fix: resolve ruff linting issues and add CI workflow (sensorium-competition#133)

* fix: resolve ruff (v0.15.6 ) linting issues and add CI workflow

* ci: exclude examples folder from ruff check

* removed unwanted addition, made the workflow to be consistent with other ,removed orphaned comment,change on class

* fix: apply ruff auto-fixes to experanto source files

* fix: convert dict() calls to literals in tests, remove C408 per-file-ignore

* remove outdated sensorium example notebooks

---------

Co-authored-by: github-actions <github-actions@github.com>
Co-authored-by: Polina Turishcheva <49938348+pollytur@users.noreply.github.com>

Author: 3 people

.github/workflows/ruff.yml

@@ -0,0 +1,29 @@
+name: CI - Ruff Linting
+
+on:
+  push:
+    branches:
+      - '**'
+  pull_request:
+    branches:
+      - '**'
+
+jobs:
+  ruff:
+    name: Ruff Linting
+    runs-on: ubuntu-latest
+    if: |
+      github.event_name == 'push' ||
+      (
+        github.event_name == 'pull_request' &&
+        github.repository != github.event.pull_request.head.repo.full_name
+      )
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Run Ruff
+        uses: astral-sh/ruff-action@v3
+        with:
+          version: "0.15.6"
+          args: "check"

.gitignore

@@ -129,6 +129,7 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+*env/
 
 # Spyder project settings
 .spyderproject
@@ -164,4 +165,4 @@ cython_debug/
 *.sif
 *.bak
 
-docs/source/generated/
+docs/source/generated/

docs/source/conf.py

@@ -78,7 +78,6 @@
     "cv2",
     "pandas",
     "hydra",
-    "omegaconf",
     "jaxtyping",
     "plotly",
     "optree",

examples/dandi_experanto_example.ipynb

@@ -137,7 +137,7 @@
     },
     {
       "cell_type": "code",
-      "execution_count": 3,
+      "execution_count": null,
       "metadata": {
         "id": "QYrgfZC2J573"
       },
@@ -158,7 +158,7 @@
     },
     {
       "cell_type": "code",
-      "execution_count": 4,
+      "execution_count": null,
       "metadata": {
         "id": "t8hE0WuTO10X"
       },
@@ -189,7 +189,7 @@
         "        elif \"ImageSeries\" in t or \"TwoPhotonSeries\" in t:\n",
         "            modalities[name.lower()] = \"ScreenInterpolator\"\n",
         "\n",
-        "    for mod_name, module in nwb.processing.items():\n",
+        "    for _mod_name, module in nwb.processing.items():\n",
         "        for dname, dobj in module.data_interfaces.items():\n",
         "            t = type(dobj).__name__\n",
         "            if \"LFP\" in t:\n",
@@ -1149,7 +1149,7 @@
     },
     {
       "cell_type": "code",
-      "execution_count": 27,
+      "execution_count": null,
       "metadata": {
         "colab": {
           "base_uri": "https://localhost:8080/",
@@ -1180,7 +1180,7 @@
         "          \"50 ms — balanced (default-like)\",\n",
         "          \"200 ms — smooth firing rate estimate, low resolution\"]\n",
         "\n",
-        "for ax, w, label in zip(axes, windows, labels):\n",
+        "for ax, w, label in zip(axes, windows, labels, strict=False):\n",
         "    si = SpikeInterpolator(\n",
         "        \"experanto_000623/spikes\",\n",
         "        cache_data=True,\n",
@@ -1214,7 +1214,7 @@
     },
     {
       "cell_type": "code",
-      "execution_count": 28,
+      "execution_count": null,
       "metadata": {
         "colab": {
           "base_uri": "https://localhost:8080/",
@@ -1247,7 +1247,7 @@
         "seq_lfp = SequenceInterpolator(\"experanto_000623/lfp_macro\")\n",
         "t_window = np.linspace(t_623[0], t_623[0] + 10, max(n_points))  # 10s window\n",
         "\n",
-        "for ax, n, label in zip(axes, n_points, labels):\n",
+        "for ax, n, label in zip(axes, n_points, labels, strict=False):\n",
         "    t_query = np.linspace(t_623[0], t_623[0] + 10, n)\n",
         "    result = seq_lfp.interpolate(t_query)\n",
         "    ax.plot(t_query, result[:, 0], lw=0.8)\n",

examples/demo.ipynb

@@ -22,7 +22,6 @@
     "\n",
     "# Standard imports\n",
     "import sys\n",
-    "import os\n",
     "from pathlib import Path\n",
     "\n",
     "# Add project root to path if needed\n",
@@ -45,13 +44,9 @@
    "outputs": [],
    "source": [
     "import matplotlib.pyplot as plt\n",
-    "from os import path\n",
     "\n",
-    "from tqdm import tqdm\n",
-    "import torch\n",
-    "from omegaconf import OmegaConf, open_dict\n",
+    "from omegaconf import OmegaConf\n",
     "\n",
-    "from experanto.datasets import ChunkDataset\n",
     "from experanto.dataloaders import get_multisession_dataloader"
    ]
   },
@@ -198,7 +193,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "3eb3e584-077f-4124-abb2-4fb8d43070c0",
    "metadata": {},
    "outputs": [
@@ -211,7 +206,7 @@
     }
    ],
    "source": [
-    "ls /data/test_upsampling_without_hamming_30.0Hz/dynamic29515-10-12-Video-021a75e56847d574b9acbcc06c675055_30hz"
+    "!ls /data/test_upsampling_without_hamming_30.0Hz/dynamic29515-10-12-Video-021a75e56847d574b9acbcc06c675055_30hz"
    ]
   },
   {
@@ -238,7 +233,6 @@
     }
    ],
    "source": [
-    "from experanto.dataloaders import get_multisession_dataloader\n",
     "\n",
     "paths = [\"/data/test_upsampling_without_hamming_30.0Hz/dynamic29515-10-12-Video-021a75e56847d574b9acbcc06c675055_30hz\"]\n",
     "train_dl = get_multisession_dataloader(paths, cfg)"
@@ -321,7 +315,7 @@
     "fig, axs = plt.subplots(1, 4, figsize=(10, 2))\n",
     "for i, ax in enumerate(axs.ravel()):\n",
     "    ax.imshow(batch[\"screen\"][i, 0, 0])  # video frames that the mouse sees\n",
-    "    ax.axis(\"off\");"
+    "    ax.axis(\"off\")"
    ]
   },
   {

examples/sensorium/data.ipynb

@@ -14,7 +14,6 @@
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
     "import matplotlib.animation as animation\n",
-    "from pathlib import Path\n",
     "from IPython.display import HTML"
    ]
   },
@@ -33,9 +32,7 @@
     "if p not in sys.path:\n",
     "    sys.path.append(p)\n",
     "\n",
-    "from experanto.experiment import Experiment\n",
-    "from experanto.interpolators import Interpolator\n",
-    "from experanto.interpolators import ScreenInterpolator"
+    "from experanto.experiment import Experiment # noqa: E402"
    ]
   },
   {
@@ -93,7 +90,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "plt.plot(data[\"running_speed\"], \"o-k\")"
+    "plt.plot(data[\"running_speed\"], \"o-k\") # noqa: F821 - `data` is defined in prior cell"
    ]
   },
   {
@@ -103,8 +100,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vid1 = e[b : b + time_steps][\"screen\"]\n",
-    "vid2 = e[b : b + time_steps, \"screen\"]\n",
+    "vid1 = e[b : b + time_steps][\"screen\"] # noqa: F821 - `b` is defined in prior cell\n",
+    "vid2 = e[b : b + time_steps, \"screen\"] # noqa: F821\n",
     "np.sum(vid1 - vid2)"
    ]
   },

examples/sensorium/experiment.ipynb

@@ -30,7 +30,7 @@
     "    sys.path.append(p)\n",
     "\n",
     "# from experanto.experiment import ImageInterpolator\n",
-    "from experanto.interpolators import ImageInterpolator"
+    "from experanto.interpolators import ImageInterpolator # noqa: E402"
    ]
   },
   {

examples/sensorium/images.ipynb

@@ -48,13 +48,13 @@
    "source": [
     "import yaml\n",
     "\n",
-    "meta = dict(\n",
-    "    modality=\"time_series\",\n",
-    "    start_time=float(si.timestamps[0]),\n",
-    "    end_time=float(si.timestamps[-1]),\n",
-    "    time_delta=float((si.timestamps[-1] - si.timestamps[0]) / (len(si.timestamps) - 1)),\n",
-    "    phase_shift_per_signal=False,\n",
-    ")\n",
+    "meta = {\n",
+    "    \"modality\": \"time_series\",\n",
+    "    \"start_time\": float(si.timestamps[0]),\n",
+    "    \"end_time\": float(si.timestamps[-1]),\n",
+    "    \"time_delta\": float((si.timestamps[-1] - si.timestamps[0]) / (len(si.timestamps) - 1)),\n",
+    "    \"phase_shift_per_signal\": False,\n",
+    "}\n",
     "\n",
     "with open(\"/Users/fabee/Data/sinzlab-data/dataset0/eye_tracker/meta.yml\", \"w\") as f:\n",
     "    yaml.safe_dump(meta, f)"