MAINT: Update nireports, boilerplate

Author: mgxd

pyproject.toml

@@ -27,7 +27,7 @@ dependencies = [
     "matplotlib >= 3.5",
     "nibabel >= 4.0.1",
     "nipype >= 1.8.5",
-    "nireports @ git+https://github.com/nipreps/nireports.git@main",
+    "nireports >= 25.2.0",
     "niworkflows >= 1.13.1",
     "numpy >= 1.24",
     "packaging >= 24",

src/smriprep/cli/run.py

@@ -470,14 +470,20 @@ def _warn_redirect(message, category, filename, lineno, file=None, line=None):
     finally:
         from nireports.assembler.tools import generate_reports
 
-        from ..utils.bids import write_bidsignore, write_derivative_description
+        from smriprep import data
+        from smriprep.utils.bids import write_bidsignore, write_derivative_description
 
         logger.log(
             25, 'Writing reports for participants: %s', _pprint_subses(subject_session_list)
         )
         # Generate reports phase
         smriprep_dir = Path(output_dir) / 'smriprep'
-        errno += generate_reports(subject_session_list, smriprep_dir, run_uuid)
+        bootstrap_file = data.load('reports-spec.yml')
+        errno += generate_reports(
+            subject_session_list,
+            smriprep_dir, run_uuid,
+            bootstrap_file=bootstrap_file,
+        )
         write_derivative_description(bids_dir, smriprep_dir)
         write_bidsignore(smriprep_dir)
     sys.exit(int(errno > 0))
@@ -643,14 +649,22 @@ def build_workflow(opts, retval):
     if opts.reports_only:
         from nireports.assembler.tools import generate_reports
 
+        from smriprep import data
+
         logger.log(
             25, 'Running --reports-only on participants %s', _pprint_subses(subject_session_list)
         )
         if opts.run_uuid is not None:
             run_uuid = opts.run_uuid
 
         smriprep_dir = output_dir / 'smriprep'
-        retval['return_code'] = generate_reports(subject_session_list, smriprep_dir, run_uuid)
+        bootstrap_file = data.load('reports-spec.yml')
+        retval['return_code'] = generate_reports(
+            subject_session_list,
+            smriprep_dir,
+            run_uuid,
+            bootstrap_file=bootstrap_file,
+        )
         return retval
 
     output_spaces = opts.output_spaces

src/smriprep/data/reports-spec.yml

@@ -0,0 +1,46 @@
+package: smriprep
+title: Visual report for participant '{subject}'
+sections:
+- name: Summary
+  reportlets:
+  - bids: { datatype: figures, desc: summary, suffix: T1w }
+- name: Anatomical
+  reportlets:
+  - bids:
+      datatype: figures
+      desc: conform
+      extension: [ .html ]
+      suffix: T1w
+  - bids: { datatype: figures, suffix: dseg }
+    caption: This panel shows the final, preprocessed T1-weighted image, with contours delineating the detected brain mask and brain tissue segmentations.
+    subtitle: Brain mask and brain tissue segmentation of the T1w
+  - bids: { datatype: figures, space: .*, suffix: T1w, regex_search: True }
+    caption: Spatial normalization of the T1w image to the <code>{space}</code> template.
+    description: Results of nonlinear alignment of the T1w reference one or more template space(s). Hover on the panels with the mouse pointer to transition between both spaces.
+    static: false
+    subtitle: Spatial normalization of the anatomical T1w reference
+  - bids: { datatype: figures, desc: reconall, suffix: T1w }
+    caption: Surfaces (white and pial) reconstructed with FreeSurfer (<code>recon-all</code>) overlaid on the participant's T1w template.
+    subtitle: Surface reconstruction
+
+- name: About
+  nested: true
+  reportlets:
+  - bids: { datatype: figures, desc: about, suffix: T1w }
+  - custom: boilerplate
+    path: '{out_dir}/logs'
+    bibfile: [ 'smriprep', 'data/boilerplate.bib' ]
+    caption: |
+      <p>We kindly ask to report results preprocessed with this tool using the following boilerplate.</p>
+      <p class="alert alert-info" role="alert">
+      <strong>Copyright Waiver</strong>.
+      The boilerplate text was automatically generated by <em>NiReports</em> with the
+      express intention that users should copy and paste this text into their manuscripts <em>unchanged</em>.
+      It is released under the
+      <a href="https://creativecommons.org/publicdomain/zero/1.0/" target="_blank">CC0 license</a>.
+      </p>
+    title: Methods
+  - custom: errors
+    path: '{out_dir}/sub-{subject}/log/{run_uuid}'
+    captions: <em>NiReports</em> may have recorded failure conditions.
+    title: Errors