From 56d1e84a1a7730bdef4d62cfcf6cb8287ed8f383 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?C=C3=A9line=20Provins?= <celine.provins@unil.ch>
Date: Fri, 17 May 2024 21:09:00 +0200
Subject: [PATCH] sty: ruff

---
 docs/notebooks/Tutorial.ipynb | 23 ++++++++++++++++-------
 1 file changed, 16 insertions(+), 7 deletions(-)

diff --git a/docs/notebooks/Tutorial.ipynb b/docs/notebooks/Tutorial.ipynb
index af9ebe68..29840f9b 100644
--- a/docs/notebooks/Tutorial.ipynb
+++ b/docs/notebooks/Tutorial.ipynb
@@ -22,7 +22,8 @@
    "source": [
     "# Silence warnings\n",
     "import warnings\n",
-    "warnings.simplefilter(action='ignore', category=UserWarning)\n",
+    "\n",
+    "warnings.simplefilter(action=\"ignore\", category=UserWarning)\n",
     "\n",
     "# Load data\n",
     "import glob\n",
@@ -40,7 +41,7 @@
     "\n",
     "# Load functional connectivity matrices\n",
     "fc_matrices = []\n",
-    "connectivity_files = glob.glob(op.join(output, '**', '*connectivity.tsv'), recursive=True)\n",
+    "connectivity_files = glob.glob(op.join(output, \"**\", \"*connectivity.tsv\"), recursive=True)\n",
     "for idx, connectivity_file in enumerate(connectivity_files):\n",
     "    fc_matrix = np.loadtxt(connectivity_file, delimiter=\"\\t\")\n",
     "    flattened = fc_matrix.reshape(-1)\n",
@@ -73,7 +74,8 @@
    "source": [
     "# Silence futureWarnings\n",
     "import warnings\n",
-    "warnings.simplefilter(action='ignore', category=FutureWarning)\n",
+    "\n",
+    "warnings.simplefilter(action=\"ignore\", category=FutureWarning)\n",
     "\n",
     "import seaborn as sns\n",
     "import matplotlib.pyplot as plt\n",
@@ -84,6 +86,7 @@
     "FC_FIGURE_SIZE: tuple = (70, 45)\n",
     "LABELSIZE: int = 60\n",
     "\n",
+    "\n",
     "def group_reportlet_fc_dist(fc_matrices: list[np.ndarray], output: str) -> None:\n",
     "    \"\"\"Plot and save the functional connectivity density distributions.\n",
     "\n",
@@ -96,7 +99,7 @@
     "    \"\"\"\n",
     "    _, ax = plt.subplots(figsize=FC_FIGURE_SIZE)\n",
     "    ax.tick_params(labelsize=LABELSIZE)\n",
-    "    mpl.rcParams['legend.fontsize'] = LABELSIZE\n",
+    "    mpl.rcParams[\"legend.fontsize\"] = LABELSIZE\n",
     "\n",
     "    fc_df = pd.DataFrame(fc_matrices, columns=[\"value\", \"session\"])\n",
     "\n",
@@ -111,8 +114,8 @@
     "    )\n",
     "\n",
     "    plt.tick_params(labelsize=LABELSIZE)\n",
-    "    plt.xlabel('Value', fontsize=LABELSIZE+4)\n",
-    "    plt.ylabel('Density', fontsize=LABELSIZE+4)\n",
+    "    plt.xlabel(\"Value\", fontsize=LABELSIZE + 4)\n",
+    "    plt.ylabel(\"Density\", fontsize=LABELSIZE + 4)\n",
     "\n",
     "    # Ensure the labels are within the figure\n",
     "    plt.tight_layout()\n",
@@ -122,6 +125,8 @@
     "\n",
     "    plt.savefig(op.join(output, savename))\n",
     "    plt.close()\n",
+    "\n",
+    "\n",
     "group_reportlet_fc_dist(fc_matrices, output)"
    ]
   },
@@ -157,6 +162,8 @@
     "\n",
     "# The literature indicates that less than 5 minutes of fMRI signal after censoring is not enough to reliably estimate functional connectivity.\n",
     "DURATION_CUT_OFF = 300\n",
+    "\n",
+    "\n",
     "# Generate each reportlets\n",
     "def group_report_censoring(good_timepoints_df, output) -> None:\n",
     "    \"\"\"\n",
@@ -233,6 +240,8 @@
     "        filename=op.join(output, \"reportlets\", \"group_desc-censoring_bold.html\"),\n",
     "        auto_open=False,\n",
     "    )\n",
+    "\n",
+    "\n",
     "group_report_censoring(good_timepoints_df, output)"
    ]
   },
@@ -356,7 +365,7 @@
     "    out_filename=\"group_report.html\",\n",
     "    bootstrap_file=op.join(\"data\", \"reports-spec.yml\"),\n",
     ")\n",
-    "robj.generate_report()\n"
+    "robj.generate_report()"
    ]
   },
   {