From d8c63ebf32c50f4f4519a93aa04f99ebd14cd42b Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 08:53:47 +0100
Subject: [PATCH 01/51] Add pre-commit

---
 .pre-commit-config.yaml | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 .pre-commit-config.yaml

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 00000000000..0d46d304fe0
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,16 @@
+default_language_version:
+    python: python3.11
+
+repos:
+- repo: https://github.com/psf/black
+  rev: 23.1.0
+  hooks:
+    - id: black
+- repo: https://github.com/charliermarsh/ruff-pre-commit
+  rev: v0.0.254
+  hooks:
+    - id: ruff
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.2.2
+  hooks:
+    - id: codespell

From 7c6f66cbedee27dd58e32e62e2700cd4ecb0dfb9 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 09:01:31 +0100
Subject: [PATCH 02/51] Add GitHub workflow

---
 .github/workflows/precommit.yml | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100644 .github/workflows/precommit.yml

diff --git a/.github/workflows/precommit.yml b/.github/workflows/precommit.yml
new file mode 100644
index 00000000000..4638064b646
--- /dev/null
+++ b/.github/workflows/precommit.yml
@@ -0,0 +1,14 @@
+name: Pre-commit
+
+on: [push, pull_request]
+
+jobs:
+  style:
+    name: Pre-commit
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+    - uses: pre-commit/action@v3.0.0

From 91b04fde4f1619e757c4474fa127f543f430312f Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 09:11:50 +0100
Subject: [PATCH 03/51] Exclude __init__.py (Ruff)

---
 pyproject.toml | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 pyproject.toml

diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 00000000000..bf1d326b04c
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,2 @@
+[tool.ruff]
+exclude = ["__init__.py"]

From 74f05ef4eeb9378ff2aa05b94ee86414d01b685c Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 09:14:01 +0100
Subject: [PATCH 04/51] Add per-file ignore

---
 pyproject.toml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index bf1d326b04c..a7bef3b73a4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,2 +1,5 @@
 [tool.ruff]
 exclude = ["__init__.py"]
+
+[tool.ruff.per-file-ignores]
+"tutorials/time-freq/10_spectrum_class.py" = ["E501"]

From 33e348ad6147c895ab0314126fd8501690faea6b Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 09:27:39 +0100
Subject: [PATCH 05/51] Quiet Black

---
 .pre-commit-config.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 0d46d304fe0..cfd94509ed7 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -6,6 +6,7 @@ repos:
   rev: 23.1.0
   hooks:
     - id: black
+      args: [--quiet]
 - repo: https://github.com/charliermarsh/ruff-pre-commit
   rev: v0.0.254
   hooks:

From 8d73a6e75a33863c23a99b10ce1d66b9f45b2e9c Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 10:23:22 +0100
Subject: [PATCH 06/51] Add Codespell config

---
 .pre-commit-config.yaml | 1 +
 pyproject.toml          | 5 +++++
 2 files changed, 6 insertions(+)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index cfd94509ed7..f53567dd432 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -15,3 +15,4 @@ repos:
   rev: v2.2.2
   hooks:
     - id: codespell
+      args: [mne/ doc/ tutorials/ examples/]
diff --git a/pyproject.toml b/pyproject.toml
index a7bef3b73a4..b7ea6e9428a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,3 +1,8 @@
+[tool.codespell]
+ignore-words = ignore_words.txt
+uri-ignore-words-list = bu
+skip = 'doc/_build,doc/auto_*,*.fif,*.eve,*.gz,*.tgz,*.zip,*.mat,*.stc,*.label,*.w,*.bz2,*.annot,*.sulc,*.log,*.local-copy,*.orig_avg,*.inflated_avg,*.gii,*.pyc,*.doctree,*.pickle,*.inv,*.png,*.edf,*.touch,*.thickness,*.nofix,*.volume,*.defect_borders,*.mgh,lh.*,rh.*,COR-*,FreeSurferColorLUT.txt,*.examples,.xdebug_mris_calc,bad.segments,BadChannels,*.hist,empty_file,*.orig,*.js,*.map,*.ipynb,searchindex.dat,install_mne_c.rst,plot_*.rst,*.rst.txt,c_EULA.rst*,*.html,gdf_encodes.txt,*.svg,references.bib,*.css,*.edf,*.bdf,*.vhdr'
+
 [tool.ruff]
 exclude = ["__init__.py"]
 

From 390f87203bce1ce891207f30744da21f31759065 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 10:28:33 +0100
Subject: [PATCH 07/51] Fix TOML

---
 pyproject.toml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index b7ea6e9428a..50bac407dd1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,7 +1,7 @@
 [tool.codespell]
-ignore-words = ignore_words.txt
-uri-ignore-words-list = bu
-skip = 'doc/_build,doc/auto_*,*.fif,*.eve,*.gz,*.tgz,*.zip,*.mat,*.stc,*.label,*.w,*.bz2,*.annot,*.sulc,*.log,*.local-copy,*.orig_avg,*.inflated_avg,*.gii,*.pyc,*.doctree,*.pickle,*.inv,*.png,*.edf,*.touch,*.thickness,*.nofix,*.volume,*.defect_borders,*.mgh,lh.*,rh.*,COR-*,FreeSurferColorLUT.txt,*.examples,.xdebug_mris_calc,bad.segments,BadChannels,*.hist,empty_file,*.orig,*.js,*.map,*.ipynb,searchindex.dat,install_mne_c.rst,plot_*.rst,*.rst.txt,c_EULA.rst*,*.html,gdf_encodes.txt,*.svg,references.bib,*.css,*.edf,*.bdf,*.vhdr'
+ignore-words = "ignore_words.txt"
+uri-ignore-words-list = "bu"
+skip = "doc/_build,doc/auto_*,*.fif,*.eve,*.gz,*.tgz,*.zip,*.mat,*.stc,*.label,*.w,*.bz2,*.annot,*.sulc,*.log,*.local-copy,*.orig_avg,*.inflated_avg,*.gii,*.pyc,*.doctree,*.pickle,*.inv,*.png,*.edf,*.touch,*.thickness,*.nofix,*.volume,*.defect_borders,*.mgh,lh.*,rh.*,COR-*,FreeSurferColorLUT.txt,*.examples,.xdebug_mris_calc,bad.segments,BadChannels,*.hist,empty_file,*.orig,*.js,*.map,*.ipynb,searchindex.dat,install_mne_c.rst,plot_*.rst,*.rst.txt,c_EULA.rst*,*.html,gdf_encodes.txt,*.svg,references.bib,*.css,*.edf,*.bdf,*.vhdr"
 
 [tool.ruff]
 exclude = ["__init__.py"]

From 1220e04cadf5063d07c7634b2ceb7c744400e2c5 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 10:36:02 +0100
Subject: [PATCH 08/51] Include instead of exclude files

---
 .pre-commit-config.yaml | 2 +-
 pyproject.toml          | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index f53567dd432..aaa37fe0748 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -15,4 +15,4 @@ repos:
   rev: v2.2.2
   hooks:
     - id: codespell
-      args: [mne/ doc/ tutorials/ examples/]
+      args: [mne/ doc/ tutorials/ examples/ *.py *.rst *.bib *.inc]
diff --git a/pyproject.toml b/pyproject.toml
index 50bac407dd1..5efd7ad0bfb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,7 +1,6 @@
 [tool.codespell]
 ignore-words = "ignore_words.txt"
 uri-ignore-words-list = "bu"
-skip = "doc/_build,doc/auto_*,*.fif,*.eve,*.gz,*.tgz,*.zip,*.mat,*.stc,*.label,*.w,*.bz2,*.annot,*.sulc,*.log,*.local-copy,*.orig_avg,*.inflated_avg,*.gii,*.pyc,*.doctree,*.pickle,*.inv,*.png,*.edf,*.touch,*.thickness,*.nofix,*.volume,*.defect_borders,*.mgh,lh.*,rh.*,COR-*,FreeSurferColorLUT.txt,*.examples,.xdebug_mris_calc,bad.segments,BadChannels,*.hist,empty_file,*.orig,*.js,*.map,*.ipynb,searchindex.dat,install_mne_c.rst,plot_*.rst,*.rst.txt,c_EULA.rst*,*.html,gdf_encodes.txt,*.svg,references.bib,*.css,*.edf,*.bdf,*.vhdr"
 
 [tool.ruff]
 exclude = ["__init__.py"]

From e638c9de1f36e098df0f5273ea2f8d94c8d3a34d Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 10:43:27 +0100
Subject: [PATCH 09/51] Try args

---
 .pre-commit-config.yaml | 2 +-
 pyproject.toml          | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index aaa37fe0748..fa5827c14a4 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -15,4 +15,4 @@ repos:
   rev: v2.2.2
   hooks:
     - id: codespell
-      args: [mne/ doc/ tutorials/ examples/ *.py *.rst *.bib *.inc]
+      args: [mne/,doc/,tutorials/,examples/,*.py,*.rst,*.bib,*.inc]
diff --git a/pyproject.toml b/pyproject.toml
index 5efd7ad0bfb..77bce780767 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,7 @@
 [tool.codespell]
 ignore-words = "ignore_words.txt"
 uri-ignore-words-list = "bu"
+builtin = "clear,rare,informal,names,usage"
 
 [tool.ruff]
 exclude = ["__init__.py"]

From 35a1139cb8497ccec1cf3e977fe95e6dbda69b39 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 11:08:49 +0100
Subject: [PATCH 10/51] Quote args

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index fa5827c14a4..1efb262f908 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -15,4 +15,4 @@ repos:
   rev: v2.2.2
   hooks:
     - id: codespell
-      args: [mne/,doc/,tutorials/,examples/,*.py,*.rst,*.bib,*.inc]
+      args: ["mne/", "doc/", "tutorials/", "examples/", "*.py", "*.rst", "*.bib"]

From df77fa68e85514c71d7b25e2fd10603aca3fce1b Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 11:13:27 +0100
Subject: [PATCH 11/51] Just one string

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 1efb262f908..b0ffdfbe8be 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -15,4 +15,4 @@ repos:
   rev: v2.2.2
   hooks:
     - id: codespell
-      args: ["mne/", "doc/", "tutorials/", "examples/", "*.py", "*.rst", "*.bib"]
+      args: ["mne/ doc/ tutorials/ examples/ *.py *.rst *.bib"]

From 7111930e5cc26c8efc8d09722d7a7459dedcfe81 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 11:18:20 +0100
Subject: [PATCH 12/51] Single quotes

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b0ffdfbe8be..3f7fb700c68 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -15,4 +15,4 @@ repos:
   rev: v2.2.2
   hooks:
     - id: codespell
-      args: ["mne/ doc/ tutorials/ examples/ *.py *.rst *.bib"]
+      args: ['mne/', 'doc/', 'tutorials/', 'examples/', '*.py', '*.rst', '*.bib']

From 1f056aad6348f95633ba46f9a3d3d763d2a5ee55 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 11:28:55 +0100
Subject: [PATCH 13/51] More Ruff excludes

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 77bce780767..04fc19dbbb6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ uri-ignore-words-list = "bu"
 builtin = "clear,rare,informal,names,usage"
 
 [tool.ruff]
-exclude = ["__init__.py"]
+exclude = ["__init__.py", "constants.py", "fixes.py", "resources.py"]
 
 [tool.ruff.per-file-ignores]
 "tutorials/time-freq/10_spectrum_class.py" = ["E501"]

From 3e3a373051903fea8cd3ee7a670cdbe60ab4038c Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 11:31:12 +0100
Subject: [PATCH 14/51] Disable Black and Ruff for now

---
 .pre-commit-config.yaml | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 3f7fb700c68..6c272aec89c 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,15 +2,15 @@ default_language_version:
     python: python3.11
 
 repos:
-- repo: https://github.com/psf/black
-  rev: 23.1.0
-  hooks:
-    - id: black
-      args: [--quiet]
-- repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.0.254
-  hooks:
-    - id: ruff
+# - repo: https://github.com/psf/black
+#   rev: 23.1.0
+#   hooks:
+#     - id: black
+#       args: [--quiet]
+# - repo: https://github.com/charliermarsh/ruff-pre-commit
+#   rev: v0.0.254
+#   hooks:
+#     - id: ruff
 - repo: https://github.com/codespell-project/codespell
   rev: v2.2.2
   hooks:

From e57737049455d26a772fedbf0b2c2b8e062bc46b Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 17:24:05 +0100
Subject: [PATCH 15/51] Filter files and types

---
 .pre-commit-config.yaml | 3 ++-
 pyproject.toml          | 1 +
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 6c272aec89c..d8e11f7abd2 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -15,4 +15,5 @@ repos:
   rev: v2.2.2
   hooks:
     - id: codespell
-      args: ['mne/', 'doc/', 'tutorials/', 'examples/', '*.py', '*.rst', '*.bib']
+      files: ^mne/|^doc/|^examples/|^tutorials/
+      types_or: [python, bib, rst]
diff --git a/pyproject.toml b/pyproject.toml
index 04fc19dbbb6..415ebdf26bb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,6 +2,7 @@
 ignore-words = "ignore_words.txt"
 uri-ignore-words-list = "bu"
 builtin = "clear,rare,informal,names,usage"
+skip = "doc/references.bib"
 
 [tool.ruff]
 exclude = ["__init__.py", "constants.py", "fixes.py", "resources.py"]

From 45d50ca83af3f4e189b444fbf20ee3837b904527 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 17:30:09 +0100
Subject: [PATCH 16/51] Add tomli dependency for codespell

---
 .pre-commit-config.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index d8e11f7abd2..3d3abfa32be 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -15,5 +15,7 @@ repos:
   rev: v2.2.2
   hooks:
     - id: codespell
+      additional_dependencies:
+        - tomli
       files: ^mne/|^doc/|^examples/|^tutorials/
       types_or: [python, bib, rst]

From 14b692a30403e96c9bd1cf56c0fb6ced64bd6aac Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 17:33:47 +0100
Subject: [PATCH 17/51] Enable Ruff

---
 .pre-commit-config.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 3d3abfa32be..371c99ec894 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,10 +7,10 @@ repos:
 #   hooks:
 #     - id: black
 #       args: [--quiet]
-# - repo: https://github.com/charliermarsh/ruff-pre-commit
-#   rev: v0.0.254
-#   hooks:
-#     - id: ruff
+- repo: https://github.com/charliermarsh/ruff-pre-commit
+  rev: v0.0.254
+  hooks:
+    - id: ruff
 - repo: https://github.com/codespell-project/codespell
   rev: v2.2.2
   hooks:

From 5f5a28eb2c39811421f03d337fa6fd72007c6ab1 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 17:41:02 +0100
Subject: [PATCH 18/51] Fix Ruff errors

---
 doc/conf.py                                    | 3 +--
 mne/beamformer/tests/test_resolution_matrix.py | 4 ++--
 mne/chpi.py                                    | 4 ++--
 mne/io/base.py                                 | 5 ++++-
 mne/viz/evoked.py                              | 2 +-
 mne/viz/topo.py                                | 2 +-
 6 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/doc/conf.py b/doc/conf.py
index c826d19228d..a537b0e85e6 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -204,7 +204,6 @@
     # MNE
     'Label': 'mne.Label', 'Forward': 'mne.Forward', 'Evoked': 'mne.Evoked',
     'Info': 'mne.Info', 'SourceSpaces': 'mne.SourceSpaces',
-    'SourceMorph': 'mne.SourceMorph',
     'Epochs': 'mne.Epochs', 'Layout': 'mne.channels.Layout',
     'EvokedArray': 'mne.EvokedArray', 'BiHemiLabel': 'mne.BiHemiLabel',
     'AverageTFR': 'mne.time_frequency.AverageTFR',
@@ -224,7 +223,7 @@
     'CrossSpectralDensity': 'mne.time_frequency.CrossSpectralDensity',
     'SourceMorph': 'mne.SourceMorph',
     'Xdawn': 'mne.preprocessing.Xdawn',
-    'Report': 'mne.Report', 'Forward': 'mne.Forward',
+    'Report': 'mne.Report',
     'TimeDelayingRidge': 'mne.decoding.TimeDelayingRidge',
     'Vectorizer': 'mne.decoding.Vectorizer',
     'UnsupervisedSpatialFilter': 'mne.decoding.UnsupervisedSpatialFilter',
diff --git a/mne/beamformer/tests/test_resolution_matrix.py b/mne/beamformer/tests/test_resolution_matrix.py
index 09ef7fe1118..e70ede5f1fa 100755
--- a/mne/beamformer/tests/test_resolution_matrix.py
+++ b/mne/beamformer/tests/test_resolution_matrix.py
@@ -86,9 +86,9 @@ def test_resolution_matrix_lcmv():
     # Some rows are off by about 0.1 - not yet clear why
     corr = []
 
-    for (f, l) in zip(resmat_fwd, resmat_lcmv):
+    for (f, lf) in zip(resmat_fwd, resmat_lcmv):
 
-        corr.append(np.corrcoef(f, l)[0, 1])
+        corr.append(np.corrcoef(f, lf)[0, 1])
 
     # all row correlations should at least be above ~0.8
     assert_allclose(corr, 1., atol=0.2)
diff --git a/mne/chpi.py b/mne/chpi.py
index 096c4e6f2bc..12d40f4cfa3 100644
--- a/mne/chpi.py
+++ b/mne/chpi.py
@@ -1213,8 +1213,8 @@ def compute_chpi_locs(info, chpi_amplitudes, t_step_max=1., too_close='raise',
         # check if data has sufficiently changed
         if last['sin_fit'] is not None:  # first iteration
             corrs = np.array(
-                [np.corrcoef(s, l)[0, 1]
-                    for s, l in zip(sin_fit, last['sin_fit'])])
+                [np.corrcoef(s, lst)[0, 1]
+                    for s, lst in zip(sin_fit, last['sin_fit'])])
             corrs *= corrs
             # check to see if we need to continue
             if fit_time - last['coil_fit_time'] <= t_step_max - 1e-7 and \
diff --git a/mne/io/base.py b/mne/io/base.py
index 55ebc33b588..91e4193e137 100644
--- a/mne/io/base.py
+++ b/mne/io/base.py
@@ -576,7 +576,10 @@ def time_as_index(self, times, use_rounding=False, origin=None):
 
     @property
     def _raw_lengths(self):
-        return [l - f + 1 for f, l in zip(self._first_samps, self._last_samps)]
+        return [
+            last - first + 1
+            for first, last in zip(self._first_samps, self._last_samps)
+        ]
 
     @property
     def annotations(self):  # noqa: D401
diff --git a/mne/viz/evoked.py b/mne/viz/evoked.py
index aff29fdd046..8c9cc4564b4 100644
--- a/mne/viz/evoked.py
+++ b/mne/viz/evoked.py
@@ -911,7 +911,7 @@ def plot_evoked_topo(evoked, layout=None, layout_scale=0.945,
     fig : instance of matplotlib.figure.Figure
         Images of evoked responses at sensor locations.
     """
-    if not type(evoked) in (tuple, list):
+    if type(evoked) not in (tuple, list):
         evoked = [evoked]
 
     background_color = _to_rgb(background_color, name='background_color')
diff --git a/mne/viz/topo.py b/mne/viz/topo.py
index 962fa283bcb..612cbaf86f8 100644
--- a/mne/viz/topo.py
+++ b/mne/viz/topo.py
@@ -658,7 +658,7 @@ def _plot_evoked_topo(evoked, layout=None, layout_scale=0.945,
     import matplotlib.pyplot as plt
     from ..cov import whiten_evoked
 
-    if not type(evoked) in (tuple, list):
+    if type(evoked) not in (tuple, list):
         evoked = [evoked]
 
     noise_cov = _check_cov(noise_cov, evoked[0].info)

From b5789ded19b36cfb2c0e8a2a3071066df9b10be8 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 17:57:06 +0100
Subject: [PATCH 19/51] Exclude *.yaml

---
 MANIFEST.in | 1 +
 1 file changed, 1 insertion(+)

diff --git a/MANIFEST.in b/MANIFEST.in
index 6c1aa9ff47f..e00b86e3e79 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -57,6 +57,7 @@ exclude tools
 exclude Makefile
 exclude .coveragerc
 exclude *.yml
+exclude *.yaml
 exclude ignore_words.txt
 exclude .mailmap
 exclude codemeta.json

From 4cf0920d30efb5b3746c56c852a8cfde3c485910 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 18:00:57 +0100
Subject: [PATCH 20/51] Try without tomli package again

---
 .pre-commit-config.yaml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 371c99ec894..4a1f44208d7 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -15,7 +15,5 @@ repos:
   rev: v2.2.2
   hooks:
     - id: codespell
-      additional_dependencies:
-        - tomli
       files: ^mne/|^doc/|^examples/|^tutorials/
       types_or: [python, bib, rst]

From 19f7e4f3aa4886d377ec3c1d29cd1fff7d537cc8 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 18:07:59 +0100
Subject: [PATCH 21/51] Even 3.11 requires tomli

---
 .pre-commit-config.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4a1f44208d7..371c99ec894 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -15,5 +15,7 @@ repos:
   rev: v2.2.2
   hooks:
     - id: codespell
+      additional_dependencies:
+        - tomli
       files: ^mne/|^doc/|^examples/|^tutorials/
       types_or: [python, bib, rst]

From 48209ee6e6da7f96c0b22446cfe2dc1d354cf07d Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 22:06:35 +0100
Subject: [PATCH 22/51] Try new Codespell without tomli

---
 .pre-commit-config.yaml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 371c99ec894..9fa57e489b2 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -12,10 +12,8 @@ repos:
   hooks:
     - id: ruff
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.2
+  rev: v2.2.3
   hooks:
     - id: codespell
-      additional_dependencies:
-        - tomli
       files: ^mne/|^doc/|^examples/|^tutorials/
       types_or: [python, bib, rst]

From adcdebfdae42a8b3164fc7715289f8cb935504a1 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 22:17:43 +0100
Subject: [PATCH 23/51] Add .inc files for codespell

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 9fa57e489b2..0f41eb4fedc 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -16,4 +16,4 @@ repos:
   hooks:
     - id: codespell
       files: ^mne/|^doc/|^examples/|^tutorials/
-      types_or: [python, bib, rst]
+      types_or: [python, bib, rst, inc]

From fc44493c58f53e6555bf13f733db6c8f162d00e4 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 22:25:05 +0100
Subject: [PATCH 24/51] Remove Codespell from old workflow

---
 .github/workflows/codespell_and_flake.yml | 45 -----------------------
 .github/workflows/flake.yml               | 33 +++++++++++++++++
 2 files changed, 33 insertions(+), 45 deletions(-)
 delete mode 100644 .github/workflows/codespell_and_flake.yml
 create mode 100644 .github/workflows/flake.yml

diff --git a/.github/workflows/codespell_and_flake.yml b/.github/workflows/codespell_and_flake.yml
deleted file mode 100644
index e191caa25d1..00000000000
--- a/.github/workflows/codespell_and_flake.yml
+++ /dev/null
@@ -1,45 +0,0 @@
-name: 'codespell_and_flake'
-# https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#concurrency
-# https://docs.github.com/en/developers/webhooks-and-events/events/github-event-types#pullrequestevent
-# workflow name, PR number (empty on push), push ref (empty on PR)
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
-  cancel-in-progress: true
-on:
-  push:
-    branches:
-      - '*'
-  pull_request:
-    branches:
-      - '*'
-
-jobs:
-  style:
-    name: 'codespell and flake'
-    runs-on: ubuntu-20.04
-    env:
-      CODESPELL_DIRS: 'mne/ doc/ tutorials/ examples/'
-      CODESPELL_SKIPS: 'doc/_build,doc/auto_*,*.fif,*.eve,*.gz,*.tgz,*.zip,*.mat,*.stc,*.label,*.w,*.bz2,*.annot,*.sulc,*.log,*.local-copy,*.orig_avg,*.inflated_avg,*.gii,*.pyc,*.doctree,*.pickle,*.inv,*.png,*.edf,*.touch,*.thickness,*.nofix,*.volume,*.defect_borders,*.mgh,lh.*,rh.*,COR-*,FreeSurferColorLUT.txt,*.examples,.xdebug_mris_calc,bad.segments,BadChannels,*.hist,empty_file,*.orig,*.js,*.map,*.ipynb,searchindex.dat,install_mne_c.rst,plot_*.rst,*.rst.txt,c_EULA.rst*,*.html,gdf_encodes.txt,*.svg,references.bib,*.css,*.edf,*.bdf,*.vhdr'
-
-    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
-        with:
-          python-version: '3.9'
-          architecture: 'x64'
-      - run: |
-          python -m pip install --upgrade pip setuptools wheel
-          python -m pip install flake8
-        name: 'Install dependencies'
-      - uses: rbialon/flake8-annotations@v1
-        name: 'Setup flake8 annotations'
-      - run: make flake
-        name: 'Run flake8'
-      - uses: codespell-project/actions-codespell@v1.0
-        with:
-          path: ${{ env.CODESPELL_DIRS }}
-          skip: ${{ env.CODESPELL_SKIPS }}
-          builtin: 'clear,rare,informal,names'
-          ignore_words_file: 'ignore_words.txt'
-          uri_ignore_words_list: 'bu'
-        name: 'Run codespell'
diff --git a/.github/workflows/flake.yml b/.github/workflows/flake.yml
new file mode 100644
index 00000000000..df085952b5a
--- /dev/null
+++ b/.github/workflows/flake.yml
@@ -0,0 +1,33 @@
+name: 'flake'
+# https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#concurrency
+# https://docs.github.com/en/developers/webhooks-and-events/events/github-event-types#pullrequestevent
+# workflow name, PR number (empty on push), push ref (empty on PR)
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:
+  push:
+    branches:
+      - '*'
+  pull_request:
+    branches:
+      - '*'
+
+jobs:
+  style:
+    name: 'flake'
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+          architecture: 'x64'
+      - run: |
+          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install flake8
+        name: 'Install dependencies'
+      - uses: rbialon/flake8-annotations@v1
+        name: 'Setup flake8 annotations'
+      - run: make flake
+        name: 'Run flake8'

From 427edb8cd45d4b07f5a47ecfeb83642a2cd0810e Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 22:40:15 +0100
Subject: [PATCH 25/51] Remove flake and codespell from Azure

---
 azure-pipelines.yml | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 74332387a67..23927beb16c 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -54,12 +54,6 @@ stages:
         python -m pip install --progress-bar off --upgrade pip setuptools wheel
         python -m pip install --progress-bar off -r requirements_base.txt -r requirements_hdf5.txt -r requirements_testing.txt
       displayName: Install dependencies
-    - bash: |
-        make flake
-      displayName: make flake
-    - bash: |
-        make codespell-error
-      displayName: make codespell
     - bash: |
         make pydocstyle
       displayName: make pydocstyle

From aeb6ecf3386904d0f0c76383ffa3a1c0074b5396 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 8 Mar 2023 22:45:14 +0100
Subject: [PATCH 26/51] Ignore .ruff_cache/

---
 .gitignore | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 40c64c7bb65..c73ee6d5257 100644
--- a/.gitignore
+++ b/.gitignore
@@ -92,5 +92,5 @@ cover
 venv/
 *.json
 .hypothesis/
-
+.ruff_cache/
 .ipynb_checkpoints/

From a614a20e480ba2b9c006247ae288a824b01efdd9 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Thu, 9 Mar 2023 07:24:16 +0100
Subject: [PATCH 27/51] Enable W rules in Ruff

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 415ebdf26bb..288e9c14081 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,6 +5,7 @@ builtin = "clear,rare,informal,names,usage"
 skip = "doc/references.bib"
 
 [tool.ruff]
+select = ["E", "F", "W"]
 exclude = ["__init__.py", "constants.py", "fixes.py", "resources.py"]
 
 [tool.ruff.per-file-ignores]

From 903c94d97359c7efe7553cb182adedcdc0537a3b Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Thu, 9 Mar 2023 07:32:51 +0100
Subject: [PATCH 28/51] Enable pydocstyle in Ruff

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 288e9c14081..0abe9b129b9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,7 +5,7 @@ builtin = "clear,rare,informal,names,usage"
 skip = "doc/references.bib"
 
 [tool.ruff]
-select = ["E", "F", "W"]
+select = ["E", "F", "W", "D"]
 exclude = ["__init__.py", "constants.py", "fixes.py", "resources.py"]
 
 [tool.ruff.per-file-ignores]

From db5bdc4264b0dff336b9592a6014fc9a09ce94e8 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Thu, 9 Mar 2023 07:44:29 +0100
Subject: [PATCH 29/51] Ignore several pydocstyle rules

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 0abe9b129b9..c670cc4f38f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,6 +6,7 @@ skip = "doc/references.bib"
 
 [tool.ruff]
 select = ["E", "F", "W", "D"]
+ignore = ["D100", "D104", "D107", "D413"]
 exclude = ["__init__.py", "constants.py", "fixes.py", "resources.py"]
 
 [tool.ruff.per-file-ignores]

From 92fd63141da3cfcd9373b45e4074fde5caa52116 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Thu, 9 Mar 2023 08:19:57 +0100
Subject: [PATCH 30/51] Check for numpydoc style

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index c670cc4f38f..6790c6ff3eb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,7 +6,7 @@ skip = "doc/references.bib"
 
 [tool.ruff]
 select = ["E", "F", "W", "D"]
-ignore = ["D100", "D104", "D107", "D413"]
+ignore = ["D107", "D203", "D212", "D213", "D402", "D413", "D415", "D416", "D417"]
 exclude = ["__init__.py", "constants.py", "fixes.py", "resources.py"]
 
 [tool.ruff.per-file-ignores]

From fd3b8ba6bb38a187a61f9278f12cfe6f806d3670 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Thu, 9 Mar 2023 08:22:59 +0100
Subject: [PATCH 31/51] Ignore more D rules

---
 pyproject.toml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6790c6ff3eb..e83ab2a6c4d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,7 +6,8 @@ skip = "doc/references.bib"
 
 [tool.ruff]
 select = ["E", "F", "W", "D"]
-ignore = ["D107", "D203", "D212", "D213", "D402", "D413", "D415", "D416", "D417"]
+ignore = ["D107", "D203", "D212", "D213", "D402", "D413", "D415", "D416", "D417"]  # numpydoc style
+ignore-extend = ["D100", "D104", "D107", "D413"]
 exclude = ["__init__.py", "constants.py", "fixes.py", "resources.py"]
 
 [tool.ruff.per-file-ignores]

From 8b91fa37ccf47361b9c19797dcef4153ce72f482 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Thu, 9 Mar 2023 08:24:22 +0100
Subject: [PATCH 32/51] Fix key

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index e83ab2a6c4d..10ee16190f2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,7 +7,7 @@ skip = "doc/references.bib"
 [tool.ruff]
 select = ["E", "F", "W", "D"]
 ignore = ["D107", "D203", "D212", "D213", "D402", "D413", "D415", "D416", "D417"]  # numpydoc style
-ignore-extend = ["D100", "D104", "D107", "D413"]
+extend-ignore = ["D100", "D104", "D107", "D413"]
 exclude = ["__init__.py", "constants.py", "fixes.py", "resources.py"]
 
 [tool.ruff.per-file-ignores]

From 83895fea7e286dccbf314ab40eb5c10fc2896ff3 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Thu, 9 Mar 2023 08:45:38 +0100
Subject: [PATCH 33/51] Pydocstyle specific excludes

---
 pyproject.toml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 10ee16190f2..19029bbcc15 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,9 +6,13 @@ skip = "doc/references.bib"
 
 [tool.ruff]
 select = ["E", "F", "W", "D"]
-ignore = ["D107", "D203", "D212", "D213", "D402", "D413", "D415", "D416", "D417"]  # numpydoc style
-extend-ignore = ["D100", "D104", "D107", "D413"]
 exclude = ["__init__.py", "constants.py", "fixes.py", "resources.py"]
 
+[tool.ruff.pydocstyle]
+convention = "numpydoc"
+extend-ignore = ["D100", "D104", "D107", "D413"]
+ignore-decorators = ^(copy_.*_doc_to_|on_trait_change|cached_property|deprecated|property|.*setter).*
+extend-exclude = ^(?!\.|doc|tutorials|examples|logo|icons).*$
+
 [tool.ruff.per-file-ignores]
 "tutorials/time-freq/10_spectrum_class.py" = ["E501"]

From 18818f6ca8de308a1690a4e1c0eba3b1cc6c2fca Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Thu, 9 Mar 2023 08:49:47 +0100
Subject: [PATCH 34/51] Fix ignores

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 19029bbcc15..3096d7295bf 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,8 +11,8 @@ exclude = ["__init__.py", "constants.py", "fixes.py", "resources.py"]
 [tool.ruff.pydocstyle]
 convention = "numpydoc"
 extend-ignore = ["D100", "D104", "D107", "D413"]
-ignore-decorators = ^(copy_.*_doc_to_|on_trait_change|cached_property|deprecated|property|.*setter).*
-extend-exclude = ^(?!\.|doc|tutorials|examples|logo|icons).*$
+ignore-decorators = ["copy_.*_doc_to_.*", "on_trait_change.*", "cached_property.*", "deprecated.*", "property.*", ".*setter.*"]
+extend-exclude = ["doc", "tutorials", "examples", "logo", "icons"]
 
 [tool.ruff.per-file-ignores]
 "tutorials/time-freq/10_spectrum_class.py" = ["E501"]

From d2502d690f16a4407fb042548672dc8448fc9ad1 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Thu, 9 Mar 2023 08:51:04 +0100
Subject: [PATCH 35/51] Fix convention

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 3096d7295bf..73ac4e8de1f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,7 +9,7 @@ select = ["E", "F", "W", "D"]
 exclude = ["__init__.py", "constants.py", "fixes.py", "resources.py"]
 
 [tool.ruff.pydocstyle]
-convention = "numpydoc"
+convention = "numpy"
 extend-ignore = ["D100", "D104", "D107", "D413"]
 ignore-decorators = ["copy_.*_doc_to_.*", "on_trait_change.*", "cached_property.*", "deprecated.*", "property.*", ".*setter.*"]
 extend-exclude = ["doc", "tutorials", "examples", "logo", "icons"]

From 8e11f3e069aae482426530838e25c4a4fe2721ca Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Thu, 9 Mar 2023 08:52:37 +0100
Subject: [PATCH 36/51] Fix ignore

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 73ac4e8de1f..ca83504255d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,7 +10,7 @@ exclude = ["__init__.py", "constants.py", "fixes.py", "resources.py"]
 
 [tool.ruff.pydocstyle]
 convention = "numpy"
-extend-ignore = ["D100", "D104", "D107", "D413"]
+ignore = ["D100", "D104", "D107", "D413"]
 ignore-decorators = ["copy_.*_doc_to_.*", "on_trait_change.*", "cached_property.*", "deprecated.*", "property.*", ".*setter.*"]
 extend-exclude = ["doc", "tutorials", "examples", "logo", "icons"]
 

From 9af3e9e6199adba527eac0bcead6dad8d73634d4 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Thu, 9 Mar 2023 08:53:41 +0100
Subject: [PATCH 37/51] Move ignore

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index ca83504255d..d20edb766fc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,10 +7,10 @@ skip = "doc/references.bib"
 [tool.ruff]
 select = ["E", "F", "W", "D"]
 exclude = ["__init__.py", "constants.py", "fixes.py", "resources.py"]
+ignore = ["D100", "D104", "D107", "D413"]
 
 [tool.ruff.pydocstyle]
 convention = "numpy"
-ignore = ["D100", "D104", "D107", "D413"]
 ignore-decorators = ["copy_.*_doc_to_.*", "on_trait_change.*", "cached_property.*", "deprecated.*", "property.*", ".*setter.*"]
 extend-exclude = ["doc", "tutorials", "examples", "logo", "icons"]
 

From befaf1067d9f81bf8dd8a2084254f98ca84a53fb Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Thu, 9 Mar 2023 08:59:10 +0100
Subject: [PATCH 38/51] Remove excludes for pydocstyle

---
 pyproject.toml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index d20edb766fc..6989b098c8f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,7 +12,6 @@ ignore = ["D100", "D104", "D107", "D413"]
 [tool.ruff.pydocstyle]
 convention = "numpy"
 ignore-decorators = ["copy_.*_doc_to_.*", "on_trait_change.*", "cached_property.*", "deprecated.*", "property.*", ".*setter.*"]
-extend-exclude = ["doc", "tutorials", "examples", "logo", "icons"]
 
 [tool.ruff.per-file-ignores]
 "tutorials/time-freq/10_spectrum_class.py" = ["E501"]

From fbb4da8644d4f20eb6bec93b85a647236a6b8765 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 20 Apr 2023 18:10:11 -0400
Subject: [PATCH 39/51] FIX: Closer

---
 .pre-commit-config.yaml | 9 ++++++++-
 pyproject.toml          | 8 +++++++-
 2 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 0f41eb4fedc..34fcd8b01fe 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -8,9 +8,16 @@ repos:
 #     - id: black
 #       args: [--quiet]
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.0.254
+  rev: v0.0.262
   hooks:
     - id: ruff
+      files: ^mne/
+- repo: https://github.com/charliermarsh/ruff-pre-commit
+  rev: v0.0.262
+  hooks:
+    - id: ruff
+      args: ["--ignore=D103,D400"]
+      files: ^tutorials/|^examples/
 - repo: https://github.com/codespell-project/codespell
   rev: v2.2.3
   hooks:
diff --git a/pyproject.toml b/pyproject.toml
index 6989b098c8f..cc30610c6fb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,7 +11,13 @@ ignore = ["D100", "D104", "D107", "D413"]
 
 [tool.ruff.pydocstyle]
 convention = "numpy"
-ignore-decorators = ["copy_.*_doc_to_.*", "on_trait_change.*", "cached_property.*", "deprecated.*", "property.*", ".*setter.*"]
+ignore-decorators = [
+    "property",
+    "setter",
+    "mne.utils.copy_function_doc_to_method_doc",
+    "mne.utils.copy_doc",
+    "mne.utils.deprecated"
+]
 
 [tool.ruff.per-file-ignores]
 "tutorials/time-freq/10_spectrum_class.py" = ["E501"]

From 8a65b160ebb60a2cb87e245ffa1de4b0b741022f Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 20 Apr 2023 18:14:33 -0400
Subject: [PATCH 40/51] FIX: TOMLY

---
 pyproject.toml |  9 +++++++++
 setup.cfg      | 42 ------------------------------------------
 2 files changed, 9 insertions(+), 42 deletions(-)
 delete mode 100644 setup.cfg

diff --git a/pyproject.toml b/pyproject.toml
index cc30610c6fb..0b0ddf24cfd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,3 +21,12 @@ ignore-decorators = [
 
 [tool.ruff.per-file-ignores]
 "tutorials/time-freq/10_spectrum_class.py" = ["E501"]
+
+[tool.pytest.ini_options]
+addopts = """--durations=20 --doctest-modules -ra --cov-report= --tb=short \
+    --doctest-ignore-import-errors --junit-xml=junit-results.xml \
+    --ignore=doc --ignore=logo --ignore=examples --ignore=tutorials \
+    --ignore=mne/gui/_*.py --ignore=mne/icons --ignore=tools \
+    --ignore=mne/report/js_and_css \
+    --color=yes --capture=sys"""
+junit_family = "xunit2"
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index 396a8906cc0..00000000000
--- a/setup.cfg
+++ /dev/null
@@ -1,42 +0,0 @@
-[aliases]
-release = egg_info -RDb ''
-# Make sure the sphinx docs are built each time we do a dist.
-# bdist = build_sphinx bdist
-# sdist = build_sphinx sdist
-# Make sure a zip file is created each time we build the sphinx docs
-# build_sphinx = generate_help build_sphinx zip_help
-# Make sure the docs are uploaded when we do an upload
-# upload = upload upload_help
-
-[egg_info]
-# tag_build = .dev
-
-[bdist_rpm]
-doc_files = doc
-
-[flake8]
-exclude = __init__.py,constants.py,fixes.py,resources.py,*doc/auto_*,*doc/_build*,build/*
-ignore = W503,W504,I100,I101,I201,N806,E201,E202,E221,E222,E241
-# We add A for the array-spacing plugin, and ignore the E ones it covers above
-select = A,E,F,W,C
-# 10_spectrum_class.py has a wide rST table
-per-file-ignores =
-    tutorials/time-freq/10_spectrum_class.py:E501
-
-[tool:pytest]
-addopts =
-    --durations=20 --doctest-modules -ra --cov-report= --tb=short
-    --doctest-ignore-import-errors --junit-xml=junit-results.xml
-    --ignore=doc --ignore=logo --ignore=examples --ignore=tutorials
-    --ignore=mne/gui/_*.py --ignore=mne/icons --ignore=tools
-    --ignore=mne/report/js_and_css
-    --color=yes --capture=sys
-junit_family = xunit2
-
-[pydocstyle]
-convention = pep257
-match_dir = ^(?!\.|doc|tutorials|examples|logo|icons).*$
-match = (?!tests/__init__\.py|fixes).*\.py
-add-ignore = D100,D104,D107,D413
-add-select = D214,D215,D404,D405,D406,D407,D408,D409,D410,D411
-ignore-decorators = ^(copy_.*_doc_to_|on_trait_change|cached_property|deprecated|property|.*setter).*

From 4655f04cf7e1a8216cb8d073ce1d4b4785b3e9d7 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 20 Apr 2023 18:25:55 -0400
Subject: [PATCH 41/51] FIX: Reqs

---
 .github/workflows/flake.yml  | 33 ------------
 Makefile                     | 98 +++---------------------------------
 azure-pipelines.yml          |  8 +--
 doc/install/contributing.rst |  5 +-
 requirements_testing.txt     |  4 +-
 5 files changed, 11 insertions(+), 137 deletions(-)
 delete mode 100644 .github/workflows/flake.yml

diff --git a/.github/workflows/flake.yml b/.github/workflows/flake.yml
deleted file mode 100644
index df085952b5a..00000000000
--- a/.github/workflows/flake.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-name: 'flake'
-# https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#concurrency
-# https://docs.github.com/en/developers/webhooks-and-events/events/github-event-types#pullrequestevent
-# workflow name, PR number (empty on push), push ref (empty on PR)
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
-  cancel-in-progress: true
-on:
-  push:
-    branches:
-      - '*'
-  pull_request:
-    branches:
-      - '*'
-
-jobs:
-  style:
-    name: 'flake'
-    runs-on: ubuntu-20.04
-    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
-        with:
-          python-version: '3.9'
-          architecture: 'x64'
-      - run: |
-          python -m pip install --upgrade pip setuptools wheel
-          python -m pip install flake8
-        name: 'Install dependencies'
-      - uses: rbialon/flake8-annotations@v1
-        name: 'Setup flake8 annotations'
-      - run: make flake
-        name: 'Run flake8'
diff --git a/Makefile b/Makefile
index 944b059aa2e..d303908ec8f 100644
--- a/Makefile
+++ b/Makefile
@@ -2,7 +2,6 @@
 
 PYTHON ?= python
 PYTESTS ?= py.test
-CTAGS ?= ctags
 CODESPELL_SKIPS ?= "doc/_build,doc/auto_*,*.fif,*.eve,*.gz,*.tgz,*.zip,*.mat,*.stc,*.label,*.w,*.bz2,*.annot,*.sulc,*.log,*.local-copy,*.orig_avg,*.inflated_avg,*.gii,*.pyc,*.doctree,*.pickle,*.inv,*.png,*.edf,*.touch,*.thickness,*.nofix,*.volume,*.defect_borders,*.mgh,lh.*,rh.*,COR-*,FreeSurferColorLUT.txt,*.examples,.xdebug_mris_calc,bad.segments,BadChannels,*.hist,empty_file,*.orig,*.js,*.map,*.ipynb,searchindex.dat,install_mne_c.rst,plot_*.rst,*.rst.txt,c_EULA.rst*,*.html,gdf_encodes.txt,*.svg,references.bib,*.css,*.edf,*.bdf,*.vhdr"
 CODESPELL_DIRS ?= mne/ doc/ tutorials/ examples/
 all: clean inplace test test-doc
@@ -25,16 +24,6 @@ clean-cache:
 
 clean: clean-build clean-pyc clean-so clean-ctags clean-cache
 
-in: inplace # just a shortcut
-inplace:
-	$(PYTHON) setup.py build_ext -i
-
-wheel:
-	$(PYTHON) setup.py sdist bdist_wheel
-
-wheel_quiet:
-	$(PYTHON) setup.py -q sdist bdist_wheel
-
 sample_data:
 	@python -c "import mne; mne.datasets.sample.data_path(verbose=True);"
 
@@ -43,22 +32,6 @@ testing_data:
 
 pytest: test
 
-test: in
-	rm -f .coverage
-	$(PYTESTS) -m 'not ultraslowtest' mne
-
-test-verbose: in
-	rm -f .coverage
-	$(PYTESTS) -m 'not ultraslowtest' mne --verbose
-
-test-fast: in
-	rm -f .coverage
-	$(PYTESTS) -m 'not slowtest' mne
-
-test-full: in
-	rm -f .coverage
-	$(PYTESTS) mne
-
 test-no-network: in
 	sudo unshare -n -- sh -c 'MNE_SKIP_NETWORK_TESTS=1 py.test mne'
 
@@ -66,56 +39,20 @@ test-no-testing-data: in
 	@MNE_SKIP_TESTING_DATASET_TESTS=true \
 	$(PYTESTS) mne
 
-test-no-sample-with-coverage: in testing_data
-	rm -rf coverage .coverage
-	$(PYTESTS) --cov=mne --cov-report html:coverage
-
 test-doc: sample_data testing_data
 	$(PYTESTS) --doctest-modules --doctest-ignore-import-errors --doctest-glob='*.rst' ./doc/ --ignore=./doc/auto_examples --ignore=./doc/auto_tutorials --ignore=./doc/_build --ignore=./doc/conf.py --ignore=doc/sphinxext --fulltrace
 
-test-coverage: testing_data
-	rm -rf coverage .coverage
-	$(PYTESTS) --cov=mne --cov-report html:coverage
-# whats the difference with test-no-sample-with-coverage?
-
-test-mem: in testing_data
-	ulimit -v 1097152 && $(PYTESTS) mne
-
-trailing-spaces:
-	find . -name "*.py" | xargs perl -pi -e 's/[ \t]*$$//'
+pre-commit:
+	@pre-commit run -a
 
-ctags:
-	# make tags for symbol based navigation in emacs and vim
-	# Install with: sudo apt-get install exuberant-ctags
-	$(CTAGS) -R *
-
-upload-pipy:
-	python setup.py sdist bdist_egg register upload
-
-flake:
-	@if command -v flake8 > /dev/null; then \
-		echo "Running flake8"; \
-		flake8 --count; \
-	else \
-		echo "flake8 not found, please install it!"; \
-		exit 1; \
-	fi;
-	@echo "flake8 passed"
+# Aliases for stuff we used to support or users might think of
+ruff: pre-commit
+flake: pre-commit
+pep: pre-commit
 
 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)
 
-codespell-error:  # running on travis
-	@codespell --builtin clear,rare,informal,names,usage -i 0 -q 7 -S $(CODESPELL_SKIPS) --ignore-words=ignore_words.txt --uri-ignore-words-list=bu $(CODESPELL_DIRS)
-
-pydocstyle:
-	@echo "Running pydocstyle"
-	@pydocstyle mne
-
-docstring:
-	@echo "Running docstring tests"
-	@$(PYTESTS) --doctest-modules mne/tests/test_docstring_parameters.py
-
 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
 
@@ -125,26 +62,3 @@ check-readme: clean wheel_quiet
 nesting:
 	@echo "Running import nesting tests"
 	@$(PYTESTS) mne/tests/test_import_nesting.py
-
-pep:
-	@$(MAKE) -k flake pydocstyle docstring codespell-error check-manifest nesting check-readme
-
-manpages:
-	@echo "I: generating manpages"
-	set -e; mkdir -p _build/manpages && \
-	cd bin && for f in mne*; do \
-			descr=$$(grep -h -e "^ *'''" -e 'DESCRIP =' $$f -h | sed -e "s,.*' *\([^'][^']*\)'.*,\1,g" | head -n 1); \
-	PYTHONPATH=../ \
-			help2man -n "$$descr" --no-discard-stderr --no-info --version-string "$(uver)" ./$$f \
-			>| ../_build/manpages/$$f.1; \
-	done
-
-build-doc-dev:
-	cd doc; make clean
-	cd doc; DISPLAY=:1.0 xvfb-run -n 1 -s "-screen 0 1280x1024x24 -noreset -ac +extension GLX +render" make html_dev
-
-build-doc-stable:
-	cd doc; make clean
-	cd doc; DISPLAY=:1.0 xvfb-run -n 1 -s "-screen 0 1280x1024x24 -noreset -ac +extension GLX +render" make html_stable
-
-docstyle: pydocstyle
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 23927beb16c..6a515889731 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -55,12 +55,8 @@ stages:
         python -m pip install --progress-bar off -r requirements_base.txt -r requirements_hdf5.txt -r requirements_testing.txt
       displayName: Install dependencies
     - bash: |
-        make pydocstyle
-      displayName: make pydocstyle
-      condition: always()
-    - bash: |
-        make docstring
-      displayName: make docstring
+        make pre-commit
+      displayName: make ruff
       condition: always()
     - bash: |
         make nesting
diff --git a/doc/install/contributing.rst b/doc/install/contributing.rst
index e6efb6814f3..4de59a0d10c 100644
--- a/doc/install/contributing.rst
+++ b/doc/install/contributing.rst
@@ -694,7 +694,7 @@ Adhere to standard Python style guidelines
 All contributions to MNE-Python are checked against style guidelines described
 in `PEP 8`_. We also check for common coding errors (such as variables that are
 defined but never used). We allow very few exceptions to these guidelines, and
-use tools such as pep8_, pyflakes_, and flake8_ to check code style
+use tools such as ruff_ to check code style
 automatically. From the :file:`mne-python` root directory, you can check for
 style violations by running::
 
@@ -1097,8 +1097,7 @@ it can serve as a useful example of what to expect from the PR review process.
 .. linting
 
 .. _PEP 8: https://www.python.org/dev/peps/pep-0008/
-.. _pyflakes: https://pypi.org/project/pyflakes
-.. _Flake8: http://flake8.pycqa.org/
+.. _ruff: https://beta.ruff.rs/docs
 
 .. misc
 
diff --git a/requirements_testing.txt b/requirements_testing.txt
index 3344f4b409e..928eba49183 100644
--- a/requirements_testing.txt
+++ b/requirements_testing.txt
@@ -3,11 +3,9 @@ pytest
 pytest-cov
 pytest-timeout
 pytest-harvest
-flake8
-flake8-array-spacing
+ruff
 numpydoc
 codespell
-pydocstyle
 check-manifest
 twine
 wheel

From 593a6250a2a28ae6a7df8d8082c761b9cc78d35d Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 20 Apr 2023 18:27:49 -0400
Subject: [PATCH 42/51] FIX: Cleaner

---
 .pre-commit-config.yaml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 34fcd8b01fe..5ac5533802e 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,17 +7,23 @@ repos:
 #   hooks:
 #     - id: black
 #       args: [--quiet]
+
+# Ruff mne
 - repo: https://github.com/charliermarsh/ruff-pre-commit
   rev: v0.0.262
   hooks:
     - id: ruff
       files: ^mne/
+
+# Ruff tutorials and examples
 - repo: https://github.com/charliermarsh/ruff-pre-commit
   rev: v0.0.262
   hooks:
     - id: ruff
       args: ["--ignore=D103,D400"]
       files: ^tutorials/|^examples/
+
+# Codespell
 - repo: https://github.com/codespell-project/codespell
   rev: v2.2.3
   hooks:

From b4509079d3fb62a2a263c72c6d3294d608aecbea Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 21 Apr 2023 11:43:38 -0400
Subject: [PATCH 43/51] FIX: Fix em

---
 .pre-commit-config.yaml                                        | 2 ++
 examples/simulation/simulate_evoked_data.py                    | 2 +-
 .../simulation/simulated_raw_data_using_subject_anatomy.py     | 3 +--
 examples/visualization/topo_customized.py                      | 3 ++-
 mne/utils/check.py                                             | 1 +
 pyproject.toml                                                 | 3 +++
 6 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 5ac5533802e..b854d5d745f 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -13,6 +13,7 @@ repos:
   rev: v0.0.262
   hooks:
     - id: ruff
+      name: ruff mne
       files: ^mne/
 
 # Ruff tutorials and examples
@@ -20,6 +21,7 @@ repos:
   rev: v0.0.262
   hooks:
     - id: ruff
+      name: ruff tutorials and examples
       args: ["--ignore=D103,D400"]
       files: ^tutorials/|^examples/
 
diff --git a/examples/simulation/simulate_evoked_data.py b/examples/simulation/simulate_evoked_data.py
index 0d4cff6a6c3..b906d2df265 100644
--- a/examples/simulation/simulate_evoked_data.py
+++ b/examples/simulation/simulate_evoked_data.py
@@ -55,7 +55,7 @@
 
 
 def data_fun(times):
-    """Function to generate random source time courses"""
+    """Generate random source time courses."""
     return (50e-9 * np.sin(30. * times) *
             np.exp(- (times - 0.15 + 0.05 * rng.randn(1)) ** 2 / 0.01))
 
diff --git a/examples/simulation/simulated_raw_data_using_subject_anatomy.py b/examples/simulation/simulated_raw_data_using_subject_anatomy.py
index b78db66c965..0edb33e7d0f 100644
--- a/examples/simulation/simulated_raw_data_using_subject_anatomy.py
+++ b/examples/simulation/simulated_raw_data_using_subject_anatomy.py
@@ -124,8 +124,7 @@
 
 
 def data_fun(times, latency, duration):
-    """Function to generate source time courses for evoked responses,
-    parametrized by latency and duration."""
+    """Generate source time courses for evoked responses."""
     f = 15  # oscillating frequency, beta band [Hz]
     sigma = 0.375 * duration
     sinusoid = np.sin(2 * np.pi * f * (times - latency))
diff --git a/examples/visualization/topo_customized.py b/examples/visualization/topo_customized.py
index cc284431246..e9106a1e8d2 100644
--- a/examples/visualization/topo_customized.py
+++ b/examples/visualization/topo_customized.py
@@ -47,7 +47,8 @@
 
 
 def my_callback(ax, ch_idx):
-    """
+    """Handle axes callback.
+
     This block of code is executed once you click on one of the channel axes
     in the plot. To work with the viz internals, this function should only take
     two parameters, the axis and the channel or data index.
diff --git a/mne/utils/check.py b/mne/utils/check.py
index 6a66fb20edc..e351184680f 100644
--- a/mne/utils/check.py
+++ b/mne/utils/check.py
@@ -1122,6 +1122,7 @@ def _to_rgb(*args, name='color', alpha=False):
 
 @deprecated('has_nibabel is deprecated and will be removed in 1.5')
 def has_nibabel():
+    """Check if nibabel is installed."""
     return check_version('nibabel')  # pragma: no cover
 
 
diff --git a/pyproject.toml b/pyproject.toml
index 0b0ddf24cfd..69e29ff04e2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,6 +21,9 @@ ignore-decorators = [
 
 [tool.ruff.per-file-ignores]
 "tutorials/time-freq/10_spectrum_class.py" = ["E501"]
+"mne/datasets/*/*.py" = ["D103"]
+"mne/utils/tests/test_docs.py" = ["D101", "D411", "D410", "D414"]
+"examples/*/*.py" = ["D205"]
 
 [tool.pytest.ini_options]
 addopts = """--durations=20 --doctest-modules -ra --cov-report= --tb=short \

From 6416b6f7223cbe2d7301d661bf4542345447851b Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 21 Apr 2023 12:46:12 -0400
Subject: [PATCH 44/51] FIX: More

---
 Makefile                 | 3 +++
 requirements_testing.txt | 1 +
 2 files changed, 4 insertions(+)

diff --git a/Makefile b/Makefile
index d303908ec8f..c0e47ada7fb 100644
--- a/Makefile
+++ b/Makefile
@@ -24,6 +24,9 @@ clean-cache:
 
 clean: clean-build clean-pyc clean-so clean-ctags clean-cache
 
+wheel_quiet:
+	$(PYTHON) setup.py -q sdist bdist_wheel
+
 sample_data:
 	@python -c "import mne; mne.datasets.sample.data_path(verbose=True);"
 
diff --git a/requirements_testing.txt b/requirements_testing.txt
index 928eba49183..c8ff7b5c5fb 100644
--- a/requirements_testing.txt
+++ b/requirements_testing.txt
@@ -9,3 +9,4 @@ codespell
 check-manifest
 twine
 wheel
+pre-commit

From f1b7076db15addc74fcc297cb8b1700f84eb4aa3 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 21 Apr 2023 12:46:39 -0400
Subject: [PATCH 45/51] FIX: Install hooks

---
 azure-pipelines.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 96c486f2947..d56a77ca841 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -50,9 +50,10 @@ stages:
         addToPath: true
       displayName: 'Get Python'
     - bash: |
-        set -e
+        set -eo pipefail
         python -m pip install --progress-bar off --upgrade pip setuptools wheel
         python -m pip install --progress-bar off -r requirements_base.txt -r requirements_hdf5.txt -r requirements_testing.txt
+        pre-commit install --install-hooks
       displayName: Install dependencies
     - bash: |
         make pre-commit

From 1414b221c40aacc8f9ae104708758dc6566d55b4 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 21 Apr 2023 13:07:06 -0400
Subject: [PATCH 46/51] FIX: Ver

---
 azure-pipelines.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index d56a77ca841..e27e056aa3f 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -39,7 +39,7 @@ stages:
     pool:
       vmImage: 'ubuntu-latest'
     variables:
-      PYTHON_VERSION: '3.9'
+      PYTHON_VERSION: '3.11'
       PYTHON_ARCH: 'x64'
     steps:
     - bash: echo $(COMMIT_MSG)

From 1f297d68b30f34c96b45f3b69ec5b0bf56693cf1 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 21 Apr 2023 13:30:09 -0400
Subject: [PATCH 47/51] FIX: Instructions

---
 doc/install/contributing.rst | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/doc/install/contributing.rst b/doc/install/contributing.rst
index 78a778d49b7..7ec42192741 100644
--- a/doc/install/contributing.rst
+++ b/doc/install/contributing.rst
@@ -696,9 +696,14 @@ in `PEP 8`_. We also check for common coding errors (such as variables that are
 defined but never used). We allow very few exceptions to these guidelines, and
 use tools such as ruff_ to check code style
 automatically. From the :file:`mne-python` root directory, you can check for
-style violations by running::
+style violations by first installing pre-commit hook
 
-    $ make flake
+    $ pip install pre-commit
+    $ pre-commit install --install-hooks
+
+Then running::
+
+    $ make ruff
 
 in the shell. Several text editors or IDEs also have Python style checking,
 which can highlight style errors while you code (and train you to make those
@@ -748,7 +753,7 @@ but complete docstrings are appropriate when private functions/methods are
 relatively complex. To run some basic tests on documentation, you can use::
 
     $ pytest mne/tests/test_docstring_parameters.py
-    $ make docstyle
+    $ make ruff
 
 
 Cross-reference everywhere

From a9427fcd29450aeb05fb572732cb9036959f5d20 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 21 Apr 2023 13:31:51 -0400
Subject: [PATCH 48/51] FIX: Explain

---
 doc/install/contributing.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/install/contributing.rst b/doc/install/contributing.rst
index 7ec42192741..5dfa97aa004 100644
--- a/doc/install/contributing.rst
+++ b/doc/install/contributing.rst
@@ -703,7 +703,7 @@ style violations by first installing pre-commit hook
 
 Then running::
 
-    $ make ruff
+    $ make ruff  # alias for `pre-commit run -a`
 
 in the shell. Several text editors or IDEs also have Python style checking,
 which can highlight style errors while you code (and train you to make those

From 61f456244b1d4ef1688b004dbe64db30ff56dbe5 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 21 Apr 2023 18:05:11 -0400
Subject: [PATCH 49/51] Apply suggestions from code review

Co-authored-by: Daniel McCloy <dan@mccloy.info>
---
 .pre-commit-config.yaml      | 2 ++
 doc/install/contributing.rst | 2 +-
 pyproject.toml               | 7 ++++++-
 3 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b854d5d745f..4814c23d8eb 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -22,6 +22,8 @@ repos:
   hooks:
     - id: ruff
       name: ruff tutorials and examples
+      # D103: missing docstring in public function
+      # D400: docstring first line must end with period
       args: ["--ignore=D103,D400"]
       files: ^tutorials/|^examples/
 
diff --git a/doc/install/contributing.rst b/doc/install/contributing.rst
index 5dfa97aa004..f7b278fe7d7 100644
--- a/doc/install/contributing.rst
+++ b/doc/install/contributing.rst
@@ -696,7 +696,7 @@ in `PEP 8`_. We also check for common coding errors (such as variables that are
 defined but never used). We allow very few exceptions to these guidelines, and
 use tools such as ruff_ to check code style
 automatically. From the :file:`mne-python` root directory, you can check for
-style violations by first installing pre-commit hook
+style violations by first installing our pre-commit hook::
 
     $ pip install pre-commit
     $ pre-commit install --install-hooks
diff --git a/pyproject.toml b/pyproject.toml
index 69e29ff04e2..a04cb2bf2d6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,7 +7,12 @@ skip = "doc/references.bib"
 [tool.ruff]
 select = ["E", "F", "W", "D"]
 exclude = ["__init__.py", "constants.py", "fixes.py", "resources.py"]
-ignore = ["D100", "D104", "D107", "D413"]
+ignore = [
+    "D100", # Missing docstring in public module
+    "D104", # Missing docstring in public package
+    "D107", # Missing docstring in __init__
+    "D413", # Missing blank line after last section
+]
 
 [tool.ruff.pydocstyle]
 convention = "numpy"

From 2545bb6c0752c318e750ce57cb180e1aae408c2a Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 21 Apr 2023 18:05:55 -0400
Subject: [PATCH 50/51] Apply suggestions from code review

Co-authored-by: Daniel McCloy <dan@mccloy.info>
---
 pyproject.toml | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index a04cb2bf2d6..24c2c22b5f8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,10 +25,21 @@ ignore-decorators = [
 ]
 
 [tool.ruff.per-file-ignores]
-"tutorials/time-freq/10_spectrum_class.py" = ["E501"]
-"mne/datasets/*/*.py" = ["D103"]
-"mne/utils/tests/test_docs.py" = ["D101", "D411", "D410", "D414"]
-"examples/*/*.py" = ["D205"]
+"tutorials/time-freq/10_spectrum_class.py" = [
+    "E501" # line too long
+]
+"mne/datasets/*/*.py" = [
+    "D103", # Missing docstring in public function
+]
+"mne/utils/tests/test_docs.py" = [
+    "D101", # Missing docstring in public class
+    "D410", # Missing blank line after section
+    "D411", # Missing blank line before section
+    "D414", # Section has no content
+]
+"examples/*/*.py" = [
+    "D205", # 1 blank line required between summary line and description
+]
 
 [tool.pytest.ini_options]
 addopts = """--durations=20 --doctest-modules -ra --cov-report= --tb=short \

From d0c00a372cb266431db4e3fbf89b97d25f2c7991 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 21 Apr 2023 18:06:09 -0400
Subject: [PATCH 51/51] FIX: D107

---
 pyproject.toml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 24c2c22b5f8..b8b664ab193 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,7 +10,6 @@ exclude = ["__init__.py", "constants.py", "fixes.py", "resources.py"]
 ignore = [
     "D100", # Missing docstring in public module
     "D104", # Missing docstring in public package
-    "D107", # Missing docstring in __init__
     "D413", # Missing blank line after last section
 ]