Merge remote-tracking branch 'upstream/main' into proj_joint

* upstream/main: MRG: In Report, allow to add multiple figure or image elements to the same content block ("section") (mne-tools#10694) CI: Add style conditional (mne-tools#10723) Fix coreg tutorial typos (mne-tools#10716) MAINT: Deal with nibabel deprecation (mne-tools#10719)
larsoner · Jun 8, 2022 · 458ebbd · 458ebbd
2 parents 1fbc3c8 + a9b139d
commit 458ebbd
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diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -54,14 +54,20 @@ stages:
         python -m pip install --progress-bar off --upgrade pip setuptools wheel
         python -m pip install --progress-bar off -r requirements_base.txt -r requirements_hdf5.txt -r requirements_testing.txt
       displayName: Install dependencies
-      condition: always()
+    - bash: |
+        make flake
+      displayName: make flake
+    - bash: |
+        make codespell-error
+      displayName: make codespell
     - bash: |
         make pydocstyle
       displayName: make pydocstyle
       condition: always()
     - bash: |
         make docstring
       displayName: make docstring
+      condition: always()
     - bash: |
         make nesting
       displayName: make nesting
@@ -77,7 +83,7 @@ stages:
 
 - stage: Test
   condition: and(succeeded(), eq(dependencies.Check.outputs['Skip.result.start_main'], 'true'))
-  dependsOn: Check
+  dependsOn: ['Style', 'Check']
   variables:
     AZURE_CI: 'true'
   jobs:

diff --git a/doc/changes/latest.inc b/doc/changes/latest.inc
@@ -89,6 +89,8 @@ Enhancements
 
 - Add timeformat ``YYYY/MM/DD`` to ``mne.io.ctf.info._convert_time`` (:gh:`10674` by `Simon Kern`_)
 
+- :meth:`mne.Report.add_figure` and :meth:`mne.Report.add_image` gained a new parameter, ``section``, allowing to put multiple figures or images into the same "content block". Previously, the only way to group figures and images was by means of a slider, which sometimes made content hard to discover. The slider remains available as an alternative. (:gh:`10694` by `Richard Höchenberger`_)
+
 Bugs
 ~~~~
 

diff --git a/doc/references.bib b/doc/references.bib
@@ -818,6 +818,16 @@ @article{HoldgrafEtAl2016
   year = {2016}
 }
 
+@article{HouckClaus2020,
+	author = {Houck, Jon M. and Claus, Eric D.},
+	doi = {10.1371/journal.pone.0232100},
+	journal = {PLOS ONE},
+	pages = {e0232100},
+	title = {A comparison of automated and manual co-registration for magnetoencephalography},
+	volume = {15},
+	year = {2020}
+}
+
 @article{Hyvarinen1999,
   author = {Hyvärinen, Aapo},
   doi = {10.1109/72.761722},

diff --git a/mne/html_templates/report/bem.html.jinja b/mne/html_templates/report/bem.html.jinja
@@ -0,0 +1,8 @@
+{% extends "section.html.jinja" %}
+{% block html_content %}
+<div class="row">
+  {{ html_slider_axial | safe }}
+  {{ html_slider_sagittal | safe }}
+  {{ html_slider_coronal | safe }}
+</div>
+{% endblock html_content %}
diff --git a/mne/html_templates/report/code.html.jinja b/mne/html_templates/report/code.html.jinja
@@ -1,24 +1,6 @@
-<div class="accordion-item code" id="{{ id }}" data-mne-tags="{% for tag in tags %} {{ tag }} {% endfor %}">
-  <div class="accordion-header" id="accordion-header-{{ id }}">
-    <button class="accordion-button pt-1 pb-1" type="button" data-bs-toggle="collapse"
-      data-bs-target="#accordion-collapse-{{ id }}" aria-expanded="true" aria-controls="accordion-collapse-{{ id }}">
-      <div class="w-100">
-        <span class="me-auto">{{ title }}</span>
-        {% for tag in tags %}
-        <span class="badge bg-primary rounded-pill float-end me-1" data-mne-tag="{{ tag }}">
-          {{ tag }}
-        </span>
-        {% endfor %}
-      </div>
-    </button>
-  </div>
-
-  <div id="accordion-collapse-{{ id }}" class="accordion-collapse collapse show"
-    aria-labelledby="accordion-header-{{ id }}">
-    <div class="accordion-body">
-      <pre class="my-0">
-        <code class="language-{{ language }}">{{ code }}</code>
-      </pre>
-    </div>
-  </div>
-</div>
+{% extends "section.html.jinja" %}
+{% block html_content %}
+<pre class="my-0">
+  <code class="language-{{ language }}">{{ code }}</code>
+</pre>
+{% endblock html_content %}
diff --git a/mne/html_templates/report/epochs.html.jinja b/mne/html_templates/report/epochs.html.jinja
diff --git a/mne/html_templates/report/evoked.html.jinja b/mne/html_templates/report/evoked.html.jinja
diff --git a/mne/html_templates/report/forward.html.jinja b/mne/html_templates/report/forward.html.jinja
@@ -1,23 +1,5 @@
-<div class="accordion-item forward-solution" id="{{ id }}" data-mne-tags="{% for tag in tags %} {{ tag }} {% endfor %}">
-  <div class="accordion-header" id="accordion-header-{{ id }}">
-    <button class="accordion-button pt-1 pb-1" type="button" data-bs-toggle="collapse"
-      data-bs-target="#accordion-collapse-{{ id }}" aria-expanded="true" aria-controls="accordion-collapse-{{ id }}">
-      <div class="w-100">
-        <span class="me-auto">{{ title }}</span>
-        {% for tag in tags %}
-        <span class="badge bg-primary rounded-pill float-end me-1" data-mne-tag="{{ tag }}">
-          {{ tag }}
-        </span>
-        {% endfor %}
-      </div>
-    </button>
-  </div>
-
-  <div id="accordion-collapse-{{ id }}" class="accordion-collapse collapse show"
-    aria-labelledby="accordion-header-{{ id }}">
-    <div class="accordion-body">
-      {{repr | safe}}
-      {{sensitivity_maps | safe }}
-    </div>
-  </div>
-</div>
+{% extends "section.html.jinja" %}
+{% block html_content %}
+{{repr | safe}}
+{{sensitivity_maps | safe}}
+{% endblock html_content %}
diff --git a/mne/html_templates/report/ica.html.jinja b/mne/html_templates/report/ica.html.jinja
diff --git a/mne/html_templates/report/image.html.jinja b/mne/html_templates/report/image.html.jinja
@@ -1,36 +1,17 @@
-<div class="accordion-item {{ div_klass }}" id="{{ id }}" data-mne-tags="{% for tag in tags %} {{ tag }} {% endfor %}"
-  {% if not show %}style="display: none" {% endif %}>
-  <div class="accordion-header" id="accordion-header-{{ id }}">
-    <button class="accordion-button pt-1 pb-1" type="button" data-bs-toggle="collapse"
-      data-bs-target="#accordion-collapse-{{ id }}" aria-expanded="true" aria-controls="accordion-collapse-{{ id }}">
-      <div class="w-100">
-        <span class="me-auto">{{ title }}</span>
-        {% for tag in tags %}
-        <span class="badge bg-primary rounded-pill float-end me-1" data-mne-tag="{{ tag }}">
-          {{ tag }}
-        </span>
-        {% endfor %}
-      </div>
-    </button>
+{% extends "section.html.jinja" %}
+{% block html_content %}
+<figure class="figure mx-auto d-block">
+  {% if image_format == 'svg' %}
+  <div class="d-flex justify-content-center">
+    {{ img }}
   </div>
+  {% else %}
+  <img class="figure-img img-fluid rounded mx-auto my-0 d-block" alt="{{ title }}"
+    src="data:image/{{ image_format }};base64,{{ img }}">
+  {% endif %}
 
-  <div id="accordion-collapse-{{ id }}" class="accordion-collapse collapse show"
-    aria-labelledby="accordion-header-{{ id }}">
-    <div class="accordion-body">
-      <figure class="figure mx-auto d-block">
-        {% if image_format == 'svg' %}
-        <div class="d-flex justify-content-center">
-          {{ img }}
-        </div>
-        {% else %}
-        <img class="figure-img img-fluid rounded mx-auto my-0 d-block" alt="{{ title }}"
-          src="data:image/{{ image_format }};base64,{{ img }}">
-        {% endif %}
-
-        {% if caption is not none %}
-        <figcaption class="figure-caption text-center">{{ caption }}</figcaption>
-        {% endif %}
-      </figure>
-    </div>
-  </div>
-</div>
+  {% if caption is not none %}
+  <figcaption class="figure-caption text-center">{{ caption }}</figcaption>
+  {% endif %}
+</figure>
+{% endblock html_content %}
diff --git a/mne/html_templates/report/inverse.html.jinja b/mne/html_templates/report/inverse.html.jinja
@@ -1,23 +1,5 @@
-<div class="accordion-item inverse-operator" id="{{ id }}" data-mne-tags="{% for tag in tags %} {{ tag }} {% endfor %}">
-  <div class="accordion-header" id="accordion-header-{{ id }}">
-    <button class="accordion-button pt-1 pb-1" type="button" data-bs-toggle="collapse"
-      data-bs-target="#accordion-collapse-{{ id }}" aria-expanded="true" aria-controls="accordion-collapse-{{ id }}">
-      <div class="w-100">
-        <span class="me-auto">{{ title }}</span>
-        {% for tag in tags %}
-        <span class="badge bg-primary rounded-pill float-end me-1" data-mne-tag="{{ tag }}">
-          {{ tag }}
-        </span>
-        {% endfor %}
-      </div>
-    </button>
-  </div>
-
-  <div id="accordion-collapse-{{ id }}" class="accordion-collapse collapse show"
-    aria-labelledby="accordion-header-{{ id }}">
-    <div class="accordion-body">
-      {{repr | safe}}
-      {{source_space | safe}}
-    </div>
-  </div>
-</div>
+{% extends "section.html.jinja" %}
+{% block html_content %}
+{{repr | safe}}
+{{source_space | safe}}
+{% endblock html_content %}
diff --git a/mne/html_templates/report/raw.html.jinja b/mne/html_templates/report/raw.html.jinja
diff --git a/mne/html_templates/report/cov.html.jinja → mne/html_templates/report/section.html.jinja b/mne/html_templates/report/cov.html.jinja → mne/html_templates/report/section.html.jinja
@@ -1,7 +1,7 @@
-<div class="accordion-item covariance" id="{{ id }}" data-mne-tags="{% for tag in tags %} {{ tag }} {% endfor %}">
-  <div class="accordion-header" id="accordion-header-{{ id }}">
+<div class="accordion-item {{ div_klass }}" id="{{ id }}" data-mne-tags="{% for tag in tags %} {{ tag }} {% endfor %}">
+  <div class="accordion-header" id="accordion-header-{{id}}">
     <button class="accordion-button pt-1 pb-1" type="button" data-bs-toggle="collapse"
-      data-bs-target="#accordion-collapse-{{ id }}" aria-expanded="true" aria-controls="accordion-collapse-{{ id }}">
+      data-bs-target="#accordion-collapse-{{ id }}" aria-expanded="true" aria-controls="accordion-collapse-{{id}}">
       <div class="w-100">
         <span class="me-auto">{{ title }}</span>
         {% for tag in tags %}
@@ -13,11 +13,15 @@
     </button>
   </div>
 
+
   <div id="accordion-collapse-{{ id }}" class="accordion-collapse collapse show"
     aria-labelledby="accordion-header-{{ id }}">
     <div class="accordion-body">
-      {{ matrix | safe }}
-      {{ svd | safe }}
+      {% block html_content %}
+      {% for html in htmls %}
+      {{ html | safe }}
+      {% endfor %}
+      {% endblock %}
     </div>
   </div>
 </div>
diff --git a/mne/html_templates/report/toc.html.jinja b/mne/html_templates/report/toc.html.jinja
@@ -3,9 +3,9 @@
     <div class="col-2 px-1 position-fixed vh-100 overflow-auto" id="toc">
       <h5 class="px-1">Table of contents</h5>
       <nav class="nav nav-pills flex-column lh-sm" id="toc-navbar">
-        {% for element in content_elements %}
-        <a class="nav-link list-group-item list-group-item-action text-break" href="#{{ element.dom_id }}"
-          data-mne-tags="{% for tag in element.tags %} {{ tag }} {% endfor %}">{{ element.name }}</a>
+        {% for title, dom_id, tags_ in titles|zip(dom_ids, tags) %}
+        <a class="nav-link list-group-item list-group-item-action text-break" href="#{{ dom_id }}"
+          data-mne-tags="{% for tag in tags_ %} {{ tag }} {% endfor %}">{{ title }}</a>
         {% endfor %}
       </nav>
     </div>
-Original file line number
+Diff line change
@@ Expand Up / @@ -89,6 +89,8 @@ Enhancements @@
     - Add timeformat ``YYYY/MM/DD`` to ``mne.io.ctf.info._convert_time`` (:gh:`10674` by `Simon Kern`_)
+    - :meth:`mne.Report.add_figure` and :meth:`mne.Report.add_image` gained a new parameter, ``section``, allowing to put multiple figures or images into the same "content block". Previously, the only way to group figures and images was by means of a slider, which sometimes made content hard to discover. The slider remains available as an alternative. (:gh:`10694` by `Richard Höchenberger`_)
     Bugs
     ~~~~
@@ Expand Down @@