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

* upstream/main:
  BUG: handle temporal discontinuities in Neuralynx `.ncs` files (mne-tools#12279)
  MAINT: Work around bad SciPy nightly wheels (mne-tools#12317)
  fix 404 link on devel landing page (mne-tools#12316)
  Switch from `epoch_data` to `data` for TFR array functions (mne-tools#12308)
  [pre-commit.ci] pre-commit autoupdate (mne-tools#12307)
  fix icon link colors (mne-tools#12301)
  Bump actions/download-artifact from 3 to 4 (mne-tools#12304)
  Bump github/codeql-action from 2 to 3 (mne-tools#12303)
  Bump actions/upload-artifact from 3 to 4 (mne-tools#12302)

.github/workflows/codeql-analysis.yml

@@ -42,7 +42,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -56,7 +56,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v2
+      uses: github/codeql-action/autobuild@v3
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
@@ -69,4 +69,4 @@ jobs:
     #   ./location_of_script_within_repo/buildscript.sh
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3

.github/workflows/release.yml

@@ -28,7 +28,7 @@ jobs:
           pip install build twine
       - run: python -m build --sdist --wheel
       - run: twine check --strict dist/*
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: dist
           path: dist
@@ -43,7 +43,7 @@ jobs:
       name: pypi
       url: https://pypi.org/p/mne
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: dist
           path: dist

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.7
+    rev: v0.1.8
     hooks:
       - id: ruff
         name: ruff lint mne
@@ -13,7 +13,7 @@ repos:
 
   # Ruff tutorials and examples
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.7
+    rev: v0.1.8
     hooks:
       - id: ruff
         name: ruff lint tutorials and examples

CONTRIBUTING.md

@@ -5,5 +5,5 @@ MNE-Python is maintained by a community of scientists and research labs. The pro
 
 Users and contributors to MNE-Python are expected to follow our [code of conduct](https://github.com/mne-tools/.github/blob/main/CODE_OF_CONDUCT.md).
 
-The [contributing guide](https://mne.tools/dev/install/contributing.html) has details on the preferred contribution workflow
+The [contributing guide](https://mne.tools/dev/development/contributing.html) has details on the preferred contribution workflow
 and the recommended system configuration for a smooth contribution/development experience.

doc/_static/style.css

@@ -17,7 +17,7 @@
 html[data-theme="light"] {
     /* topbar logo links */
     --mne-color-github: #000;
-    --mne-color-discourse: #000;
+    --mne-color-discourse: #d0232b;
     --mne-color-mastodon: #2F0C7A;
     /* code block copy button */
     --copybtn-opacity: 0.75;
@@ -222,16 +222,16 @@ aside.footnote:last-child {
 }
 
 /* ******************************************************* navbar icon links */
-#navbar-icon-links i.fa-square-github::before {
+.navbar-icon-links i.fa-square-github::before {
     color: var(--mne-color-github);
 }
-#navbar-icon-links i.fa-discourse::before {
+.navbar-icon-links i.fa-discourse::before {
     color: var(--mne-color-discourse);
 }
-#navbar-icon-links i.fa-discord::before {
+.navbar-icon-links i.fa-discord::before {
     color: var(--mne-color-discord);
 }
-#navbar-icon-links i.fa-mastodon::before {
+.navbar-icon-links i.fa-mastodon::before {
     color: var(--mne-color-mastodon);
 }
 

doc/changes/devel/12279.bugfix.rst

@@ -0,0 +1 @@
+Correctly handle temporal gaps in Neuralynx .ncs files via :func:`mne.io.read_raw_neuralynx`, by `Kristijan Armeni`_ and `Eric Larson`_.

doc/changes/devel/12308.deprecation.rst

@@ -0,0 +1 @@
+The parameter for providing data to :func:`mne.time_frequency.tfr_array_morlet` and :func:`mne.time_frequency.tfr_array_multitaper` has been switched from ``epoch_data`` to ``data``. Only use the ``data`` parameter to avoid a warning. Changes by `Thomas Binns`_.

doc/development/index.rst

@@ -24,7 +24,7 @@ experience.
 .. _`opening an issue`: https://github.com/mne-tools/mne-python/issues/new/choose
 .. _`MNE Forum`: https://mne.discourse.group
 .. _`code of conduct`: https://github.com/mne-tools/.github/blob/main/CODE_OF_CONDUCT.md
-.. _`contributing guide`: https://mne.tools/dev/install/contributing.html
+.. _`contributing guide`: https://mne.tools/dev/development/contributing.html
 
 .. toctree::
    :hidden:

environment.yml

@@ -61,3 +61,4 @@ dependencies:
   - mamba
   - lazy_loader
   - defusedxml
+  - python-neo

mne/datasets/config.py

@@ -88,7 +88,7 @@
 # respective repos, and make a new release of the dataset on GitHub. Then
 # update the checksum in the MNE_DATASETS dict below, and change version
 # here:                  ↓↓↓↓↓         ↓↓↓
-RELEASES = dict(testing="0.150", misc="0.27")
+RELEASES = dict(testing="0.151", misc="0.27")
 TESTING_VERSIONED = f'mne-testing-data-{RELEASES["testing"]}'
 MISC_VERSIONED = f'mne-misc-data-{RELEASES["misc"]}'
 
@@ -112,7 +112,7 @@
 # Testing and misc are at the top as they're updated most often
 MNE_DATASETS["testing"] = dict(
     archive_name=f"{TESTING_VERSIONED}.tar.gz",
-    hash="md5:0b7452daef4d19132505b5639d695628",
+    hash="md5:5832b4d44f0423d22305fa61cb75bc25",
     url=(
         "https://codeload.github.com/mne-tools/mne-testing-data/"
         f'tar.gz/{RELEASES["testing"]}'