Merge branch 'main' into equalize_epochs_tfr

CarinaFo · Dec 1, 2023 · 2449290 · 2449290
2 parents 75c3142 + 20174f4
commit 2449290
Show file tree

Hide file tree

Showing 49 changed files with 801 additions and 731 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -296,8 +296,14 @@ jobs:
       # Build docs
       - run:
           name: make html
+          command: |  # we have -o pipefail in #BASH_ENV so we should be okay
+            set -x
+            PATTERN=$(cat pattern.txt) make -C doc $(cat build.txt) 2>&1 | tee sphinx_log.txt
+      - run:
+          name: Check sphinx log for warnings (which are treated as errors)
+          when: always
           command: |
-            PATTERN=$(cat pattern.txt) make -C doc $(cat build.txt);
+            ! grep "^.* WARNING: .*$" sphinx_log.txt
       - run:
           name: Show profiling output
           when: always

diff --git a/.git_archival.txt b/.git_archival.txt
@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1 @@
+.git_archival.txt  export-subst
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -63,16 +63,16 @@ jobs:
             python: '3.11'
             kind: pip-pre
           - os: macos-latest
-            python: '3.8'
+            python: '3.9'
             kind: mamba
           - os: windows-latest
             python: '3.10'
             kind: mamba
           - os: ubuntu-latest
-            python: '3.8'
+            python: '3.9'
             kind: minimal
           - os: ubuntu-20.04
-            python: '3.8'
+            python: '3.9'
             kind: old
     steps:
       - uses: actions/checkout@v4

diff --git a/.mailmap b/.mailmap
@@ -240,6 +240,7 @@ Olaf Hauk <[email protected]> olafhauk <[email protected]>
 Omer Shubi <[email protected]> Omer S <[email protected]>
 Paul Pasler <[email protected]> ppasler <[email protected]>
 Paul Roujansky <[email protected]> Paul ROUJANSKY <[email protected]>
+Paul Roujansky <[email protected]> paulroujansky <[email protected]>
 Pedro Silva <[email protected]> pbnsilva <[email protected]>
 Phillip Alday <[email protected]> Phillip Alday <[email protected]>
 Phillip Alday <[email protected]> Phillip Alday <[email protected]>
@@ -254,6 +255,7 @@ Praveen Sripad <[email protected]> prav <[email protected]>
 Proloy Das <[email protected]> pdas6 <[email protected]>
 Ram Pari <[email protected]> Ram <[email protected]>
 Ramonapariciog Apariciogarcia <[email protected]> ramonapariciog <[email protected]>
+Rasmus Aagaard <[email protected]> roraa <[email protected]>
 Reza Nasri <[email protected]> Reza <[email protected]>
 Reza Nasri <[email protected]> RezaNasri <[email protected]>
 Roan LaPlante <[email protected]> aestrivex <[email protected]>

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ repos:
 
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.5
+    rev: v0.1.6
     hooks:
       - id: ruff
         name: ruff mne
@@ -16,7 +16,7 @@ repos:
 
   # Ruff tutorials and examples
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.5
+    rev: v0.1.6
     hooks:
       - id: ruff
         name: ruff tutorials and examples
@@ -50,3 +50,6 @@ repos:
         additional_dependencies:
           - tomli
         files: ^doc/.*\.(rst|inc)$
+
+ci:
+  autofix_prs: false
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: 1.5.0
-date-released: "2023-08-15"
-commit: 5645d375f52727eb563bd46a45422fc1a55e9f1a
+version: 1.6.0
+date-released: "2023-11-20"
+commit: 498cf789685ede0b29e712a1e7220c69443e8744
 doi: 10.5281/zenodo.592483
 keywords:
   - MEG
@@ -61,14 +61,14 @@ authors:
     given-names: Joan
   - family-names: Bekhti
     given-names: Yousra
+  - family-names: Scheltienne
+    given-names: Mathieu
   - family-names: Appelhoff
     given-names: Stefan
   - family-names: Leggitt
     given-names: Alan
   - family-names: Dykstra
     given-names: Andrew
-  - family-names: Scheltienne
-    given-names: Mathieu
   - family-names: Luke
     given-names: Rob
   - family-names: Trachel
@@ -121,10 +121,14 @@ authors:
     given-names: Cathy
   - family-names: García Alanis
     given-names: José C
+  - family-names: Huberty
+    given-names: Scott
   - family-names: Hauk
     given-names: Olaf
   - family-names: Maddox
     given-names: Ross
+  - family-names: Orfanos
+    given-names: Dimitri Papadopoulos
   - family-names: LaPlante
     given-names: Roan
   - family-names: Drew
@@ -133,16 +137,12 @@ authors:
     given-names: Christoph
   - family-names: Dumas
     given-names: Guillaume
-  - family-names: Huberty
-    given-names: Scott
+  - family-names: Benerradi
+    given-names: Johann
   - family-names: Hartmann
     given-names: Thomas
-  - family-names: Orfanos
-    given-names: Dimitri Papadopoulos
   - family-names: Ort
     given-names: Eduard
-  - family-names: Benerradi
-    given-names: Johann
   - family-names: Pasler
     given-names: Paul
   - family-names: Repplinger
@@ -185,6 +185,8 @@ authors:
     given-names: Tanay
   - family-names: Nunes
     given-names: Adonay
+  - family-names: Gramfort
+    given-names: Alexandre
   - family-names: Gütlin
     given-names: Dirk
   - name: kjs
@@ -196,6 +198,10 @@ authors:
     given-names: Catalina María
   - family-names: Moënne-Loccoz
     given-names: Cristóbal
+  - family-names: Altukhov
+    given-names: Dmitrii
+  - family-names: Peterson
+    given-names: Erica
   - family-names: Heinila
     given-names: Erkka
   - family-names: Hanna
@@ -206,6 +212,8 @@ authors:
     given-names: Michiru
   - family-names: Klein
     given-names: Natalie
+  - family-names: Roujansky
+    given-names: Paul
   - family-names: Kern
     given-names: Simon
   - family-names: Rantala
@@ -214,24 +222,26 @@ authors:
     given-names: Burkhard
   - family-names: O'Reilly
     given-names: Christian
-  - family-names: Peterson
-    given-names: Erica
   - family-names: Kolkhorst
     given-names: Henrich
   - family-names: Banville
     given-names: Hubert
+  - family-names: Zhang
+    given-names: Jack
+  - family-names: Woessner
+    given-names: Jacob
   - family-names: Maksymenko
     given-names: Kostiantyn
   - family-names: Clarke
     given-names: Maggie
   - family-names: Anelli
     given-names: Matteo
+  - family-names: Chapochnikov
+    given-names: Nikolai
   - family-names: Bannier
     given-names: Pierre-Antoine
   - family-names: Choudhary
     given-names: Saket
-  - family-names: Gramfort
-    given-names: Alexandre
   - family-names: Forster
     given-names: Carina
   - family-names: Kim
@@ -242,8 +252,6 @@ authors:
     given-names: Fu-Te
   - family-names: Kojcic
     given-names: Ivana
-  - family-names: Zhang
-    given-names: Jack
   - family-names: Nielsen
     given-names: Jesper Duemose
   - family-names: Lankinen
@@ -258,6 +266,10 @@ authors:
     given-names: Nathalie
   - family-names: Ward
     given-names: Nick
+  - family-names: Ruuskanen
+    given-names: Santeri
+  - family-names: Radanovic
+    given-names: Ana
   - family-names: Quinn
     given-names: Andrew
   - family-names: Gauthier
@@ -266,6 +278,8 @@ authors:
     given-names: Basile
   - family-names: Welke
     given-names: Dominik
+  - family-names: Welke
+    given-names: Dominik
   - family-names: Stephen
     given-names: Emily
   - family-names: Hornberger
@@ -326,12 +340,8 @@ authors:
     given-names: Chetan
   - family-names: Zhao
     given-names: Christina
-  - family-names: Altukhov
-    given-names: Dmitrii
   - family-names: Krzemiński
     given-names: Dominik
-  - family-names: Welke
-    given-names: Dominik
   - family-names: Makowski
     given-names: Dominique
   - family-names: Mikulan
@@ -340,16 +350,22 @@ authors:
     given-names: Gennadiy
   - family-names: O'Neill
     given-names: George
-  - family-names: Woessner
-    given-names: Jacob
+  - family-names: Abdelhedi
+    given-names: Hamza
   - family-names: Schiratti
     given-names: Jean-Baptiste
   - family-names: Evans
     given-names: Jen
+  - family-names: Veillette
+    given-names: John
   - family-names: Drew
     given-names: Jordan
   - family-names: Teves
     given-names: Joshua
+  - family-names: Zhu
+    given-names: Judy D
+  - family-names: Armeni
+    given-names: Kristijan
   - family-names: Mathewson
     given-names: Kyle
   - family-names: Gwilliams
@@ -375,8 +391,6 @@ authors:
     given-names: Naveen
   - family-names: Wilming
     given-names: Niklas
-  - family-names: Chapochnikov
-    given-names: Nikolai
   - family-names: Kozynets
     given-names: Oleh
   - family-names: Ablin
@@ -427,6 +441,8 @@ authors:
     given-names: Adina
   - family-names: Ciok
     given-names: Alex
+  - family-names: Gilbert
+    given-names: Andy
   - family-names: Pradhan
     given-names: Aniket
   - family-names: Padee
@@ -510,10 +526,10 @@ authors:
   - family-names: O'Neill
     given-names: George
   - name: Giulio
+  - family-names: Reina
+    given-names: Gonzalo
   - family-names: Maymandi
     given-names: Hamid
-  - family-names: Abdelhedi
-    given-names: Hamza
   - family-names: Sonntag
     given-names: Hermann
   - family-names: Ye
@@ -524,6 +540,10 @@ authors:
     given-names: Hüseyin Orkun
   - family-names: Machairas
     given-names: Ilias
+  - family-names: Skelin
+    given-names: Ivan
+  - family-names: Zubarev
+    given-names: Ivan
   - family-names: Kaczmarzyk
     given-names: Jakub
   - family-names: Zerfowski
@@ -536,14 +556,10 @@ authors:
     given-names: Johan
   - family-names: Niediek
     given-names: Johannes
-  - family-names: Veillette
-    given-names: John
   - family-names: Koen
     given-names: Josh
   - family-names: Bear
     given-names: Joshua J
-  - family-names: Zhu
-    given-names: Judy D
   - family-names: Dammers
     given-names: Juergen
   - family-names: Galán
@@ -566,6 +582,8 @@ authors:
     given-names: Lorenzo
   - family-names: Hejtmánek
     given-names: Lukáš
+  - family-names: Balatsko
+    given-names: Maksym
   - family-names: Kitzbichler
     given-names: Manfred
   - family-names: Kumar
@@ -578,6 +596,8 @@ authors:
     given-names: Marcin
   - family-names: Henney
     given-names: Mark Alexander
+  - family-names: Schulz
+    given-names: Martin
   - family-names: van Harmelen
     given-names: Martin
   - name: MartinBaBer
@@ -613,16 +633,18 @@ authors:
     given-names: Nikolas
   - family-names: Shubi
     given-names: Omer
+  - family-names: Mainar
+    given-names: Pablo
   - family-names: Sundaram
     given-names: Padma
-  - family-names: Roujansky
-    given-names: Paul
   - family-names: Silva
     given-names: Pedro
   - family-names: Molfese
     given-names: Peter J
   - family-names: Das
     given-names: Proloy
+  - family-names: Chu
+    given-names: Qian
   - family-names: Li
     given-names: Quanliang
   - family-names: Barthélemy
@@ -633,6 +655,8 @@ authors:
     given-names: Ramiro
   - family-names: Apariciogarcia
     given-names: Ramonapariciog
+  - family-names: Aagaard
+    given-names: Rasmus
   - family-names: Nasri
     given-names: Reza
   - family-names: Koehler
@@ -653,8 +677,6 @@ authors:
     given-names: Sam
   - family-names: Louviot
     given-names: Samuel
-  - family-names: Ruuskanen
-    given-names: Santeri
   - family-names: Saha
     given-names: Sawradip
   - family-names: Mathot

diff --git a/Makefile b/Makefile
@@ -55,7 +55,7 @@ codespell:  # running manually
 	@codespell --builtin clear,rare,informal,names,usage -w -i 3 -q 3 -S $(CODESPELL_SKIPS) --ignore-words=ignore_words.txt --uri-ignore-words-list=bu $(CODESPELL_DIRS)
 
 check-manifest:
-	check-manifest -q --ignore .circleci/config.yml,doc,logo,mne/io/*/tests/data*,mne/io/tests/data,mne/preprocessing/tests/data,.DS_Store,mne/_version.py
+	check-manifest -q --ignore .circleci/config.yml,doc,logo,mne/io/*/tests/data*,mne/io/tests/data,mne/preprocessing/tests/data,.DS_Store,.git_archival.txt
 
 check-readme: clean wheel
 	twine check dist/*