mne-tools · DerAndereJohannes · Sep 17, 2025 · Sep 17, 2025 · Sep 17, 2025 · Sep 22, 2025
@@ -36,7 +36,8 @@ jobs:
       - restore_cache:
           keys:
             - source-cache
-      - checkout
+      - checkout:
+          method: full
       - run:
           name: Complete checkout
           command: |
@@ -461,7 +462,11 @@ jobs:
           at: /tmp/build
       - restore_cache:
           keys:
-            - website-cache
+            - website-cache-1
+      - add_ssh_keys:
+          fingerprints:
+            # SHA256:N4qvp6MSbXcTz/27xz96VPsNuTDRT92zoRP8EW0I/8I
+            - "19:fe:1d:c3:c7:af:7e:16:94:4c:e1:e7:0a:56:13:bd"
       - run:
           name: Set BASH_ENV
           command: |
@@ -489,6 +494,7 @@ jobs:
           command: |
             git config --global user.email "circle@mne.tools";
             git config --global user.name "Circle CI";
+            ssh-add -D && ssh-add ~/.ssh/id_rsa_19fe1dc3c7af7e16944ce1e70a5613bd
             cd ~/mne-tools.github.io;
             git checkout main
             git remote -v
@@ -510,9 +516,9 @@ jobs:
             fi;
             git push origin main;
       - save_cache:
-          key: website-cache
+          key: website-cache-1
           paths:
-            - ~/mne_data/MNE-visual_92_categories-data
+            - ~/mne-tools.github.io
 
 workflows:
   default:

@@ -44,7 +44,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v3
+      uses: github/codeql-action/init@v4
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -58,7 +58,7 @@ 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@v3
+      uses: github/codeql-action/autobuild@v4
 
     # 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
@@ -71,4 +71,4 @@ jobs:
     #   ./location_of_script_within_repo/buildscript.sh
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v3
+      uses: github/codeql-action/analyze@v4
@@ -50,7 +50,7 @@ jobs:
   pytest:
     name: '${{ matrix.os }} / ${{ matrix.kind }} / ${{ matrix.python }}'
     needs: style
-    timeout-minutes: 90
+    timeout-minutes: 120
     runs-on: ${{ matrix.os }}
     defaults:
       run:
@@ -78,7 +78,7 @@ jobs:
           - os: macos-latest  # arm64 (Apple Silicon): Sequoia
             python: '3.13'
             kind: mamba
-          - os: macos-14  # arm64 (Apple Silicon): Sonoma
+          - os: macos-15-intel  # intel: Sequoia
             python: '3.13'
             kind: mamba
           - os: windows-latest
@@ -128,12 +128,18 @@ jobs:
           # For some reason on Linux we get crashes
           if [[ "$RUNNER_OS" == "Linux" ]]; then
             sed -i "/numba/d" environment.yml
+          fi
           # And on Windows and macOS PySide6.9.0 segfaults
-          elif [[ "$RUNNER_OS" == "macOS" ]]; then
-            sed -i "" "s/  - PySide6 .*/  - PySide6 =6.7.3/g" environment.yml
-            sed -i "" "s/  - vtk .*/  - vtk =9.3.1/g" environment.yml
-          elif [[ "$RUNNER_OS" == "Windows" ]]; then
-            sed -i "s/  - PySide6 .*/  - PySide6 <6.8/g" environment.yml
+          if [[ "$RUNNER_OS" == "macOS" ]]; then
+            sed -i "" "s/  - PySide6 .*/  - PySide6 =6.9.2/g" environment.yml
+            sed -i "" "s/  - vtk .*/  - vtk =9.5.1/g" environment.yml
+
+          else
+            sed -i "s/  - PySide6 .*/  - PySide6 =6.9.2/g" environment.yml
+            sed -i "s/  - vtk .*/  - vtk =9.5.1/g" environment.yml
+            if [[ "$RUNNER_OS" == "Windows" ]]; then
+              echo "MNE_IS_OSMESA=true" | tee -a $GITHUB_ENV
+            fi
           fi
         if: matrix.kind == 'conda' || matrix.kind == 'mamba'
       - uses: mamba-org/setup-micromamba@v2

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.13.0
+    rev: v0.14.0
     hooks:
       - id: ruff-check
         name: ruff lint mne
@@ -82,7 +82,7 @@ repos:
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.13.0
+    rev: v1.14.2
     hooks:
       - id: zizmor
 

@@ -0,0 +1 @@
+Add ``on_few_samples`` parameter to :func:`mne.compute_covariance` and :func:`mne.compute_raw_covariance` for controlling behavior when there are fewer samples than channels, which can lead to inaccurate covariance estimates, by :newcontrib:`Emmanuel Ferdman`.
@@ -0,0 +1 @@
+Added `annotation_regex` parameter to :func:`mne.viz.raw.plot_raw` and :func:`mne.viz.ica.plot_sources`, automatically hiding annotations not matching the regex, by `Johannes Herforth`_.
@@ -0,0 +1 @@
+Preserve event-to-epoch mapping when exporting EEGLAB .set files by `Scott Huberty`_
@@ -0,0 +1 @@
+Add support for BDF export in :func:`mne.export.export_raw`, by `Clemens Brunner`_
@@ -0,0 +1 @@
+Fix and update osf.io links to new format, by :newcontrib:`Johannes Herforth`.
@@ -0,0 +1 @@
+Improve precision of fiducial clicking in ``mne coreg``, by `Eric Larson`_.
@@ -76,6 +76,7 @@
 .. _Eduard Ort: https://github.com/eort
 .. _Emily Stephen: https://github.com/emilyps14
 .. _Emma Bailey: https://www.cbs.mpg.de/employees/bailey
+.. _Emmanuel Ferdman: https://github.com/emmanuel-ferdman
 .. _Emrecan Çelik: https://github.com/emrecncelik
 .. _Enrico Varano: https://github.com/enricovara/
 .. _Enzo Altamiranda: https://www.linkedin.com/in/enzoalt
@@ -142,6 +143,7 @@
 .. _jeythekey: https://github.com/jeythekey
 .. _Joan Massich: https://github.com/massich
 .. _Johann Benerradi: https://github.com/HanBnrd
+.. _Johannes Herforth: https://herforth.net
 .. _Johannes Niediek: https://github.com/jniediek
 .. _John Samuelsson: https://github.com/johnsam7
 .. _John Veillette: https://psychology.uchicago.edu/directory/john-veillette

@@ -62,12 +62,24 @@
 
 # We need to triage which date type we use so that incremental builds work
 # (Sphinx looks at variable changes and rewrites all files if some change)
-copyright = (  # noqa: A001
-    f'2012–{td.year}, MNE Developers. Last updated <time datetime="{td.isoformat()}" class="localized">{td.strftime("%Y-%m-%d %H:%M %Z")}</time>\n'  # noqa: E501
-    '<script type="text/javascript">function formatTimestamp() {document.querySelectorAll("time.localized").forEach(el => el.textContent = new Date(el.getAttribute("datetime")).toLocaleString([], {dateStyle: "medium", timeStyle: "long"}));};if (document.readyState != "loading") formatTimestamp();else document.addEventListener("DOMContentLoaded", formatTimestamp);</script>'  # noqa: E501
+project_copyright = (
+    f'2012–{td.year}, MNE Developers. Last updated <time datetime="{td.isoformat()}" class="localized">{td.strftime("%Y-%m-%d %H:%M %Z")}</time>.\n'  # noqa: E501
+    """<script type="text/javascript">
+function formatTimestamp() {
+    document.querySelectorAll("time.localized").forEach(el => {
+        const d = new Date(el.getAttribute("datetime"));
+        el.textContent = d.toLocaleString("sv-SE", { "timeZoneName": "short" });
+    });
+}
+if (document.readyState !== "loading") {
+    formatTimestamp();
+} else {
+    document.addEventListener("DOMContentLoaded", formatTimestamp);
+}
+</script>"""
 )
 if os.getenv("MNE_FULL_DATE", "false").lower() != "true":
-    copyright = f"2012–{td.year}, MNE Developers. Last updated locally."  # noqa: A001
+    project_copyright = f"2012–{td.year}, MNE Developers. Last updated locally."
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

@@ -224,7 +224,7 @@ in certain operating systems, for example CentOS. This may lead to incomplete
 rendering of some 3D plots. A solution is described in this `Github comment <https://github.com/mne-tools/mne-python/issues/7977#issuecomment-729921035>`_.
 It boils down to building a newer version (e.g., 18.3.6)
 locally following a variant of `these instructions <https://xorg-team.pages.debian.net/xorg/howto/build-mesa.html#_preparing_mesa_sources>`_.
-If you have CentOS 7 or newer, you can also try some `prebuilt binaries <https://osf.io/sp9qg/download>`_ we made.
+If you have CentOS 7 or newer, you can also try some `prebuilt binaries <https://osf.io/download/sp9qg>`_ we made.
 After downloading the files, untar them and add them to the appropriate library paths
 using the following commands:
 

@@ -17,7 +17,7 @@ Platform-specific installers
         :class-content: text-center
         :name: install-linux
 
-        .. button-link:: https://github.com/mne-tools/mne-installers/releases/download/v1.10.1/MNE-Python-1.10.1_0-Linux.sh
+        .. button-link:: https://github.com/mne-tools/mne-installers/releases/download/v1.10.2/MNE-Python-1.10.2_0-Linux.sh
             :ref-type: ref
             :color: primary
             :shadow:
@@ -31,14 +31,14 @@ Platform-specific installers
 
         .. code-block:: console
 
-            $ sh ./MNE-Python-1.10.1_0-Linux.sh
+            $ sh ./MNE-Python-1.10.2_0-Linux.sh
 
 
     .. tab-item:: macOS (Intel)
         :class-content: text-center
         :name: install-macos-intel
 
-        .. button-link:: https://github.com/mne-tools/mne-installers/releases/download/v1.10.1/MNE-Python-1.10.1_0-macOS_Intel.pkg
+        .. button-link:: https://github.com/mne-tools/mne-installers/releases/download/v1.10.2/MNE-Python-1.10.2_0-macOS_Intel.pkg
             :ref-type: ref
             :color: primary
             :shadow:
@@ -54,7 +54,7 @@ Platform-specific installers
         :class-content: text-center
         :name: install-macos-apple
 
-        .. button-link:: https://github.com/mne-tools/mne-installers/releases/download/v1.10.1/MNE-Python-1.10.1_0-macOS_M1.pkg
+        .. button-link:: https://github.com/mne-tools/mne-installers/releases/download/v1.10.2/MNE-Python-1.10.2_0-macOS_M1.pkg
             :ref-type: ref
             :color: primary
             :shadow:
@@ -70,7 +70,7 @@ Platform-specific installers
         :class-content: text-center
         :name: install-windows
 
-        .. button-link:: https://github.com/mne-tools/mne-installers/releases/download/v1.10.1/MNE-Python-1.10.1_0-Windows.exe
+        .. button-link:: https://github.com/mne-tools/mne-installers/releases/download/v1.10.2/MNE-Python-1.10.2_0-Windows.exe
             :ref-type: ref
             :color: primary
             :shadow:
@@ -156,7 +156,7 @@ To remove the MNE-Python distribution provided by our installers above:
            .. code-block:: bash
 
                $ which python
-               /home/username/mne-python/1.10.1_0/bin/python
+               /home/username/mne-python/1.10.2_0/bin/python
                $ rm -Rf /home/$USER/mne-python
                $ rm /home/$USER/.local/share/applications/mne-python-*.desktop
 
@@ -170,7 +170,7 @@ To remove the MNE-Python distribution provided by our installers above:
            .. code-block:: bash
 
                $ which python
-               /Users/username/Applications/MNE-Python/1.10.1_0/.mne-python/bin/python
+               /Users/username/Applications/MNE-Python/1.10.2_0/.mne-python/bin/python
                $ rm -Rf /Users/$USER/Applications/MNE-Python  # if user-specific
                $ rm -Rf /Applications/MNE-Python              # if system-wide
 

@@ -0,0 +1,51 @@
+{
+  "merge_commit_sha": "3fbf9865c8e27f6cffe15fa5335e922e82933af7",
+  "authors": [
+    {
+      "n": "Emmanuel Ferdman",
+      "e": null
+    },
+    {
+      "n": "pre-commit-ci[bot]",
+      "e": "66853113+pre-commit-ci[bot]@users.noreply.github.com"
+    },
+    {
+      "n": "Eric Larson",
+      "e": "larson.eric.d@gmail.com"
+    }
+  ],
+  "changes": {
+    "doc/changes/dev/13350.apichange.rst": {
+      "a": 1,
+      "d": 0
+    },
+    "doc/changes/names.inc": {
+      "a": 1,
+      "d": 0
+    },
+    "mne/cov.py": {
+      "a": 33,
+      "d": 7
+    },
+    "mne/decoding/_covs_ged.py": {
+      "a": 3,
+      "d": 0
+    },
+    "mne/decoding/tests/test_csp.py": {
+      "a": 1,
+      "d": 1
+    },
+    "mne/rank.py": {
+      "a": 54,
+      "d": 8
+    },
+    "mne/simulation/tests/test_evoked.py": {
+      "a": 2,
+      "d": 1
+    },
+    "mne/tests/test_rank.py": {
+      "a": 10,
+      "d": 0
+    }
+  }
+}
@@ -0,0 +1,27 @@
+{
+  "merge_commit_sha": "97fd038b2add2b5a08923d735af72e3688d6ebf0",
+  "authors": [
+    {
+      "n": "Thomas S. Binns",
+      "e": "t.s.binns@outlook.com"
+    }
+  ],
+  "changes": {
+    "doc/changes/dev/13375.bugfix.rst": {
+      "a": 1,
+      "d": 0
+    },
+    "mne/channels/channels.py": {
+      "a": 8,
+      "d": 2
+    },
+    "mne/time_frequency/spectrum.py": {
+      "a": 4,
+      "d": 0
+    },
+    "mne/time_frequency/tests/test_spectrum.py": {
+      "a": 29,
+      "d": 3
+    }
+  }
+}
@@ -0,0 +1,27 @@
+{
+  "merge_commit_sha": "17c4e03b50b1f504ea607db68a616e677891cf75",
+  "authors": [
+    {
+      "n": "Emrecan Çelik",
+      "e": "emrecncelik@gmail.com"
+    },
+    {
+      "n": "Eric Larson",
+      "e": "larson.eric.d@gmail.com"
+    }
+  ],
+  "changes": {
+    "doc/changes/dev/13395.bugfix.rst": {
+      "a": 1,
+      "d": 0
+    },
+    "doc/changes/names.inc": {
+      "a": 1,
+      "d": 0
+    },
+    "mne/io/eeglab/eeglab.py": {
+      "a": 3,
+      "d": 3
+    }
+  }
+}
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Add ``on_few_samples`` parameter to :func:`mne.compute_covariance` and :func:`mne.compute_raw_covariance` for controlling behavior when there are fewer samples than channels, which can lead to inaccurate covariance estimates, by :newcontrib:`Emmanuel Ferdman`.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Added `annotation_regex` parameter to :func:`mne.viz.raw.plot_raw` and :func:`mne.viz.ica.plot_sources`, automatically hiding annotations not matching the regex, by `Johannes Herforth`_.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Preserve event-to-epoch mapping when exporting EEGLAB .set files by `Scott Huberty`_
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Add support for BDF export in :func:`mne.export.export_raw`, by `Clemens Brunner`_
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Fix and update osf.io links to new format, by :newcontrib:`Johannes Herforth`.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Improve precision of fiducial clicking in ``mne coreg``, by `Eric Larson`_.