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

* upstream/main: (37 commits)
  Use constrained layout in matplotlib visualization (mne-tools#12050)
  Add raw stc (mne-tools#12001)
  [MRG] update codeowners (mne-tools#12089)
  DOC: Morlet wavelet length in tfr_morlet (mne-tools#12073)
  BUG: Fix bug with mne browser backend (mne-tools#12078)
  Cache avatars (mne-tools#12077)
  BUG: Fix bug with ch_name resolution (mne-tools#12086)
  add unicode roundtrip for FIF (mne-tools#12080)
  add Ivan to names.inc (mne-tools#12081)
  MAINT: Work around PySide 6.5.3 event loop error (mne-tools#12076)
  mne-tools#11608, buggfix and docstring update (mne-tools#12066)
  MAINT: Fix broken examples (mne-tools#12074)
  Add UI Event linking to DraggableColorbar (mne-tools#12057)
  handle lazy loading through .pyi type stubs (mne-tools#12072)
  BUG: Fix bug with sensor_colors (mne-tools#12068)
  clean  up some deprecations (mne-tools#12067)
  Allow not dropping bads when creating or plotting Spectrum objs (mne-tools#12006)
  Collapsible html repr for raw/info (mne-tools#12064)
  BUG: Fix bug with pickling MNEBadsList (mne-tools#12063)
  add details for Denis (mne-tools#12065)
  ...

Author: larsoner

.github/CODEOWNERS

@@ -24,7 +24,7 @@
 #################################################
 
 # Artifact regression
-/mne/preprocessing/_regress.py @wmvanvliet @cbrnr
+/mne/preprocessing/_regress.py @wmvanvliet
 /mne/preprocessing/tests/test_regress.py @wmvanvliet
 
 # Beamforming
@@ -33,25 +33,26 @@
 *lcmv*.py @britta-wstnr
 
 # Channels
-/mne/channels @cbrnr @agramfort @mscheltienne
+/mne/channels @agramfort @mscheltienne @dengemann @jasmainak
 
 # Core sensor-space classes
-/mne/epochs.py @drammock @agramfort @mscheltienne
-/mne/evoked.py @drammock @agramfort @mscheltienne
-/mne/io/*.* @drammock @cbrnr @agramfort @mscheltienne
+/mne/epochs.py @drammock @agramfort @mscheltienne @dengemann
+/mne/evoked.py @drammock @agramfort @mscheltienne @dengemann
+/mne/io/*.* @drammock @cbrnr @agramfort @mscheltienne @dengemann
 
 # Current-source density
-/mne/preprocessing/_csd.py  @alexrockhill
+/mne/preprocessing/_csd.py  @alexrockhill @dengemann
 
 # Decoding
-/mne/decoding/csp.py @cbrnr @agramfort
+/mne/decoding/csp.py @cbrnr @agramfort @dengemann
+/mne/decoding/*.py @jasmainak
 
 # fNIRS
 /mne/preprocessing/nirs @rob-luke
 *fnirs*.py @rob-luke
 
 # forward
-/mne/forward/ @agramfort
+/mne/forward/ @agramfort @jasmainak
 *forward*.py @agramfort
 
 # Intracranial
@@ -69,19 +70,21 @@
 /mne/io/nirx @rob-luke
 /mne/io/snirf @rob-luke
 /mne/export @sappelhoff @cbrnr
+/mne/io/eeglab.py @jasmainak
+/mne/io/eeglab/tests/test_eeglab.py @jasmainak
 
 # Minimum Norm
 /mne/minimum_norm @agramfort
 
 # Preprocessing
-/mne/preprocessing/ica.py @cbrnr @adam2392 @agramfort @mscheltienne
-/mne/preprocessing/infomax_.py @cbrnr @adam2392 @mscheltienne
+/mne/preprocessing/ica.py @cbrnr @adam2392 @agramfort @mscheltienne @dengemann
+/mne/preprocessing/infomax_.py @cbrnr @adam2392 @mscheltienne @dengemann
 /mne/preprocessing/*annotate*.py @mscheltienne
 /mne/preprocessing/bads.py @mscheltienne
 /mne/preprocessing/e*g.py @mscheltienne
 
 # Report
-/mne/report @hoechenberger
+/mne/report @hoechenberger @dengemann @jasmainak
 
 # Simulation
 /mne/simulation/ @agramfort
@@ -93,25 +96,28 @@
 /mne/_freesurfer.py @alexrockhill @larsoner
 
 # TFR
-/mne/time_frequency @drammock @cbrnr @adam2392 @mscheltienne
+/mne/time_frequency @drammock @adam2392 @mscheltienne
 
 # Viz
-/mne/viz @drammock @cbrnr
+/mne/viz @drammock @dengemann
 /mne/viz/_brain @larsoner @wmvanvliet
 /mne/viz/ui_events.py @wmvanvliet
-/tutorials/visualization @larsoner @wmvanvliet
-/examples/visualization @larsoner
+/tutorials/visualization @larsoner @wmvanvliet @dengemann
+/examples/visualization @larsoner @dengemann
+
+# Datasets
+/mne/datasets/brainstorm @jasmainak
 
 #########################
 # Project-level / other #
 #########################
 
 # Examples and tutorials
-/examples @drammock @agramfort
-/tutorials @drammock @agramfort
+/examples @drammock @agramfort @dengemann
+/tutorials @drammock @agramfort @dengemann
 
 # Non-tutorial documentation text and infrastructure
-/doc @larsoner @drammock @agramfort
+/doc @larsoner @drammock @agramfort @dengemann
 /logo @drammock
 
 # Installation documentation
@@ -120,5 +126,5 @@
 # Project infrastructure and CIs
 /*.* @larsoner @drammock  # files in the root directory
 /.circleci @larsoner
-/.github @larsoner @cbrnr
+/.github @larsoner
 /tools @larsoner @drammock

.github/workflows/release.yml

@@ -18,7 +18,7 @@ jobs:
   package:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: '3.10'

.pre-commit-config.yaml

@@ -7,15 +7,15 @@ repos:
 
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.291
+    rev: v0.0.292
     hooks:
       - id: ruff
         name: ruff mne
         files: ^mne/
 
   # Ruff tutorials and examples
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.291
+    rev: v0.0.292
     hooks:
       - id: ruff
         name: ruff tutorials and examples
@@ -26,7 +26,7 @@ repos:
 
   # Codespell
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.2.6
     hooks:
       - id: codespell
         additional_dependencies:

MANIFEST.in

@@ -15,6 +15,7 @@ recursive-include tutorials *.py
 recursive-include tutorials *.txt
 
 recursive-include mne *.py
+recursive-include mne *.pyi
 recursive-include mne/data *
 recursive-include mne/icons *
 recursive-include mne/data/helmets *

Makefile

@@ -33,8 +33,6 @@ sample_data:
 testing_data:
 	@python -c "import mne; mne.datasets.testing.data_path(verbose=True);"
 
-pytest: test
-
 test-no-network: in
 	sudo unshare -n -- sh -c 'MNE_SKIP_NETWORK_TESTS=1 py.test mne'
 

README.rst

@@ -96,7 +96,7 @@ The minimum required dependencies to run MNE-Python are:
 - Python >= 3.8
 - NumPy >= 1.21.2
 - SciPy >= 1.7.1
-- Matplotlib >= 3.4.3
+- Matplotlib >= 3.5.0
 - pooch >= 1.5
 - tqdm
 - Jinja2

doc/overview/images/flow_diagram.svg renamed to doc/_static/flow_diagram.svg

@@ -47,7 +47,7 @@ async function putAvatarsInPage() {
     }
     // finish
     outer.append(title, inner);
-    document.getElementById("institution-logos").after(outer);
+    document.body.append(outer);
 }
 
 putAvatarsInPage();

doc/_static/js/contrib-avatars.js

@@ -0,0 +1,32 @@
+/* inspired by https://tobiasahlin.com/blog/move-from-jquery-to-vanilla-javascript/ */
+
+function documentReady(callback) {
+    if (document.readyState != "loading") callback();
+    else document.addEventListener("DOMContentLoaded", callback);
+}
+
+function setTabs() {
+    var platform = "linux";
+    if (navigator.userAgent.indexOf("Win") !== -1) {
+        platform = "windows";
+    }
+    if (navigator.userAgent.indexOf("Mac") !== -1) {
+        // there's no good way to distinguish intel vs M1 in javascript so we
+        // just default to showing the first of the 2 macOS tabs
+        platform = "macos-intel";
+    }
+    let all_tab_nodes = document.querySelectorAll(
+        '.platform-selector-tabset')[0].children;
+    let input_nodes = [...all_tab_nodes].filter(
+        child => child.nodeName === "INPUT");
+    let tab_label_nodes = [...document.querySelectorAll('.sd-tab-label')];
+    let correct_label = tab_label_nodes.filter(
+        // label.id is drawn from :name: property in the rST, which must
+        // be unique across the whole site (*sigh*)
+        label => label.id.startsWith(platform))[0];
+    let input_id = correct_label.getAttribute('for');
+    let correct_input = input_nodes.filter(node => node.id === input_id)[0];
+    correct_input.checked = true;
+}
+
+documentReady(setTabs);

doc/_static/js/set_installer_tab.js

@@ -0,0 +1,61 @@
+/* inspired by https://tobiasahlin.com/blog/move-from-jquery-to-vanilla-javascript/ */
+
+function documentReady(callback) {
+    if (document.readyState != "loading") callback();
+    else document.addEventListener("DOMContentLoaded", callback);
+}
+
+async function getRelease() {
+    result = await fetch("https://api.github.com/repos/mne-tools/mne-installers/releases/latest");
+    data = await result.json();
+    return data;
+}
+async function warnVersion() {
+    data = await getRelease();
+    // Take v1.5.1 for example and change to 1.5
+    ids = ["linux-installers", "macos-intel-installers", "macos-apple-installers", "windows-installers"];
+    warn = false;
+    ids.forEach((id) => {
+        label_id = document.getElementById(id);
+        // tab is immediately after label
+        children = [].slice.call(label_id.parentNode.children);
+        div = children[children.indexOf(label_id) + 1];
+        a = div.children[0].children[0];  // div->p->a
+        ending = a.href.split("-").slice(-1)[0];  // Should be one of: ["macOS_Intel.pkg", "macOS_M1.pkg", "Linux.sh", "Windows.exe"]
+        data["assets"].every((asset) => {
+            // find the matching asset
+            if (!asset["browser_download_url"].endsWith(ending)) {
+                return true;  // continue
+            }
+            old_stem = a.href.split("/").slice(-1)[0];
+            new_stem = asset["browser_download_url"].split("/").slice(-1)[0];
+            a.href = asset["browser_download_url"];
+            // also replace the command on Linux
+            if (ending === "Linux.sh") {
+                code = document.getElementById("codecell0");
+            }
+            if (!warn) {
+                // MNE-Python-1.5.1_0-Linux.sh to 1.5 for example
+                old_ver = old_stem.split("-").slice(2)[0].split("_")[0].split(".").slice(0, 2).join(".");
+                new_ver = new_stem.split("-").slice(2)[0].split("_")[0].split(".").slice(0, 2).join(".");
+                if (old_ver !== new_ver) {
+                    warn = `The installers below are for version ${new_ver} as ${old_ver} is no longer supported`;
+                }
+            }
+            return false;  // do not continue
+        });
+    });
+    if (warn) {
+        let outer = document.createElement("div");
+        let title = document.createElement("p");
+        let inner = document.createElement("p");
+        outer.setAttribute("class", "admonition warning");
+        title.setAttribute("class", "admonition-title");
+        title.innerText = "Warning";
+        inner.innerText = warn;
+        outer.append(title, inner);
+        document.querySelectorAll('.platform-selector-tabset')[0].before(outer);
+    }
+}
+
+documentReady(warnVersion);