Merge pull request #34 from ComputationalPhysiology/pre-commit-ci-upd…

…ate-config [pre-commit.ci] pre-commit autoupdate
ComputationalPhysiology · Aug 21, 2024 · 3991f86 · 3991f86
2 parents 5538151 + 71262d6
commit 3991f86
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Showing 4 changed files with 28 additions and 25 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -12,7 +12,7 @@ repos:
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.5.7'
+    rev: 'v0.6.1'
     hooks:
        # Run the linter.
       - id: ruff

diff --git a/docs/features.ipynb b/docs/features.ipynb
@@ -20,9 +20,9 @@
    "outputs": [],
    "source": [
     "from pathlib import Path\n",
-    "import matplotlib.pyplot as plt # For plotting\n",
-    "import mps # Package to load data\n",
-    "import mps_motion # Package for motion analysis\n",
+    "import matplotlib.pyplot as plt  # For plotting\n",
+    "import mps  # Package to load data\n",
+    "import mps_motion  # Package for motion analysis\n",
     "import ap_features as apf  # Package for analzying traces\n",
     "import numpy as np\n",
     "import logging\n",
@@ -124,11 +124,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "reference_frame_index = (\n",
-    "    mps_motion.motion_tracking.estimate_referece_image_from_velocity(\n",
-    "        t=data.time_stamps[:-5],\n",
-    "        v=v_mean_norm,\n",
-    "    )\n",
+    "reference_frame_index = mps_motion.motion_tracking.estimate_referece_image_from_velocity(\n",
+    "    t=data.time_stamps[:-5],\n",
+    "    v=v_mean_norm,\n",
     ")\n",
     "reference_frame = data.time_stamps[reference_frame_index]"
    ]
@@ -221,9 +219,11 @@
     "    t=data.time_stamps[start : end - spacing],\n",
     ")\n",
     "\n",
+    "\n",
     "def normalize(y):\n",
     "    return (y - np.min(y)) / (np.max(y) - np.min(y))\n",
     "\n",
+    "\n",
     "u_norm = normalize(u.y)\n",
     "v_norm = normalize(v.y)\n",
     "time = normalize(u.t)\n",
@@ -235,6 +235,7 @@
     "indices_u = [7, 16, 31, 43, 56]\n",
     "indices_v = [i - spacing // 2 for i in indices_u]\n",
     "\n",
+    "\n",
     "def arrow_annotate(axi, y, t1, t2, label):\n",
     "    mid_t = 0.5 * (t1 + t2)\n",
     "    axi.annotate(\n",
@@ -250,7 +251,8 @@
     "        size=\"large\",\n",
     "        bbox=dict(boxstyle=\"circle\", fc=\"w\", ec=\"k\"),\n",
     "    )\n",
-    "    \n",
+    "\n",
+    "\n",
     "def adjust_spines(ax, spines):\n",
     "    for loc, spine in ax.spines.items():\n",
     "        if loc in spines:\n",
@@ -271,6 +273,7 @@
     "        # no xaxis ticks\n",
     "        ax.xaxis.set_ticks([])\n",
     "\n",
+    "\n",
     "fig, ax = plt.subplots(2, 1, sharex=True, figsize=(8, 8))\n",
     "\n",
     "\n",
@@ -293,7 +296,7 @@
     "        size=\"large\",\n",
     "        bbox=dict(boxstyle=\"circle\", fc=\"w\", ec=\"k\"),\n",
     "    )\n",
-    "    \n",
+    "\n",
     "# Beat duratiom\n",
     "arrow_annotate(\n",
     "    ax[0],\n",
@@ -372,12 +375,12 @@
     "ax[1].set_xticks(points)\n",
     "ax[1].set_xticklabels([f\"{vi:.0f}\" for vi in t_points])\n",
     "ax[1].set_xlabel(\"Time [ms]\")\n",
-    "    \n",
+    "\n",
     "for axi in ax:\n",
     "    axi.grid()\n",
-    "    \n",
-    "ax[0].set_ylabel(\"Displacement [\\u00B5m]\")\n",
-    "ax[1].set_ylabel(\"Velocity [\\u00B5m / s]\")\n",
+    "\n",
+    "ax[0].set_ylabel(\"Displacement [\\u00b5m]\")\n",
+    "ax[1].set_ylabel(\"Velocity [\\u00b5m / s]\")\n",
     "\n",
     "legend = \"\\n\".join(\n",
     "    [\n",

diff --git a/docs/gui.ipynb b/docs/gui.ipynb
@@ -36,6 +36,7 @@
    "outputs": [],
    "source": [
     "from IPython.display import Video\n",
+    "\n",
     "Video(\"mps-motion-gui.mp4\", width=700, height=400)"
    ]
   }

diff --git a/docs/quickstart.ipynb b/docs/quickstart.ipynb
@@ -47,9 +47,9 @@
    "outputs": [],
    "source": [
     "from pathlib import Path\n",
-    "import matplotlib.pyplot as plt # For plotting\n",
-    "import mps # Package to load data\n",
-    "import mps_motion # Package for motion analysis\n",
+    "import matplotlib.pyplot as plt  # For plotting\n",
+    "import mps  # Package to load data\n",
+    "import mps_motion  # Package for motion analysis\n",
     "import logging\n",
     "\n",
     "# Set loglevel to WARNING to not spill the output\n",
@@ -167,11 +167,9 @@
    "outputs": [],
    "source": [
     "v_norm = v.norm().mean().compute()\n",
-    "reference_frame_index = (\n",
-    "    mps_motion.motion_tracking.estimate_referece_image_from_velocity(\n",
-    "        t=data.time_stamps[:-5],\n",
-    "        v=v_norm,\n",
-    "    )\n",
+    "reference_frame_index = mps_motion.motion_tracking.estimate_referece_image_from_velocity(\n",
+    "    t=data.time_stamps[:-5],\n",
+    "    v=v_norm,\n",
     ")\n",
     "reference_frame = data.time_stamps[reference_frame_index]\n",
     "print(f\"Found reference frame at index {reference_frame_index} and time {reference_frame:.2f}\")"
@@ -233,7 +231,7 @@
    "outputs": [],
    "source": [
     "u_norm = u.norm()\n",
-    "print(u_norm) # FrameSequence((817, 469, 267), dx=0.8125, scale=0.4)"
+    "print(u_norm)  # FrameSequence((817, 469, 267), dx=0.8125, scale=0.4)"
    ]
   },
   {
@@ -313,6 +311,7 @@
    "outputs": [],
    "source": [
     "from IPython.display import Video\n",
+    "\n",
     "Video(movie_path)"
    ]
   },
@@ -376,7 +375,7 @@
    "outputs": [],
    "source": [
     "# Green-Lagrange strain\n",
-    "print(mech.E) # TensorFrameSequence((817, 469, 267, 2, 2), dx=0.8125, scale=0.4)\n",
+    "print(mech.E)  # TensorFrameSequence((817, 469, 267, 2, 2), dx=0.8125, scale=0.4)\n",
     "\n",
     "# Plot the X-component of the Green-Lagrange strain\n",
     "fig, ax = plt.subplots()\n",