: true,
-          sourceUrl: 'https://raw.githubusercontent.com/nipreps/nipreps.github.io/mkdocs/docs/assets/bhd2020/presentation.md',
+          sourceUrl: 'presentation.md',
           ratio: '16:9'
       });
     </script>

assets/bhd2020/presentation/index.html

@@ -968,7 +968,7 @@ <h1 id="nipreps"><em>NiPreps</em><a class="headerlink" href="#nipreps" title="Pe
 <br />
 <br /></p>
 <p align="center">
-<img src="../nipreps-qr.svg" width="70%" />
+<object type="text/xml+svg" data="https://raw.githubusercontent.com/nipreps/identity/refs/heads/main/nipreps-general/qr-code.svg" style="width: 70%"></object>
 </p>
 <p><br /></p>
 <p align="center">
@@ -988,7 +988,7 @@ <h1 id="nipreps_1"><em>NiPreps</em><a class="headerlink" href="#nipreps_1" title
 <br />
 <br /></p>
 <p align="center">
-<img src="../nipreps-qr.svg" width="70%" />
+<object type="text/xml+svg" data="https://raw.githubusercontent.com/nipreps/identity/refs/heads/main/nipreps-general/qr-code.svg" style="width: 70%"></object>
 </p>
 <p><br /></p>
 <p align="center">
@@ -1097,7 +1097,7 @@ <h3 id="fmriprep-produces-analysis-ready-data-from-diverse-data">fMRIPrep produc
 <ul>
 <li>minimal requirements (<a href="https://bids-standard.github.io/bids-validator/">BIDS-compliant</a>);</li>
 <li><em>agnostic</em> to downstream steps of the workflow</li>
-<li>produces <a href="https://bids-specification.readthedocs.io/en/derivatives/05-derivatives/01-introduction.html">BIDS-Derivatives</a>;</li>
+<li>produces <a href="https://bids-specification.readthedocs.io/en/stable/derivatives/introduction.html">BIDS-Derivatives</a>;</li>
 <li>robust against inhomogeneity of data across studies</li>
 </ul>
 <p>???</p>

assets/torw2020/presentation/index.html

@@ -884,6 +884,10 @@
 
 
 
+<!-- markdown-link-check-disable -->
+<p>name: title
+layout: true
+class: center</p>
 <hr />
 <p>layout: false
 count: false</p>
@@ -962,7 +966,7 @@ <h3 id="fmriprep-produces-analysis-ready-data-from-acquired-fmri-data">fMRIPrep
 <ul>
 <li>minimal requirements (<a href="https://bids-standard.github.io/bids-validator/">BIDS-compliant</a>);</li>
 <li><em>agnostic</em> to downstream steps of the workflow</li>
-<li>produces <a href="https://bids-specification.readthedocs.io/en/derivatives/05-derivatives/01-introduction.html">BIDS-Derivatives</a>;</li>
+<li>produces <a href="https://bids-specification.readthedocs.io/en/stable/derivatives/introduction.html">BIDS-Derivatives</a>;</li>
 </ul>
 <p>???</p>
 <p>fMRIPrep takes in a task-based or resting-state
@@ -1785,16 +1789,14 @@ <h1 id="open-phd-student-position">Open PhD student position!<a class="headerlin
 <h1 id="thanks">Thanks!<a class="headerlink" href="#thanks" title="Permanent link">&para;</a></h1>
 <h2 id="questions">Questions?<a class="headerlink" href="#questions" title="Permanent link">&para;</a></h2>
 <p>]</p>
+<!-- markdown-link-check-enable -->
 
 
 
 
 
 
 
-  
-  
-
 
 
 

community/CONTRIBUTING/index.html

@@ -1394,7 +1394,7 @@ <h2 id="making-a-change">Making a change<a class="headerlink" href="#making-a-ch
 <p><strong>Make the changes you've discussed, following the <a href="#nipreps-coding-style-guide">NiPreps coding style guide</a>.</strong><br />
   Try to keep the changes focused: it is generally easy to review changes that address one feature or bug at a time.
   It can also be helpful to test your changes locally,
-  using a <a href="https://fmriprep.readthedocs.io/en/latest/contributors.html">NiPreps development environment</a>.
+  using a <a href="../../devs/devenv/">NiPreps development environment</a>.
   Once you are satisfied with your local changes, <a href="https://help.github.com/articles/adding-a-file-to-a-repository-using-the-command-line">add/commit/push them</a>
   to the branch on your forked repository.
   Note that that each commit must include changes that serve a coherent

community/features/index.html

@@ -1107,7 +1107,7 @@ <h3 id="some-questions-will-always-be-asked-about-a-new-feature">Some questions
 <p>It also seems that some new features add more confusion than others.
 Especially when the CLI is affected, and yet another option is added,
 that makes the tool more complex to use.</p>
-<p>-- <cite>Alejandro (<a href="https://github.com/nipreps/fmriprep/    issues/1963#issuecomment-582174814">source</a>)</cite>.</p>
+<p>-- <cite>Alejandro (<a href="https://github.com/nipreps/fmriprep/issues/1963#issuecomment-582174814">source</a>)</cite>.</p>
 </blockquote>
 </li>
 <li>