Merge branch 'main' into add_tfr_weights

mne-tools · Dec 19, 2024 · 0d3d85d · 0d3d85d
2 parents 5b150aa + 05bd738
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diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml
@@ -0,0 +1,17 @@
+name: Bot auto-merge
+on: pull_request  # yamllint disable-line rule:truthy
+
+jobs:
+  autobot:
+    permissions:
+      contents: write
+      pull-requests: write
+    runs-on: ubuntu-latest
+    # Names can be found with gh api /repos/mne-tools/mne-python/pulls/12998 -q .user.login for example
+    if: (github.event.pull_request.user.login == 'dependabot[bot]' || github.event.pull_request.user.login == 'pre-commit-ci[bot]' || github.event.pull_request.user.login == 'github-actions[bot]') && github.repository == 'mne-tools/mne-python'
+    steps:
+      - name: Enable auto-merge for bot PRs
+        run: gh pr merge --auto --squash "$PR_URL"
+        env:
+          PR_URL: ${{github.event.pull_request.html_url}}
+          GH_TOKEN: ${{secrets.GITHUB_TOKEN}}
diff --git a/.github/workflows/credit.yml b/.github/workflows/credit.yml
@@ -19,7 +19,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          persist-credentials: false
+          persist-credentials: true
       - uses: actions/setup-python@v5
         with:
           python-version: '3.12'
@@ -38,8 +38,8 @@ jobs:
           git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
           git config --global user.name "github-actions[bot]"
           git checkout -b credit
-          git commit -am "MAINT: Update code credit [ci skip]"
+          git commit -am "MAINT: Update code credit"
           git push origin credit
-          PR_NUM=$(gh pr create --base main --head credit --title "MAINT: Update code credit" --body "Created by credit GitHub action." --label "no-changelog-entry-needed")
+          PR_NUM=$(gh pr create --base main --head credit --title "MAINT: Update code credit" --body "Created by credit [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }})." --label "no-changelog-entry-needed")
           echo "Opened https://github.com/mne-tools/mne-python/pull/${PR_NUM}" >> $GITHUB_STEP_SUMMARY
         if: steps.status.outputs.dirty == 'true'
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -120,11 +120,11 @@ jobs:
       - run: ./tools/github_actions_dependencies.sh
       # Minimal commands on Linux (macOS stalls)
       - run: ./tools/get_minimal_commands.sh
-        if: ${{ startswith(matrix.os, 'ubuntu') }}
+        if: startswith(matrix.os, 'ubuntu') && matrix.kind != 'minimal' && matrix.kind != 'old'
       - run: ./tools/github_actions_infos.sh
       # Check Qt
       - run: ./tools/check_qt_import.sh $MNE_QT_BACKEND
-        if: ${{ env.MNE_QT_BACKEND != '' }}
+        if: env.MNE_QT_BACKEND != ''
       - name: Run tests with no testing data
         run: MNE_SKIP_TESTING_DATASET_TESTS=true pytest -m "not (ultraslowtest or pgtest)" --tb=short --cov=mne --cov-report xml -vv -rfE mne/
         if: matrix.kind == 'minimal'

diff --git a/.mailmap b/.mailmap
@@ -2,6 +2,7 @@ Adam Li <[email protected]> Adam Li <[email protected]>
 Adam Li <[email protected]> Adam Li <[email protected]>
 Alan Leggitt <[email protected]> leggitta <[email protected]>
 Alessandro Tonin <[email protected]> Lychfindel <[email protected]>
+Alex Lepauvre <[email protected]> Alex lepauvre <[email protected]>
 Alex Rockhill <[email protected]> Alex <[email protected]>
 Alex Rockhill <[email protected]> Alex <[email protected]>
 Alex Rockhill <[email protected]> Alex Rockhill <[email protected]>
@@ -356,4 +357,4 @@ Yousra Bekhti <[email protected]> Yousra BEKHTI <[email protected]>
 Yousra Bekhti <[email protected]> yousrabk <[email protected]>
 Zhi Zhang <[email protected]> ZHANG Zhi <[email protected]>
 Zhi Zhang <[email protected]> ZHANG Zhi <[email protected]>
-Ziyi ZENG <[email protected]>
+Ziyi ZENG <[email protected]> ZIYI ZENG <[email protected]>
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.2
+    rev: v0.8.3
     hooks:
       - id: ruff
         name: ruff lint mne
@@ -82,7 +82,7 @@ repos:
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v0.8.0
+    rev: v0.9.2
     hooks:
       - id: zizmor
 

diff --git a/CITATION.cff b/CITATION.cff
@@ -1,9 +1,9 @@
 cff-version: 1.2.0
 title: "MNE-Python"
 message: "If you use this software, please cite both the software itself, and the paper listed in the preferred-citation field."
-version: 1.8.0
-date-released: "2024-08-18"
-commit: 9a760d76971e845b67b619804c1156cc04c9c948
+version: 1.9.0
+date-released: "2024-12-18"
+commit: 14938b9657b255a38aa96482a4aaf410e8865859
 doi: 10.5281/zenodo.592483
 keywords:
   - MEG
@@ -40,15 +40,15 @@ authors:
   - family-names: Luessi
     given-names: Martin
   - family-names: King
-    given-names: Jean-Remi
+    given-names: Jean-Rémi
   - family-names: Höchenberger
     given-names: Richard
   - family-names: Goj
     given-names: Roman
-  - family-names: Favelier
-    given-names: Guillaume
   - family-names: Brunner
     given-names: Clemens
+  - family-names: Favelier
+    given-names: Guillaume
   - family-names: van Vliet
     given-names: Marijn
   - family-names: Wronkiewicz
@@ -57,22 +57,22 @@ authors:
     given-names: Alex
   - family-names: Holdgraf
     given-names: Chris
-  - family-names: Massich
-    given-names: Joan
-  - family-names: Bekhti
-    given-names: Yousra
   - family-names: Scheltienne
     given-names: Mathieu
+  - family-names: Massich
+    given-names: Joan
   - family-names: Appelhoff
     given-names: Stefan
+  - family-names: Bekhti
+    given-names: Yousra
   - family-names: Leggitt
     given-names: Alan
   - family-names: Dykstra
     given-names: Andrew
-  - family-names: Luke
-    given-names: Rob
   - family-names: Trachel
     given-names: Romain
+  - family-names: Luke
+    given-names: Robert
   - family-names: De Santis
     given-names: Lorenzo
   - family-names: Panda
@@ -111,12 +111,12 @@ authors:
     given-names: Jair
   - family-names: Woodman
     given-names: Marmaduke
+  - family-names: Huberty
+    given-names: Scott
   - family-names: Lee
     given-names: Ingoo
   - family-names: Schulz
     given-names: Martin
-  - family-names: Huberty
-    given-names: Scott
   - family-names: Foti
     given-names: Nick
   - family-names: Nangini
@@ -156,6 +156,8 @@ authors:
     given-names: Ana
   - family-names: Buran
     given-names: Brad
+  - family-names: Woessner
+    given-names: Jacob
   - family-names: Massias
     given-names: Mathurin
   - family-names: Hämäläinen
@@ -168,8 +170,6 @@ authors:
     given-names: Christopher
   - family-names: Raimundo
     given-names: Félix
-  - family-names: Woessner
-    given-names: Jacob
   - family-names: Kaneda
     given-names: Michiru
   - family-names: Alday
@@ -192,6 +192,8 @@ authors:
     given-names: Mads
   - family-names: Gahlot
     given-names: Tanay
+  - family-names: Binns
+    given-names: Thomas S
   - family-names: Nunes
     given-names: Adonay
   - family-names: Gütlin
@@ -221,6 +223,10 @@ authors:
     given-names: Natalie
   - family-names: Roujansky
     given-names: Paul
+  - family-names: Luke
+    given-names: Rob
+  - family-names: Ruuskanen
+    given-names: Santeri
   - family-names: Kern
     given-names: Simon
   - family-names: Rantala
@@ -275,10 +281,10 @@ authors:
     given-names: Nathalie
   - family-names: Ward
     given-names: Nick
-  - family-names: Ruuskanen
-    given-names: Santeri
   - family-names: Herbst
     given-names: Sophie
+  - family-names: Férat
+    given-names: Victor
   - family-names: Radanovic
     given-names: Ana
   - family-names: Quinn
@@ -299,6 +305,8 @@ authors:
     given-names: Evgenii
   - family-names: Mamashli
     given-names: Fahimeh
+  - family-names: Belonosov
+    given-names: Gennadiy
   - family-names: O'Neill
     given-names: George
   - family-names: Marinato
@@ -327,6 +335,8 @@ authors:
     given-names: Nicolas
   - family-names: Kapralov
     given-names: Nikolai
+  - family-names: Chu
+    given-names: Qian
   - family-names: Falach
     given-names: Rotem
   - family-names: Deslauriers-Gauthier
@@ -337,14 +347,10 @@ authors:
     given-names: Steve
   - family-names: Bierer
     given-names: Steven
-  - family-names: Binns
-    given-names: Thomas S
   - family-names: Binns
     given-names: Thomas Samuel
   - family-names: Stenner
     given-names: Tristan
-  - family-names: Férat
-    given-names: Victor
   - family-names: Peterson
     given-names: Victoria
   - family-names: Baratz
@@ -369,8 +375,8 @@ authors:
     given-names: Dominique
   - family-names: Mikulan
     given-names: Ezequiel
-  - family-names: Belonosov
-    given-names: Gennadiy
+  - family-names: Hofer
+    given-names: Florian
   - family-names: Schiratti
     given-names: Jean-Baptiste
   - family-names: Evans
@@ -416,12 +422,14 @@ authors:
     given-names: Peter J
   - family-names: Ablin
     given-names: Pierre
-  - family-names: Chu
-    given-names: Qian
+  - family-names: Das
+    given-names: Proloy
   - family-names: Bertrand
     given-names: Quentin
   - family-names: Shoorangiz
     given-names: Reza
+  - family-names: Scholz
+    given-names: Richard
   - family-names: Hübner
     given-names: Rodrigo
   - family-names: Sommariva
@@ -460,6 +468,8 @@ authors:
     given-names: Adina
   - family-names: Ciok
     given-names: Alex
+  - family-names: Lepauvre
+    given-names: Alex
   - family-names: Kiefer
     given-names: Alexander
   - family-names: Gilbert
@@ -534,12 +544,12 @@ authors:
     given-names: Etienne
   - family-names: Goldstein
     given-names: Evgeny
+  - family-names: Mamashli
+    given-names: Fahimeh
   - family-names: Negahbani
     given-names: Farzin
   - family-names: Zamberlan
     given-names: Federico
-  - family-names: Hofer
-    given-names: Florian
   - family-names: Pop
     given-names: Florin
   - family-names: Weber
@@ -573,6 +583,8 @@ authors:
     given-names: Ivan
   - family-names: de Jong
     given-names: Ivo
+  - family-names: Phelan
+    given-names: Jacob
   - family-names: Kaczmarzyk
     given-names: Jakub
   - family-names: Zerfowski
@@ -603,6 +615,8 @@ authors:
     given-names: Laetitia
   - family-names: Andersen
     given-names: Lau Møller
+  - family-names: Almeida
+    given-names: Leonardo Rochael
   - family-names: Barbosa
     given-names: Leonardo S
   - family-names: Alfine
@@ -671,8 +685,6 @@ authors:
     given-names: Padma
   - family-names: Silva
     given-names: Pedro
-  - family-names: Das
-    given-names: Proloy
   - family-names: Li
     given-names: Quanliang
   - family-names: Barthélemy
@@ -689,8 +701,6 @@ authors:
     given-names: Reza
   - family-names: Koehler
     given-names: Richard
-  - family-names: Scholz
-    given-names: Richard
   - family-names: Stargardsky
     given-names: Riessarius
   - family-names: Oostenveld
@@ -727,6 +737,8 @@ authors:
     given-names: Simeon
   - family-names: Wong
     given-names: Simeon
+  - family-names: Hofmann
+    given-names: Simon M
   - family-names: Poil
     given-names: Simon-Shlomo
   - family-names: Foslien
@@ -769,6 +781,8 @@ authors:
     given-names: Yiping
   - family-names: Zhang
     given-names: Zhi
+  - family-names: ZENG
+    given-names: Ziyi
   - name: btkcodedev
   - name: buildqa
   - name: luzpaz

diff --git a/SECURITY.md b/SECURITY.md
@@ -10,9 +10,9 @@ without a proper 6-month deprecation cycle.
 
 | Version | Supported                |
 | ------- | ------------------------ |
-| 1.8.x   | :heavy_check_mark: (dev) |
-| 1.7.x   | :heavy_check_mark:       |
-| < 1.7   | :x:                      |
+| 1.9.x   | :heavy_check_mark: (dev) |
+| 1.8.x   | :heavy_check_mark:       |
+| < 1.8   | :x:                      |
 
 ## Reporting a Vulnerability
 

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -171,8 +171,7 @@ stages:
               python -m pip install --progress-bar off --upgrade pip
               python -m pip install --progress-bar off --upgrade --pre --only-binary=\"numpy,scipy,matplotlib,vtk\" numpy scipy matplotlib vtk
               python -c "import vtk"
-              # Bug on 2.5.13 https://github.com/openmeeg/openmeeg/issues/700
-              python -m pip install --progress-bar off --upgrade -ve .[full,test_extra] "openmeeg==2.5.12"
+              python -m pip install --progress-bar off --upgrade -ve .[full,test_extra]
             displayName: 'Install dependencies with pip'
           - bash: |
               set -e