From 4f8436a5414131f4e04f742eee83f4ad35c76a24 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Wed, 17 Sep 2025 14:44:36 +0200
Subject: [PATCH 01/14] maint: run `ruff check`

---
 .github/workflows/pythonpackage.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index 1ec634f7..f2fc1d7d 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -79,7 +79,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - run: pipx run ruff format --diff
+    - run: |
+        pipx run ruff check --output-format=github
+        pipx run ruff format --diff
 
   codespell:
     runs-on: ubuntu-latest

From b011355c0db956f4297285b9a0f68d45d1403ca8 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Wed, 17 Sep 2025 14:49:34 +0200
Subject: [PATCH 02/14] maint: update ruff rule selection

- No need to specify `F` and `E` rules with `extend-select`.
- Update rules to ignore.
---
 pyproject.toml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index cf5917f5..b929f1cc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -193,8 +193,6 @@ line-length = 99
 
 [tool.ruff.lint]
 extend-select = [
-  "F",
-  "E",
   "W",
   "I",
   "UP",
@@ -202,10 +200,9 @@ extend-select = [
   "S",
   "BLE",
   "B",
-  "A", # "CPY",
   "C4",
   "DTZ",
-  "T10", # "EM",
+  "T10",
   "EXE",
   "FA",
   "ISC",
@@ -216,6 +213,7 @@ extend-select = [
 ignore = [
   "F841",
   "S311", # We are not using random for cryptographic purposes
+  "S310",
   "S603",
 ]
 
@@ -224,6 +222,7 @@ inline-quotes = "single"
 
 [tool.ruff.lint.extend-per-file-ignores]
 "*/test_*.py" = ["S101"]
+"docs/notebooks/*.ipynb" = ["B018", "F401", "F821"]
 "docs/source/conf.py" = ["A001"]
 "mriqc/bin/nib_hash.py" = ["S324"]
 "mriqc/config.py" = ["S105"]

From 8547540354b9b94694521e71fe7cb2aa3da3851f Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Wed, 17 Sep 2025 14:50:03 +0200
Subject: [PATCH 03/14] Apply ruff/pycodestyle rule E741

E741 Ambiguous variable name: `l`
---
 docs/notebooks/MRIQC Web API.ipynb | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/docs/notebooks/MRIQC Web API.ipynb b/docs/notebooks/MRIQC Web API.ipynb
index b0e6cfcd..bfd59e5c 100644
--- a/docs/notebooks/MRIQC Web API.ipynb	
+++ b/docs/notebooks/MRIQC Web API.ipynb	
@@ -224,11 +224,11 @@
     "print(\n",
     "    ','.join(\n",
     "        [\n",
-    "            l\n",
-    "            for l in df_t1w.columns\n",
-    "            if not l.startswith('_')\n",
-    "            and not l.startswith('bids_meta')\n",
-    "            and not l.startswith('provenance')\n",
+    "            line\n",
+    "            for line in df_t1w.columns\n",
+    "            if not line.startswith('_')\n",
+    "            and not line.startswith('bids_meta')\n",
+    "            and not line.startswith('provenance')\n",
     "        ]\n",
     "    )\n",
     ")"
@@ -291,11 +291,11 @@
     "print(\n",
     "    ','.join(\n",
     "        [\n",
-    "            l\n",
-    "            for l in df_bold.columns\n",
-    "            if not l.startswith('_')\n",
-    "            and not l.startswith('bids_meta')\n",
-    "            and not l.startswith('provenance')\n",
+    "            line\n",
+    "            for line in df_bold.columns\n",
+    "            if not line.startswith('_')\n",
+    "            and not line.startswith('bids_meta')\n",
+    "            and not line.startswith('provenance')\n",
     "        ]\n",
     "    )\n",
     ")"

From a91d78a2f58b7e596736e44ef6a8657c4aef0ab5 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Wed, 17 Sep 2025 14:52:05 +0200
Subject: [PATCH 04/14] Apply ruff/pycodestyle rule E401

E401 Multiple imports on one line
---
 docs/notebooks/MRIQC Web API.ipynb  | 3 ++-
 docs/notebooks/finding_spikes.ipynb | 4 +++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/docs/notebooks/MRIQC Web API.ipynb b/docs/notebooks/MRIQC Web API.ipynb
index bfd59e5c..d56a8adb 100644
--- a/docs/notebooks/MRIQC Web API.ipynb	
+++ b/docs/notebooks/MRIQC Web API.ipynb	
@@ -21,7 +21,8 @@
    "source": [
     "import pandas as pd\n",
     "from json import load\n",
-    "import urllib.request, json\n",
+    "import urllib.request\n",
+    "import json\n",
     "from pandas.io.json import json_normalize\n",
     "import seaborn as sns\n",
     "import pylab as plt\n",
diff --git a/docs/notebooks/finding_spikes.ipynb b/docs/notebooks/finding_spikes.ipynb
index a2e68867..41643412 100644
--- a/docs/notebooks/finding_spikes.ipynb
+++ b/docs/notebooks/finding_spikes.ipynb
@@ -8,7 +8,9 @@
    },
    "outputs": [],
    "source": [
-    "import nibabel, nipy, nilearn\n",
+    "import nibabel\n",
+    "import nipy\n",
+    "import nilearn\n",
     "from nipy.labs.mask import compute_mask\n",
     "from nilearn.masking import compute_epi_mask\n",
     "from nilearn.image import mean_img, new_img_like\n",

From 1ee311a4f0cf1cdca8ae6bc3082ccb6fcf354e9d Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Wed, 17 Sep 2025 14:53:04 +0200
Subject: [PATCH 05/14] Apply ruff/pycodestyle rule W605

W605 Invalid escape sequence
---
 docs/notebooks/Paper-v1.0.ipynb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/notebooks/Paper-v1.0.ipynb b/docs/notebooks/Paper-v1.0.ipynb
index 5fbda5fe..3ed6feb6 100644
--- a/docs/notebooks/Paper-v1.0.ipynb
+++ b/docs/notebooks/Paper-v1.0.ipynb
@@ -213,7 +213,7 @@
     "    draw_line(mean + std, ax=ax, color=color, extend=True)\n",
     "\n",
     "    ax.annotate(\n",
-    "        '$\\mu$=%0.3f' % mean,\n",
+    "        r'$\\mu$=%0.3f' % mean,\n",
     "        xy=(mean_coord[0], 0.75 * ymax),\n",
     "        xytext=(-35, 30),\n",
     "        textcoords='offset points',\n",
@@ -239,7 +239,7 @@
     "        arrowprops=dict(arrowstyle='<->'),\n",
     "    )\n",
     "    ax.annotate(\n",
-    "        '$2\\sigma$=%0.3f' % (2 * std),\n",
+    "        r'$2\\sigma$=%0.3f' % (2 * std),\n",
     "        xy=(mean_coord[0], 0.70 * ymax),\n",
     "        xytext=(-25, -12),\n",
     "        textcoords='offset points',\n",

From 719e939dfeb18b05bb6c8e99479cc4f3a8be0ac4 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Wed, 17 Sep 2025 14:53:42 +0200
Subject: [PATCH 06/14] Apply ruff/pycodestyle rule I001

I001 Import block is un-sorted or un-formatted
---
 docs/notebooks/MRIQC Web API.ipynb          | 16 +++++++++-------
 docs/notebooks/Paper-v1.0.ipynb             |  5 +++--
 docs/notebooks/Paper-v2.0.ipynb             |  8 ++++----
 docs/notebooks/Supplemental Materials.ipynb |  1 +
 docs/notebooks/finding_spikes.ipynb         | 12 ++++++------
 mriqc/cli/run.py                            |  2 +-
 6 files changed, 24 insertions(+), 20 deletions(-)

diff --git a/docs/notebooks/MRIQC Web API.ipynb b/docs/notebooks/MRIQC Web API.ipynb
index d56a8adb..b73760f4 100644
--- a/docs/notebooks/MRIQC Web API.ipynb	
+++ b/docs/notebooks/MRIQC Web API.ipynb	
@@ -19,15 +19,16 @@
    },
    "outputs": [],
    "source": [
-    "import pandas as pd\n",
-    "from json import load\n",
-    "import urllib.request\n",
     "import json\n",
-    "from pandas.io.json import json_normalize\n",
-    "import seaborn as sns\n",
-    "import pylab as plt\n",
     "import multiprocessing as mp\n",
+    "import urllib.request\n",
+    "from json import load\n",
+    "\n",
     "import numpy as np\n",
+    "import pandas as pd\n",
+    "import pylab as plt\n",
+    "import seaborn as sns\n",
+    "from pandas.io.json import json_normalize\n",
     "\n",
     "%matplotlib inline"
    ]
@@ -151,8 +152,9 @@
    ],
    "source": [
     "import datetime\n",
-    "from dateutil import parser\n",
+    "\n",
     "import matplotlib.dates as mdates\n",
+    "from dateutil import parser\n",
     "\n",
     "dates_t1w = [parser.parse(d) for d in df_t1w['_created'].values]\n",
     "dates_t1w.sort()\n",
diff --git a/docs/notebooks/Paper-v1.0.ipynb b/docs/notebooks/Paper-v1.0.ipynb
index 3ed6feb6..52aee2f9 100644
--- a/docs/notebooks/Paper-v1.0.ipynb
+++ b/docs/notebooks/Paper-v1.0.ipynb
@@ -11,10 +11,11 @@
     "%matplotlib inline\n",
     "%load_ext autoreload\n",
     "%autoreload 2\n",
-    "import matplotlib.pyplot as plt\n",
     "import os.path as op\n",
-    "import pandas as pd\n",
+    "\n",
+    "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
+    "import pandas as pd\n",
     "import seaborn as sn\n",
     "\n",
     "sn.set(style='whitegrid')"
diff --git a/docs/notebooks/Paper-v2.0.ipynb b/docs/notebooks/Paper-v2.0.ipynb
index 02f2c03e..8cc52a21 100644
--- a/docs/notebooks/Paper-v2.0.ipynb
+++ b/docs/notebooks/Paper-v2.0.ipynb
@@ -24,12 +24,12 @@
     "%load_ext autoreload\n",
     "%autoreload 2\n",
     "import os.path as op\n",
+    "\n",
     "import numpy as np\n",
     "import pandas as pd\n",
-    "from pkg_resources import resource_filename as pkgrf\n",
-    "\n",
+    "from mriqc.classifier.data import combine_datasets, read_dataset\n",
     "from mriqc.viz import misc as mviz\n",
-    "from mriqc.classifier.data import read_dataset, combine_datasets\n",
+    "from pkg_resources import resource_filename as pkgrf\n",
     "\n",
     "# Where the outputs should be saved\n",
     "outputs_path = '../../mriqc-data/'\n",
@@ -776,8 +776,8 @@
    "outputs": [],
    "source": [
     "import matplotlib.pyplot as plt\n",
-    "from mriqc.viz.utils import plot_slice\n",
     "import nibabel as nb\n",
+    "from mriqc.viz.utils import plot_slice\n",
     "\n",
     "for im, z in fn_clear:\n",
     "    image_path = op.join(ds030_path, 'sub-%s' % im, 'anat', 'sub-%s_T1w.nii.gz' % im)\n",
diff --git a/docs/notebooks/Supplemental Materials.ipynb b/docs/notebooks/Supplemental Materials.ipynb
index 0758f348..965a30a4 100644
--- a/docs/notebooks/Supplemental Materials.ipynb	
+++ b/docs/notebooks/Supplemental Materials.ipynb	
@@ -23,6 +23,7 @@
     "%load_ext autoreload\n",
     "%autoreload 2\n",
     "import os.path as op\n",
+    "\n",
     "import numpy as np\n",
     "import pandas as pd\n",
     "from mriqc.viz import misc as mviz\n",
diff --git a/docs/notebooks/finding_spikes.ipynb b/docs/notebooks/finding_spikes.ipynb
index 41643412..b7d42d90 100644
--- a/docs/notebooks/finding_spikes.ipynb
+++ b/docs/notebooks/finding_spikes.ipynb
@@ -9,15 +9,15 @@
    "outputs": [],
    "source": [
     "import nibabel\n",
-    "import nipy\n",
     "import nilearn\n",
-    "from nipy.labs.mask import compute_mask\n",
-    "from nilearn.masking import compute_epi_mask\n",
-    "from nilearn.image import mean_img, new_img_like\n",
+    "import nipy\n",
+    "import numpy as np\n",
     "import pylab as plt\n",
     "import seaborn as sns\n",
-    "from nilearn.plotting import plot_epi, plot_anat, plot_roi\n",
-    "import numpy as np\n",
+    "from nilearn.image import mean_img, new_img_like\n",
+    "from nilearn.masking import compute_epi_mask\n",
+    "from nilearn.plotting import plot_anat, plot_epi, plot_roi\n",
+    "from nipy.labs.mask import compute_mask\n",
     "\n",
     "%matplotlib inline"
    ]
diff --git a/mriqc/cli/run.py b/mriqc/cli/run.py
index efbe345d..bd872f28 100644
--- a/mriqc/cli/run.py
+++ b/mriqc/cli/run.py
@@ -35,11 +35,11 @@ def format_elapsed_time(elapsed_timedelta):
 def main(argv=None):
     """Entry point for MRIQC's CLI."""
     import atexit
+    import datetime
     import gc
     import os
     import sys
     import time
-    import datetime
     from tempfile import mkstemp
 
     from mriqc import config, messages

From 39378170120d0e318ee215a6afcd989064d19479 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Wed, 17 Sep 2025 14:54:27 +0200
Subject: [PATCH 07/14] Apply ruff/flake8-comprehensions rule C408

C408 Unnecessary `dict()` call (rewrite as a literal)
---
 docs/notebooks/Paper-v1.0.ipynb | 51 +++++++++++++++++++--------------
 1 file changed, 29 insertions(+), 22 deletions(-)

diff --git a/docs/notebooks/Paper-v1.0.ipynb b/docs/notebooks/Paper-v1.0.ipynb
index 52aee2f9..165b769b 100644
--- a/docs/notebooks/Paper-v1.0.ipynb
+++ b/docs/notebooks/Paper-v1.0.ipynb
@@ -221,23 +221,23 @@
     "        va='center',\n",
     "        color='w',\n",
     "        size=14,\n",
-    "        bbox=dict(boxstyle='round', fc=color, ec='none', color='none', lw=0),\n",
-    "        arrowprops=dict(\n",
-    "            arrowstyle='wedge,tail_width=0.8',\n",
-    "            lw=0,\n",
-    "            patchA=None,\n",
-    "            patchB=None,\n",
-    "            fc=color,\n",
-    "            ec='none',\n",
-    "            relpos=(0.5, 0.5),\n",
-    "        ),\n",
+    "        bbox={'boxstyle': 'round', 'fc': color, 'ec': 'none', 'color': 'none', 'lw': 0},\n",
+    "        arrowprops={\n",
+    "            'arrowstyle': 'wedge,tail_width=0.8',\n",
+    "            'lw': 0,\n",
+    "            'patchA': None,\n",
+    "            'patchB': None,\n",
+    "            'fc': color,\n",
+    "            'ec': 'none',\n",
+    "            'relpos': (0.5, 0.5),\n",
+    "        },\n",
     "    )\n",
     "    sigmay = 0.70 * ymax\n",
     "    ax.annotate(\n",
     "        s='',\n",
     "        xy=(mean - std, sigmay),\n",
     "        xytext=(mean + std, sigmay),\n",
-    "        arrowprops=dict(arrowstyle='<->'),\n",
+    "        arrowprops={'arrowstyle': '<->'},\n",
     "    )\n",
     "    ax.annotate(\n",
     "        r'$2\\sigma$=%0.3f' % (2 * std),\n",
@@ -247,7 +247,14 @@
     "        va='center',\n",
     "        color='k',\n",
     "        size=12,\n",
-    "        bbox=dict(boxstyle='round', fc='w', ec='none', color='none', alpha=0.7, lw=0),\n",
+    "        bbox={\n",
+    "            'boxstyle': 'round',\n",
+    "            'fc': 'w',\n",
+    "            'ec': 'none',\n",
+    "            'color': 'none',\n",
+    "            'alpha': 0.7,\n",
+    "            'lw': 0,\n",
+    "        },\n",
     "    )\n",
     "\n",
     "    if ds030_score is not None:\n",
@@ -260,16 +267,16 @@
     "            va='center',\n",
     "            color='w',\n",
     "            size=16,\n",
-    "            bbox=dict(boxstyle='round', fc=color, ec='none', color='none', lw=0),\n",
-    "            arrowprops=dict(\n",
-    "                arrowstyle='wedge,tail_width=0.8',\n",
-    "                lw=0,\n",
-    "                patchA=None,\n",
-    "                patchB=None,\n",
-    "                fc=color,\n",
-    "                ec='none',\n",
-    "                relpos=(0.5, 0.5),\n",
-    "            ),\n",
+    "            bbox={'boxstyle': 'round', 'fc': color, 'ec': 'none', 'color': 'none', 'lw': 0},\n",
+    "            arrowprops={\n",
+    "                'arrowstyle': 'wedge,tail_width=0.8',\n",
+    "                'lw': 0,\n",
+    "                'patchA': None,\n",
+    "                'patchB': None,\n",
+    "                'fc': color,\n",
+    "                'ec': 'none',\n",
+    "                'relpos': (0.5, 0.5),\n",
+    "            },\n",
     "        )\n",
     "\n",
     "\n",

From 5cc3b829f841d8e0b8d4b7e40c5a6044e2448e49 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Wed, 17 Sep 2025 14:55:12 +0200
Subject: [PATCH 08/14] Apply ruff/flake8-comprehensions rule C413

C413 Unnecessary `list()` call around `sorted()`
---
 docs/notebooks/Paper-v1.0.ipynb             | 2 +-
 docs/notebooks/Paper-v2.0.ipynb             | 2 +-
 docs/notebooks/Supplemental Materials.ipynb | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/notebooks/Paper-v1.0.ipynb b/docs/notebooks/Paper-v1.0.ipynb
index 165b769b..5d102774 100644
--- a/docs/notebooks/Paper-v1.0.ipynb
+++ b/docs/notebooks/Paper-v1.0.ipynb
@@ -32,7 +32,7 @@
     "from mriqc.classifier import data as mcd\n",
     "\n",
     "abide, _ = mcd.read_dataset(x_path, y_path, rate_label='rater_1')\n",
-    "sites = list(sorted(set(abide.site.values.ravel())))\n",
+    "sites = sorted(set(abide.site.values.ravel()))\n",
     "\n",
     "fmt = r'{site} & \\pixmat{{{size[0]:d}$\\pm${sr[0]:d}}}{{{size[1]:d}$\\pm${sr[1]:d}}}{{{size[2]:d}$\\pm${sr[1]:d}}}'\n",
     "fmt += r'& \\pixmat[mm]{{{sp[0]:.2f}$\\pm${spr[0]:.2f}}}{{{sp[1]:.2f}$\\pm${spr[1]:.2f}}}{{{sp[2]:.2f}$\\pm${spr[1]:.2f}}}'\n",
diff --git a/docs/notebooks/Paper-v2.0.ipynb b/docs/notebooks/Paper-v2.0.ipynb
index 8cc52a21..cc522033 100644
--- a/docs/notebooks/Paper-v2.0.ipynb
+++ b/docs/notebooks/Paper-v2.0.ipynb
@@ -63,7 +63,7 @@
     "rater_types = {'rater_1': float, 'rater_2': float, 'rater_3': float}\n",
     "mdata = pd.read_csv(y_path, index_col=False, dtype=rater_types)\n",
     "\n",
-    "sites = list(sorted(list(set(mdata.site.values.ravel().tolist()))))"
+    "sites = sorted(list(set(mdata.site.values.ravel().tolist())))"
    ]
   },
   {
diff --git a/docs/notebooks/Supplemental Materials.ipynb b/docs/notebooks/Supplemental Materials.ipynb
index 965a30a4..c599b0a1 100644
--- a/docs/notebooks/Supplemental Materials.ipynb	
+++ b/docs/notebooks/Supplemental Materials.ipynb	
@@ -48,7 +48,7 @@
     "rater_types = {'rater_1': float, 'rater_2': float, 'rater_3': float}\n",
     "mdata = pd.read_csv(y_path, index_col=False, dtype=rater_types)\n",
     "\n",
-    "sites = list(sorted(list(set(mdata.site.values.ravel().tolist()))))"
+    "sites = sorted(list(set(mdata.site.values.ravel().tolist())))"
    ]
   },
   {

From b47c5ebfe87b2c06e58b6f7a5a4040b1c527f52d Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Wed, 17 Sep 2025 14:56:03 +0200
Subject: [PATCH 09/14] Apply ruff/flake8-comprehensions rule C414

C414 Unnecessary `list()` call within `sorted()`
---
 docs/notebooks/Paper-v1.0.ipynb             | 2 +-
 docs/notebooks/Paper-v2.0.ipynb             | 2 +-
 docs/notebooks/Supplemental Materials.ipynb | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/notebooks/Paper-v1.0.ipynb b/docs/notebooks/Paper-v1.0.ipynb
index 5d102774..18cd62e3 100644
--- a/docs/notebooks/Paper-v1.0.ipynb
+++ b/docs/notebooks/Paper-v1.0.ipynb
@@ -404,7 +404,7 @@
    },
    "outputs": [],
    "source": [
-    "sites = sorted(list(set(loso_outer.site.ravel().tolist())))\n",
+    "sites = sorted(set(loso_outer.site.ravel().tolist()))\n",
     "palette = sn.color_palette('husl', len(sites))\n",
     "fig = plt.figure()\n",
     "for i, site in enumerate(sites):\n",
diff --git a/docs/notebooks/Paper-v2.0.ipynb b/docs/notebooks/Paper-v2.0.ipynb
index cc522033..2e444171 100644
--- a/docs/notebooks/Paper-v2.0.ipynb
+++ b/docs/notebooks/Paper-v2.0.ipynb
@@ -63,7 +63,7 @@
     "rater_types = {'rater_1': float, 'rater_2': float, 'rater_3': float}\n",
     "mdata = pd.read_csv(y_path, index_col=False, dtype=rater_types)\n",
     "\n",
-    "sites = sorted(list(set(mdata.site.values.ravel().tolist())))"
+    "sites = sorted(set(mdata.site.values.ravel().tolist()))"
    ]
   },
   {
diff --git a/docs/notebooks/Supplemental Materials.ipynb b/docs/notebooks/Supplemental Materials.ipynb
index c599b0a1..dc680d8d 100644
--- a/docs/notebooks/Supplemental Materials.ipynb	
+++ b/docs/notebooks/Supplemental Materials.ipynb	
@@ -48,7 +48,7 @@
     "rater_types = {'rater_1': float, 'rater_2': float, 'rater_3': float}\n",
     "mdata = pd.read_csv(y_path, index_col=False, dtype=rater_types)\n",
     "\n",
-    "sites = sorted(list(set(mdata.site.values.ravel().tolist())))"
+    "sites = sorted(set(mdata.site.values.ravel().tolist()))"
    ]
   },
   {

From dd212a08a111d5f73f24ae22220b68e5d6e1c8a9 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Wed, 17 Sep 2025 14:56:38 +0200
Subject: [PATCH 10/14] Apply ruff/flake8-comprehensions rule C420

C420 Unnecessary dict comprehension for iterable; use `dict.fromkeys` instead
---
 mriqc/bin/dfcheck.py   | 2 +-
 mriqc/reports/group.py | 4 +---
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/mriqc/bin/dfcheck.py b/mriqc/bin/dfcheck.py
index 832b3fd5..346b6a68 100644
--- a/mriqc/bin/dfcheck.py
+++ b/mriqc/bin/dfcheck.py
@@ -40,7 +40,7 @@ def read_iqms(feat_file):
     feat_file = Path(feat_file)
 
     if feat_file.suffix == '.csv':
-        x_df = pd.read_csv(feat_file, index_col=False, dtype={col: str for col in BIDS_COMP})
+        x_df = pd.read_csv(feat_file, index_col=False, dtype=dict.fromkeys(BIDS_COMP, str))
         # Find present bids bits and sort by them
         bids_comps_present = list(set(x_df.columns) & set(BIDS_COMP))
         bids_comps_present = [bit for bit in BIDS_COMP if bit in bids_comps_present]
diff --git a/mriqc/reports/group.py b/mriqc/reports/group.py
index 4fa17772..4ef5e7fe 100644
--- a/mriqc/reports/group.py
+++ b/mriqc/reports/group.py
@@ -45,9 +45,7 @@ def gen_html(csv_file, mod, csv_failed=None, out_file=None):
     load_data = Loader('mriqc')
 
     if csv_file.suffix == '.csv':
-        dataframe = pd.read_csv(
-            csv_file, index_col=False, dtype={comp: object for comp in BIDS_COMP}
-        )
+        dataframe = pd.read_csv(csv_file, index_col=False, dtype=dict.fromkeys(BIDS_COMP, object))
 
         id_labels = list(set(BIDS_COMP) & set(dataframe.columns))
         dataframe['label'] = dataframe[id_labels].apply(_format_labels, args=(id_labels,), axis=1)

From 924ff8bea9c16d5bc32cf10be6e30663e2ba4c78 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Wed, 17 Sep 2025 14:57:17 +0200
Subject: [PATCH 11/14] Apply ruff/flake8-pytest-style PT001

PT001 Use `@pytest.fixture` over `@pytest.fixture()`
---
 mriqc/conftest.py                 | 6 +++---
 mriqc/qc/tests/test_anatomical.py | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/mriqc/conftest.py b/mriqc/conftest.py
index 7d0d55a7..da06ce4b 100644
--- a/mriqc/conftest.py
+++ b/mriqc/conftest.py
@@ -70,16 +70,16 @@ def expand_namespace(doctest_namespace):
     tmpdir.cleanup()
 
 
-@pytest.fixture()
+@pytest.fixture
 def testdata_path():
     return _datadir
 
 
-@pytest.fixture()
+@pytest.fixture
 def workdir():
     return None if test_workdir is None else Path(test_workdir)
 
 
-@pytest.fixture()
+@pytest.fixture
 def outdir():
     return None if test_output_dir is None else Path(test_output_dir)
diff --git a/mriqc/qc/tests/test_anatomical.py b/mriqc/qc/tests/test_anatomical.py
index b89fa1aa..5fa4799b 100644
--- a/mriqc/qc/tests/test_anatomical.py
+++ b/mriqc/qc/tests/test_anatomical.py
@@ -60,7 +60,7 @@ def get_data(self, sigma, noise='normal'):
         return test_data, wmdata, bgdata
 
 
-@pytest.fixture()
+@pytest.fixture
 def gtruth():
     return GroundTruth()
 

From 2f0a013ca05c5280c1acc773889ae336312eea64 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Wed, 17 Sep 2025 15:22:14 +0200
Subject: [PATCH 12/14] Apply ruff/pyupgrade rule UP031

UP031 Use format specifiers instead of percent format
---
 docs/notebooks/MRIQC Web API.ipynb          |  9 ++++-----
 docs/notebooks/Paper-v1.0.ipynb             |  2 +-
 docs/notebooks/Paper-v2.0.ipynb             | 14 +++++++-------
 docs/notebooks/Supplemental Materials.ipynb |  4 ++--
 mriqc/bin/fs2gif.py                         | 13 +++++--------
 mriqc/synthstrip/model.py                   |  4 ++--
 6 files changed, 21 insertions(+), 25 deletions(-)

diff --git a/docs/notebooks/MRIQC Web API.ipynb b/docs/notebooks/MRIQC Web API.ipynb
index b73760f4..f0e10716 100644
--- a/docs/notebooks/MRIQC Web API.ipynb	
+++ b/docs/notebooks/MRIQC Web API.ipynb	
@@ -64,14 +64,13 @@
     "            query = []\n",
     "\n",
     "            if software is not None:\n",
-    "                query.append('\"provenance.software\":\"%s\"' % software)\n",
+    "                query.append(f'\"provenance.software\":\"{software}\"')\n",
     "\n",
     "            if version != '*':\n",
-    "                query.append('\"provenance.version\":\"%s\"' % version)\n",
+    "                query.append(f'\"provenance.version\":\"{version}\"')\n",
     "\n",
-    "            page_url = url_root.format(\n",
-    "                modality=modality, query='where={%s}&page=%d' % (','.join(query), page)\n",
-    "            )\n",
+    "            where = ','.join(query)\n",
+    "            page_url = url_root.format(modality=modality, query=f'where={where}&page={page}')\n",
     "            with urllib.request.urlopen(page_url) as url:\n",
     "                data = json.loads(url.read().decode())\n",
     "                dfs.append(json_normalize(data['_items']))\n",
diff --git a/docs/notebooks/Paper-v1.0.ipynb b/docs/notebooks/Paper-v1.0.ipynb
index 18cd62e3..955f09a8 100644
--- a/docs/notebooks/Paper-v1.0.ipynb
+++ b/docs/notebooks/Paper-v1.0.ipynb
@@ -214,7 +214,7 @@
     "    draw_line(mean + std, ax=ax, color=color, extend=True)\n",
     "\n",
     "    ax.annotate(\n",
-    "        r'$\\mu$=%0.3f' % mean,\n",
+    "        rf'$\\mu$={mean:0.3f}',\n",
     "        xy=(mean_coord[0], 0.75 * ymax),\n",
     "        xytext=(-35, 30),\n",
     "        textcoords='offset points',\n",
diff --git a/docs/notebooks/Paper-v2.0.ipynb b/docs/notebooks/Paper-v2.0.ipynb
index 2e444171..8547cf67 100644
--- a/docs/notebooks/Paper-v2.0.ipynb
+++ b/docs/notebooks/Paper-v2.0.ipynb
@@ -283,14 +283,14 @@
     "    y1, y2, out_file=op.join(outputs_path, 'figures', 'fig02-irv.pdf')\n",
     ")\n",
     "\n",
-    "print(\"Cohen's Kappa %f\" % cohen_kappa_score(y1, y2))\n",
+    "print(f\"Cohen's Kappa {cohen_kappa_score(y1, y2):f}\")\n",
     "\n",
     "y1 = overlap.rater_1.values.ravel()\n",
     "y1[y1 == 0] = 1\n",
     "\n",
     "y2 = overlap.rater_2.values.ravel()\n",
     "y2[y2 == 0] = 1\n",
-    "print(\"Cohen's Kappa (binarized): %f\" % cohen_kappa_score(y1, y2))"
+    "print(f\"Cohen's Kappa (binarized): {cohen_kappa_score(y1, y2):f}\")"
    ]
   },
   {
@@ -667,7 +667,7 @@
     "fig = plt.figure(figsize=(20, 6))\n",
     "# plt.title(\"Feature importance plot\")\n",
     "sn.boxplot(x='Feature', y='Importance', data=pd.DataFrame(df), linewidth=1, notch=True)\n",
-    "plt.xlabel('Features selected (%d)' % len(features))\n",
+    "plt.xlabel(f'Features selected ({len(features)})')\n",
     "# plt.bar(range(nft), importances[indices],\n",
     "#        color=\"r\", yerr=std[indices], align=\"center\")\n",
     "plt.xticks(range(nft))\n",
@@ -780,13 +780,13 @@
     "from mriqc.viz.utils import plot_slice\n",
     "\n",
     "for im, z in fn_clear:\n",
-    "    image_path = op.join(ds030_path, 'sub-%s' % im, 'anat', 'sub-%s_T1w.nii.gz' % im)\n",
+    "    image_path = op.join(ds030_path, f'sub-{im}', 'anat', f'sub-{im}_T1w.nii.gz')\n",
     "    imdata = nb.load(image_path).get_data()\n",
     "\n",
     "    fig, ax = plt.subplots()\n",
     "    plot_slice(imdata[..., z], annotate=True)\n",
     "    fig.savefig(\n",
-    "        op.join(outputs_path, 'figures', 'fig-06_sub-%s_slice-%03d.svg' % (im, z)),\n",
+    "        op.join(outputs_path, 'figures', f'fig-06_sub-{im}_slice-{z:03}.svg'),\n",
     "        dpi=300,\n",
     "        bbox_inches='tight',\n",
     "    )\n",
@@ -807,13 +807,13 @@
     "    ('50073', 162),\n",
     "]\n",
     "for im, z in fp_clear:\n",
-    "    image_path = op.join(ds030_path, 'sub-%s' % im, 'anat', 'sub-%s_T1w.nii.gz' % im)\n",
+    "    image_path = op.join(ds030_path, f'sub-{im}', 'anat', f'sub-{im}_T1w.nii.gz')\n",
     "    imdata = nb.load(image_path).get_data()\n",
     "\n",
     "    fig, ax = plt.subplots()\n",
     "    plot_slice(imdata[..., z], annotate=True)\n",
     "    fig.savefig(\n",
-    "        op.join(outputs_path, 'figures', 'fig-06_sub-%s_slice-%03d.svg' % (im, z)),\n",
+    "        op.join(outputs_path, 'figures', f'fig-06_sub-{im}_slice-{z:03}.svg'),\n",
     "        dpi=300,\n",
     "        bbox_inches='tight',\n",
     "    )\n",
diff --git a/docs/notebooks/Supplemental Materials.ipynb b/docs/notebooks/Supplemental Materials.ipynb
index dc680d8d..5068aaa0 100644
--- a/docs/notebooks/Supplemental Materials.ipynb	
+++ b/docs/notebooks/Supplemental Materials.ipynb	
@@ -87,14 +87,14 @@
     "    out_file=op.join(outputs_path, 'figures', 'suppl-intrarv.pdf'),\n",
     ")\n",
     "\n",
-    "print(\"Cohen's Kappa %f\" % cohen_kappa_score(y1, y2))\n",
+    "print(f\"Cohen's Kappa {cohen_kappa_score(y1, y2):f}\")\n",
     "\n",
     "y1 = overlap.rater_2.values.ravel()\n",
     "y1[y1 == 0] = 1\n",
     "\n",
     "y2 = overlap.rater_3.values.ravel()\n",
     "y2[y2 == 0] = 1\n",
-    "print(\"Cohen's Kappa (binarized): %f\" % cohen_kappa_score(y1, y2))"
+    "print(f\"Cohen's Kappa (binarized): {cohen_kappa_score(y1, y2):f}\")"
    ]
   },
   {
diff --git a/mriqc/bin/fs2gif.py b/mriqc/bin/fs2gif.py
index 762a13d8..18d5a712 100644
--- a/mriqc/bin/fs2gif.py
+++ b/mriqc/bin/fs2gif.py
@@ -125,8 +125,7 @@ def main():
             with open(tcl_file, 'w') as tclfp:
                 tclfp.write(tcl_contents)
                 tclfp.write(
-                    'for { set slice %d } { $slice < %d } { incr slice } {'
-                    % (bbox_min[2], bbox_max[2])
+                    f'for {{ set slice {bbox_min[2]} }} {{ $slice < {bbox_max[2]} }} {{ incr slice }} {{'
                 )
                 tclfp.write('    SetSlice $slice\n')
                 tclfp.write('    RedrawScreen\n')
@@ -170,10 +169,9 @@ def main():
                 tclfp.write(tcl_contents)
                 tclfp.write('SetZoomLevel 2')
                 tclfp.write(
-                    'for { set slice %d } { $slice < %d } { incr slice } {'
-                    % (bbox_min[2], bbox_max[2])
+                    'for {{ set slice {bbox_min[2]} }} {{ $slice < {bbox_max[2]} }} {{ incr slice }} {{'
                 )
-                tclfp.write('    SetZoomCenter %d %d $slice\n' % (center[0] + 30, center[1] - 10))
+                tclfp.write(f'    SetZoomCenter {center[0] + 30} {center[1] - 10} $slice\n')
                 tclfp.write('    SetSlice $slice\n')
                 tclfp.write('    RedrawScreen\n')
                 tclfp.write(f'    SaveTIFF [format "{tmp_sub}/{subid}-lh-%03d.tif" $i]\n')
@@ -195,10 +193,9 @@ def main():
                 tclfp.write(tcl_contents)
                 tclfp.write('SetZoomLevel 2')
                 tclfp.write(
-                    'for { set slice %d } { $slice < %d } { incr slice } {'
-                    % (bbox_min[2], bbox_max[2])
+                    'for {{ set slice {bbox_min[2]} }} {{ $slice < {bbox_max[2]} }} {{ incr slice }} {{'
                 )
-                tclfp.write('    SetZoomCenter %d %d $slice\n' % (center[0] - 30, center[1] - 10))
+                tclfp.write(f'    SetZoomCenter {center[0] - 30} {center[1] - 10} $slice\n')
                 tclfp.write('    SetSlice $slice\n')
                 tclfp.write('    RedrawScreen\n')
                 tclfp.write(f'    SaveTIFF [format "{tmp_sub}/{subid}-rh-%03d.tif" $slice]\n')
diff --git a/mriqc/synthstrip/model.py b/mriqc/synthstrip/model.py
index 3081d2d7..74eba9cf 100644
--- a/mriqc/synthstrip/model.py
+++ b/mriqc/synthstrip/model.py
@@ -89,7 +89,7 @@ def __init__(
             max_pool = [max_pool] * self.nb_levels
 
         # cache downsampling / upsampling operations
-        MaxPooling = getattr(nn, 'MaxPool%dd' % ndims)
+        MaxPooling = getattr(nn, f'MaxPool{ndims}d')
         self.pooling = [MaxPooling(s) for s in max_pool]
         self.upsampling = [nn.Upsample(scale_factor=s, mode='nearest') for s in max_pool]
 
@@ -164,7 +164,7 @@ class ConvBlock(nn.Module):
     def __init__(self, ndims, in_channels, out_channels, stride=1, activation='leaky'):
         super().__init__()
 
-        Conv = getattr(nn, 'Conv%dd' % ndims)
+        Conv = getattr(nn, f'Conv{ndims}d')
         self.conv = Conv(in_channels, out_channels, 3, stride, 1)
         if activation == 'leaky':
             self.activation = nn.LeakyReLU(0.2)

From 675996966762f6551bbbb3377fefcc8d604ecaaa Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Wed, 17 Sep 2025 15:26:12 +0200
Subject: [PATCH 13/14] Apply ruff/pyupgrade rule UP035

UP035 Import from `collections.abc` instead
---
 mriqc/config.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/mriqc/config.py b/mriqc/config.py
index 898cf94a..c1aca569 100644
--- a/mriqc/config.py
+++ b/mriqc/config.py
@@ -93,10 +93,11 @@
 import os
 import pickle
 import sys
+from collections.abc import Iterable
 from contextlib import suppress
 from pathlib import Path
 from time import strftime
-from typing import TYPE_CHECKING, Any, Iterable
+from typing import TYPE_CHECKING, Any
 from uuid import uuid4
 
 try:

From 595401ed34164b4671d7426c10134839f8139adc Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Wed, 17 Sep 2025 15:28:08 +0200
Subject: [PATCH 14/14] Apply ruff/flake8-import-conventions rule ICN001

ICN001 `seaborn` should be imported as `sns`
---
 docs/notebooks/Paper-v1.0.ipynb | 18 +++++++++---------
 docs/notebooks/Paper-v2.0.ipynb | 14 +++++++-------
 2 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/docs/notebooks/Paper-v1.0.ipynb b/docs/notebooks/Paper-v1.0.ipynb
index 955f09a8..ba0655d8 100644
--- a/docs/notebooks/Paper-v1.0.ipynb
+++ b/docs/notebooks/Paper-v1.0.ipynb
@@ -16,9 +16,9 @@
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "import pandas as pd\n",
-    "import seaborn as sn\n",
+    "import seaborn as sns\n",
     "\n",
-    "sn.set(style='whitegrid')"
+    "sns.set(style='whitegrid')"
    ]
   },
   {
@@ -192,7 +192,7 @@
     "        ax = plt.gca()\n",
     "\n",
     "    outer_score = data.loc[data[score].notnull(), [score, 'zscored']]\n",
-    "    sn.distplot(\n",
+    "    sns.distplot(\n",
     "        outer_score.loc[outer_score.zscored == zscored, score],\n",
     "        hist=True,\n",
     "        norm_hist=True,\n",
@@ -318,12 +318,12 @@
    },
    "outputs": [],
    "source": [
-    "sn.set(style='whitegrid')\n",
+    "sns.set(style='whitegrid')\n",
     "\n",
     "fig = plt.figure(figsize=(20, 8))\n",
     "ax1 = plt.subplot2grid((2, 4), (0, 0), colspan=2, rowspan=2)\n",
     "\n",
-    "sn.violinplot(\n",
+    "sns.violinplot(\n",
     "    x='Classifier',\n",
     "    y='AUC',\n",
     "    hue='Split scheme',\n",
@@ -390,8 +390,8 @@
    "outputs": [],
    "source": [
     "zscoreddf = loso_outer.loc[loso_outer.zscored == 0, ['auc', 'acc', 'site']]\n",
-    "palette = sn.color_palette('cubehelix', len(set(zscoreddf.site)))\n",
-    "sn.pairplot(\n",
+    "palette = sns.color_palette('cubehelix', len(set(zscoreddf.site)))\n",
+    "sns.pairplot(\n",
     "    zscoreddf.loc[zscoreddf.auc.notnull(), ['auc', 'acc', 'site']], hue='site', palette=palette\n",
     ")"
    ]
@@ -405,12 +405,12 @@
    "outputs": [],
    "source": [
     "sites = sorted(set(loso_outer.site.ravel().tolist()))\n",
-    "palette = sn.color_palette('husl', len(sites))\n",
+    "palette = sns.color_palette('husl', len(sites))\n",
     "fig = plt.figure()\n",
     "for i, site in enumerate(sites):\n",
     "    sitedf = loso_outer.loc[loso_outer.site == site]\n",
     "    accdf = sitedf.loc[sitedf.zscored == 0]\n",
-    "    sn.distplot(accdf.acc.values.ravel(), bins=20, kde=0, label=site, color=palette[i])\n",
+    "    sns.distplot(accdf.acc.values.ravel(), bins=20, kde=0, label=site, color=palette[i])\n",
     "\n",
     "fig.gca().legend()\n",
     "fig.gca().set_xlim([0.5, 1.0])"
diff --git a/docs/notebooks/Paper-v2.0.ipynb b/docs/notebooks/Paper-v2.0.ipynb
index 8547cf67..0fb4f959 100644
--- a/docs/notebooks/Paper-v2.0.ipynb
+++ b/docs/notebooks/Paper-v2.0.ipynb
@@ -309,7 +309,7 @@
    "outputs": [],
    "source": [
     "import matplotlib.pyplot as plt\n",
-    "import seaborn as sn\n",
+    "import seaborn as sns\n",
     "\n",
     "rfc_acc = [\n",
     "    0.842,\n",
@@ -391,13 +391,13 @@
     "\n",
     "fig = plt.figure(figsize=(10, 3))\n",
     "ax2 = plt.subplot2grid((1, 4), (0, 3))\n",
-    "plot = sn.violinplot(\n",
+    "plot = sns.violinplot(\n",
     "    data=df, x='Model', y='accuracy', ax=ax2, palette=colors, bw=0.1, linewidth=0.7\n",
     ")\n",
     "for i in range(dim):\n",
     "    ax2.axhline(np.average(allvals[i]), ls='--', color=colors[i], lw=0.8)\n",
     "#     ax2.axhline(np.percentile(allvals[i], 50), ls='--', color=colors[i], lw=.8)\n",
-    "# sn.swarmplot(x=\"model\", y=\"accuracy\", data=df, color=\"w\", alpha=.5, ax=ax2);\n",
+    "# sns.swarmplot(x=\"model\", y=\"accuracy\", data=df, color=\"w\", alpha=.5, ax=ax2);\n",
     "ax2.yaxis.tick_right()\n",
     "ax2.set_ylabel('')\n",
     "ax2.set_xticklabels(ax2.get_xticklabels(), rotation=40)\n",
@@ -506,7 +506,7 @@
     "\n",
     "fig = plt.figure(figsize=(10, 3))\n",
     "ax2 = plt.subplot2grid((1, 4), (0, 3))\n",
-    "plot = sn.violinplot(data=df, x='Model', y='auc', ax=ax2, palette=colors, bw=0.1, linewidth=0.7)\n",
+    "plot = sns.violinplot(data=df, x='Model', y='auc', ax=ax2, palette=colors, bw=0.1, linewidth=0.7)\n",
     "for i in range(dim):\n",
     "    ax2.axhline(np.average(allvals[i]), ls='--', color=colors[i], lw=0.8)\n",
     "\n",
@@ -584,10 +584,10 @@
    },
    "outputs": [],
    "source": [
-    "import seaborn as sn\n",
+    "import seaborn as sns\n",
     "from sklearn.externals.joblib import load as loadpkl\n",
     "\n",
-    "sn.set_style('white')\n",
+    "sns.set_style('white')\n",
     "\n",
     "# Get the RFC\n",
     "estimator = loadpkl(\n",
@@ -666,7 +666,7 @@
     "        df['Importance'] += [tree.feature_importances_[i]]\n",
     "fig = plt.figure(figsize=(20, 6))\n",
     "# plt.title(\"Feature importance plot\")\n",
-    "sn.boxplot(x='Feature', y='Importance', data=pd.DataFrame(df), linewidth=1, notch=True)\n",
+    "sns.boxplot(x='Feature', y='Importance', data=pd.DataFrame(df), linewidth=1, notch=True)\n",
     "plt.xlabel(f'Features selected ({len(features)})')\n",
     "# plt.bar(range(nft), importances[indices],\n",
     "#        color=\"r\", yerr=std[indices], align=\"center\")\n",