Backport PR #13076 on branch maint/1.9 (MAINT: Fix doc build) (#13077)

Co-authored-by: Eric Larson <[email protected]>

Author: meeseeksmachine

doc/sphinxext/mne_doc_utils.py

@@ -97,6 +97,8 @@ def reset_warnings(gallery_conf, fname):
         r"numpy\.core is deprecated and has been renamed to numpy\._core",
         # matplotlib
         "__array_wrap__ must accept context and return_scalar.*",
+        # nibabel
+        "__array__ implementation doesn't accept.*",
     ):
         warnings.filterwarnings(  # deal with other modules having bad imports
             "ignore", message=f".*{key}.*", category=DeprecationWarning

doc/sphinxext/related_software.py

@@ -173,6 +173,7 @@ def _get_packages() -> dict[str, str]:
     packages = sorted(packages, key=lambda x: x.lower())
     packages = [RENAMES.get(package, package) for package in packages]
     out = dict()
+    reasons = []
     for package in status_iterator(
         packages, f"Adding {len(packages)} related software packages: "
     ):
@@ -183,12 +184,17 @@ def _get_packages() -> dict[str, str]:
             else:
                 md = importlib.metadata.metadata(package)
         except importlib.metadata.PackageNotFoundError:
-            pass  # raise a complete error later
+            reasons.append(f"{package}: not found, needs to be installed")
+            continue  # raise a complete error later
         else:
             # Every project should really have this
+            do_continue = False
             for key in ("Summary",):
                 if key not in md:
-                    raise ExtensionError(f"Missing {repr(key)} for {package}")
+                    reasons.extend(f"{package}: missing {repr(key)}")
+                    do_continue = True
+            if do_continue:
+                continue
             # It is annoying to find the home page
             url = None
             if "Home-page" in md:
@@ -204,15 +210,17 @@ def _get_packages() -> dict[str, str]:
                     if url is not None:
                         break
                 else:
-                    raise RuntimeError(
-                        f"Could not find Home-page for {package} in:\n"
-                        f"{sorted(set(md))}\nwith Summary:\n{md['Summary']}"
+                    reasons.append(
+                        f"{package}: could not find Home-page in {sorted(md)}"
                     )
+                    continue
             out[package]["url"] = url
             out[package]["description"] = md["Summary"].replace("\n", "")
-    bad = [package for package in packages if not out[package]]
-    if bad and REQUIRE_METADATA:
-        raise ExtensionError(f"Could not find metadata for:\n{' '.join(bad)}")
+    reason_str = "\n".join(reasons)
+    if reason_str and REQUIRE_METADATA:
+        raise ExtensionError(
+            f"Could not find suitable metadata for related software:\n{reason_str}"
+        )
 
     return out
 

tools/circleci_dependencies.sh

@@ -13,4 +13,4 @@ python -m pip install --upgrade --progress-bar off \
     mne-icalabel mne-lsl mne-microstates mne-nirs mne-rsa \
     neurodsp neurokit2 niseq nitime openneuro-py pactools \
     plotly pycrostates pyprep pyriemann python-picard sesameeg \
-    sleepecg tensorpac yasa meegkit eeg_positions
+    sleepecg tensorpac yasa meegkit eeg_positions wfdb

tutorials/intro/70_report.py

@@ -12,11 +12,11 @@
 and after each preprocessing step, epoch rejection statistics, MRI slices with overlaid
 BEM shells, all the way up to plots of estimated cortical activity.
 
-Compared to a Jupyter notebook, :class:`mne.Report` is easier to deploy, as the
-HTML pages it generates are self-contained and do not require a running Python
-environment. However, it is less flexible as you can't change code and re-run
-something directly within the browser. This tutorial covers the basics of
-building a report. As usual, we will start by importing the modules and data we need:
+Compared to a Jupyter notebook, :class:`mne.Report` is easier to deploy, as the HTML
+pages it generates are self-contained and do not require a running Python environment.
+However, it is less flexible as you can't change code and re-run something directly
+within the browser. This tutorial covers the basics of building a report. As usual,
+we will start by importing the modules and data we need:
 """
 
 # Authors: The MNE-Python contributors.

tutorials/inverse/20_dipole_fit.py

@@ -87,6 +87,7 @@
 # %%
 # Calculate and visualise magnetic field predicted by dipole with maximum GOF
 # and compare to the measured data, highlighting the ipsilateral (right) source
+
 fwd, stc = make_forward_dipole(dip, fname_bem, evoked.info, fname_trans)
 pred_evoked = simulate_evoked(fwd, stc, evoked.info, cov=None, nave=np.inf)