From 827d9fcc896733572503b423ecfccc99aa7effcb Mon Sep 17 00:00:00 2001
From: binary69 <220374295+binary69@users.noreply.github.com>
Date: Sun, 15 Mar 2026 15:41:04 +0530
Subject: [PATCH 1/6] fix: resolve ruff linting issues and add CI workflow

---
 .github/workflows/ruff.yml                    | 10 ++++++++++
 .gitignore                                    |  1 +
 examples/sensorium/data.ipynb                 |  4 +---
 examples/sensorium/experiment.ipynb           |  5 +----
 .../sensorium/sensorium_min_example.ipynb     |  4 ----
 experanto/configs.py                          |  3 +--
 experanto/dataloaders.py                      |  9 ++-------
 experanto/datasets.py                         | 12 ++++--------
 experanto/experiment.py                       |  4 +---
 experanto/interpolators.py                    |  5 ++---
 experanto/intervals.py                        |  2 +-
 experanto/utils.py                            | 19 +++----------------
 12 files changed, 27 insertions(+), 51 deletions(-)
 create mode 100644 .github/workflows/ruff.yml

diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml
new file mode 100644
index 00000000..3de066bb
--- /dev/null
+++ b/.github/workflows/ruff.yml
@@ -0,0 +1,10 @@
+name: Ruff
+
+on: [push, pull_request]
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/ruff-action@v3
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
index 2bc61f88..22b40f7c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -165,3 +165,4 @@ cython_debug/
 *.bak
 
 docs/source/generated/
+gsoc_env/
\ No newline at end of file
diff --git a/examples/sensorium/data.ipynb b/examples/sensorium/data.ipynb
index 5324dea4..6db7901d 100644
--- a/examples/sensorium/data.ipynb
+++ b/examples/sensorium/data.ipynb
@@ -11,9 +11,7 @@
     "%load_ext autoreload\n",
     "%autoreload 2\n",
     "\n",
-    "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
-    "import torch"
+    "import matplotlib.pyplot as plt"
    ]
   },
   {
diff --git a/examples/sensorium/experiment.ipynb b/examples/sensorium/experiment.ipynb
index 54dc7c75..21423733 100644
--- a/examples/sensorium/experiment.ipynb
+++ b/examples/sensorium/experiment.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"
    ]
   },
   {
diff --git a/examples/sensorium/sensorium_min_example.ipynb b/examples/sensorium/sensorium_min_example.ipynb
index 0b1d1ee2..82ca25cf 100644
--- a/examples/sensorium/sensorium_min_example.ipynb
+++ b/examples/sensorium/sensorium_min_example.ipynb
@@ -32,7 +32,6 @@
     "import numpy as np\n",
     "from tqdm import tqdm\n",
     "import matplotlib.pyplot as plt\n",
-    "from torch.utils.data import DataLoader\n",
     "from collections import OrderedDict"
    ]
   },
@@ -444,8 +443,6 @@
     "\n",
     "set_random_seed(seed)\n",
     "\n",
-    "from sensorium.datasets.mouse_video_loaders import mouse_video_loader\n",
-    "from sensorium.utility.scores import get_correlations\n",
     "from nnfabrik.builder import get_trainer\n",
     "from sensorium.models.make_model import make_video_model"
    ]
@@ -744,7 +741,6 @@
    "source": [
     "import yaml\n",
     "import os\n",
-    "from tqdm import tqdm\n",
     "from collections import Counter"
    ]
   },
diff --git a/experanto/configs.py b/experanto/configs.py
index 5f3a0beb..de7293ba 100644
--- a/experanto/configs.py
+++ b/experanto/configs.py
@@ -37,8 +37,7 @@
 
 from pathlib import Path
 
-from hydra import compose, initialize, initialize_config_dir
-from omegaconf import OmegaConf, open_dict
+from omegaconf import OmegaConf
 
 # get config relative to this file
 script_dir = Path(__file__).parent
diff --git a/experanto/dataloaders.py b/experanto/dataloaders.py
index f891bd57..c4a29414 100644
--- a/experanto/dataloaders.py
+++ b/experanto/dataloaders.py
@@ -1,13 +1,8 @@
 import logging
-import os
-import time
 import warnings
-from pathlib import Path
-from typing import Any, Dict, List, Optional, Type, Union
+from typing import Dict, List, Optional, Union
 
-import numpy as np
 from omegaconf import DictConfig
-from torch.utils.data import DataLoader
 
 from .datasets import ChunkDataset
 from .utils import (
@@ -158,7 +153,7 @@ def get_multisession_concat_dataloader(
     datasets = []
     session_names = []
 
-    start_time = time.time()
+    
     for i, (path, cfg) in enumerate(zip(paths, configs)):
         # Create dataset with deterministic seed
         path_hash = hash(path) % 10000
diff --git a/experanto/datasets.py b/experanto/datasets.py
index 31682cda..24a67627 100644
--- a/experanto/datasets.py
+++ b/experanto/datasets.py
@@ -1,35 +1,31 @@
 from __future__ import annotations
 
-import functools
 import importlib
 import json
 import logging
 import os
 from collections.abc import Iterable
 from pathlib import Path
-from typing import Any, Dict, List, Optional, Union
+from typing import Any, Dict, List, Optional
 
 import numpy as np
 import torch
 import torchvision
 from hydra.utils import instantiate
-from omegaconf import DictConfig, ListConfig, OmegaConf
+from omegaconf import DictConfig, ListConfig
 from torch.utils.data import Dataset
-from torchvision.transforms import v2
 from torchvision.transforms.v2 import Compose, Lambda, ToTensor
 
 from .configs import DEFAULT_MODALITY_CONFIG
 from .experiment import Experiment
-from .interpolators import ImageTrial, VideoTrial
 from .intervals import (
     TimeInterval,
     find_intersection_between_two_interval_arrays,
     get_stats_for_valid_interval,
 )
-from .utils import add_behavior_as_channels, replace_nan_with_batch_mean
+from .utils import add_behavior_as_channels
 
 # see .configs.py for the definition of DEFAULT_MODALITY_CONFIG
-DEFAULT_MODALITY_CONFIG = dict()
 
 logger = logging.getLogger(__name__)
 
@@ -768,7 +764,7 @@ def __getitem__(self, idx: int) -> dict:
         for device_name in self.device_names:
             sampling_rate = self.sampling_rates[device_name]
             chunk_size = self.chunk_sizes[device_name]
-            chunk_s = chunk_size / sampling_rate
+           
 
             # convert everything to int to avoid numerical issues
             start_time = int(round(s * self.scale_precision))
diff --git a/experanto/experiment.py b/experanto/experiment.py
index faa2fed1..b5c4850f 100644
--- a/experanto/experiment.py
+++ b/experanto/experiment.py
@@ -1,11 +1,9 @@
 from __future__ import annotations
 
 import logging
-import re
 import warnings
-from collections.abc import Sequence
 from pathlib import Path
-from typing import Optional, Union
+from typing import Union
 
 import numpy as np
 from hydra.utils import instantiate
diff --git a/experanto/interpolators.py b/experanto/interpolators.py
index 4928fd85..027e87c8 100644
--- a/experanto/interpolators.py
+++ b/experanto/interpolators.py
@@ -12,7 +12,6 @@
 
 import cv2
 import numpy as np
-import numpy.lib.format as fmt
 import yaml
 from numba import njit, prange
 from scipy.ndimage import gaussian_filter1d
@@ -326,7 +325,7 @@ def interpolate(
 
         else:
             raise NotImplementedError(
-                f"interpolation_mode should be linear or nearest_neighbor"
+                "interpolation_mode should be linear or nearest_neighbor"
             )
 
     def close(self) -> None:
@@ -454,7 +453,7 @@ def interpolate(
 
         else:
             raise NotImplementedError(
-                f"interpolation_mode should be linear or nearest_neighbor"
+                "interpolation_mode should be linear or nearest_neighbor"
             )
 
 
diff --git a/experanto/intervals.py b/experanto/intervals.py
index 16079857..9a1d6c02 100644
--- a/experanto/intervals.py
+++ b/experanto/intervals.py
@@ -236,7 +236,7 @@ def get_stats_for_valid_interval(
     """
     total_duration = end_time - start_time
     if total_duration <= 0:
-        return f"Error: Invalid time range (end_time <= start_time). Total duration must be positive."
+        return "Error: Invalid time range (end_time <= start_time). Total duration must be positive."
 
     # Ensure intervals are unique and sorted, then clamp them to the analysis window
     unique_intervals = uniquefy_interval_array(intervals)
diff --git a/experanto/utils.py b/experanto/utils.py
index bd0c7f85..f30ac279 100644
--- a/experanto/utils.py
+++ b/experanto/utils.py
@@ -1,28 +1,15 @@
 import bisect
 import logging
-import math
-import multiprocessing
 
 # inbuilt libraries
-import os
-import queue
-import random
-import threading
-import time
-import warnings
 from collections import defaultdict
-from copy import deepcopy
-from functools import partial
-from typing import Any, Dict, Iterator, List, Optional, Tuple, Union
 
 # third-party libraries
 import numpy as np
 import torch
-from omegaconf import DictConfig
-from torch.utils.data import ConcatDataset, DataLoader, Dataset, Sampler
+from torch.utils.data import DataLoader, Dataset, Sampler
 
 # local libraries
-from .intervals import TimeInterval
 
 logger = logging.getLogger(__name__)
 
@@ -58,7 +45,7 @@ def add_behavior_as_channels(data: dict[str, torch.Tensor]) -> dict:
 
     # Process eye_tracker
     if len(eye_tracker.shape) == 2:  # (t, c_eye)
-        c_eye = eye_tracker.shape[1]
+        
         # Reshape to (c_eye, t, h, w)
         eye_tracker = eye_tracker.transpose(0, 1)  # (c_eye, t)
         eye_tracker = eye_tracker.unsqueeze(-1).unsqueeze(-1)  # (c_eye, t, 1, 1)
@@ -69,7 +56,7 @@ def add_behavior_as_channels(data: dict[str, torch.Tensor]) -> dict:
 
     # Process treadmill
     if len(treadmill.shape) == 2:  # (t, c_tread)
-        c_tread = treadmill.shape[1]
+        
         # Reshape to (c_tread, t, h, w)
         treadmill = treadmill.transpose(0, 1)  # (c_tread, t)
         treadmill = treadmill.unsqueeze(-1).unsqueeze(-1)  # (c_tread, t, 1, 1)

From ebca0d2da6203aa14be29e0d09dd14ae4a2793fc Mon Sep 17 00:00:00 2001
From: github-actions <github-actions@github.com>
Date: Sun, 15 Mar 2026 10:11:31 +0000
Subject: [PATCH 2/6] style: auto-format with black and isort

---
 experanto/dataloaders.py | 1 -
 experanto/datasets.py    | 1 -
 experanto/utils.py       | 4 ++--
 3 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/experanto/dataloaders.py b/experanto/dataloaders.py
index c4a29414..316a4828 100644
--- a/experanto/dataloaders.py
+++ b/experanto/dataloaders.py
@@ -153,7 +153,6 @@ def get_multisession_concat_dataloader(
     datasets = []
     session_names = []
 
-    
     for i, (path, cfg) in enumerate(zip(paths, configs)):
         # Create dataset with deterministic seed
         path_hash = hash(path) % 10000
diff --git a/experanto/datasets.py b/experanto/datasets.py
index 24a67627..c2454a26 100644
--- a/experanto/datasets.py
+++ b/experanto/datasets.py
@@ -764,7 +764,6 @@ def __getitem__(self, idx: int) -> dict:
         for device_name in self.device_names:
             sampling_rate = self.sampling_rates[device_name]
             chunk_size = self.chunk_sizes[device_name]
-           
 
             # convert everything to int to avoid numerical issues
             start_time = int(round(s * self.scale_precision))
diff --git a/experanto/utils.py b/experanto/utils.py
index f30ac279..f40c862b 100644
--- a/experanto/utils.py
+++ b/experanto/utils.py
@@ -45,7 +45,7 @@ def add_behavior_as_channels(data: dict[str, torch.Tensor]) -> dict:
 
     # Process eye_tracker
     if len(eye_tracker.shape) == 2:  # (t, c_eye)
-        
+
         # Reshape to (c_eye, t, h, w)
         eye_tracker = eye_tracker.transpose(0, 1)  # (c_eye, t)
         eye_tracker = eye_tracker.unsqueeze(-1).unsqueeze(-1)  # (c_eye, t, 1, 1)
@@ -56,7 +56,7 @@ def add_behavior_as_channels(data: dict[str, torch.Tensor]) -> dict:
 
     # Process treadmill
     if len(treadmill.shape) == 2:  # (t, c_tread)
-        
+
         # Reshape to (c_tread, t, h, w)
         treadmill = treadmill.transpose(0, 1)  # (c_tread, t)
         treadmill = treadmill.unsqueeze(-1).unsqueeze(-1)  # (c_tread, t, 1, 1)

From 38ad1aab7043e79ca8fa8f1b58999dcfa3db4875 Mon Sep 17 00:00:00 2001
From: binary69 <220374295+binary69@users.noreply.github.com>
Date: Mon, 16 Mar 2026 05:21:34 +0530
Subject: [PATCH 3/6] ci: pin ruff to v0.15.6 and avoid duplicate CI runs

---
 .github/workflows/ruff.yml | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml
index 3de066bb..48b790fd 100644
--- a/.github/workflows/ruff.yml
+++ b/.github/workflows/ruff.yml
@@ -1,10 +1,15 @@
 name: Ruff
 
-on: [push, pull_request]
+on:
+  push:
+    branches: ["main"]
+  pull_request:
 
 jobs:
   ruff:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: astral-sh/ruff-action@v3
\ No newline at end of file
+      - uses: astral-sh/ruff-action@v3
+        with:
+          version: "0.15.6"
\ No newline at end of file

From 7597f9545bd08a680a54fa8f36f8e176d8a2cd20 Mon Sep 17 00:00:00 2001
From: binary69 <220374295+binary69@users.noreply.github.com>
Date: Mon, 16 Mar 2026 14:27:28 +0530
Subject: [PATCH 4/6] ci: exclude examples folder from ruff check

---
 .github/workflows/ruff.yml | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml
index 48b790fd..37b0c585 100644
--- a/.github/workflows/ruff.yml
+++ b/.github/workflows/ruff.yml
@@ -1,15 +1,14 @@
 name: Ruff
 
-on:
-  push:
-    branches: ["main"]
-  pull_request:
+on: [push, pull_request]
 
 jobs:
   ruff:
+    if: github.event_name == 'push' || (github.event_name == 'pull_request' && github.event.pull_request.head.repo.fork == true)
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - uses: astral-sh/ruff-action@v3
         with:
-          version: "0.15.6"
\ No newline at end of file
+          version: "0.15.6"
+          args: "check --exclude examples/"
\ No newline at end of file

From 7f720c45494417d324acc8dddd0c958819395dca Mon Sep 17 00:00:00 2001
From: binary69 <220374295+binary69@users.noreply.github.com>
Date: Mon, 16 Mar 2026 15:17:33 +0530
Subject: [PATCH 5/6] test: upadted comments

---
 tests/test_experiment.py | 165 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 165 insertions(+)
 create mode 100644 tests/test_experiment.py

diff --git a/tests/test_experiment.py b/tests/test_experiment.py
new file mode 100644
index 00000000..a21e8196
--- /dev/null
+++ b/tests/test_experiment.py
@@ -0,0 +1,165 @@
+import shutil
+from contextlib import contextmanager
+from pathlib import Path
+
+import numpy as np
+import pytest
+import yaml
+
+from experanto.experiment import Experiment
+
+EXPERIMENT_ROOT = Path("tests/experiment_data")
+
+
+@contextmanager
+def create_two_device_experiment(
+    device0_start=0.0,
+    device0_end=10.0,
+    device1_start=1.0,
+    device1_end=8.0,
+    sampling_rate=10.0,
+):
+    """Create a temporary experiment with two sequence devices with different time ranges."""
+    try:
+        for device_name, start, end in [
+            ("device_0", device0_start, device0_end),
+            ("device_1", device1_start, device1_end),
+        ]:
+            device_root = EXPERIMENT_ROOT / device_name
+            (device_root / "meta").mkdir(parents=True, exist_ok=True)
+
+            n_samples = int((end - start) * sampling_rate) + 1
+            timestamps = np.linspace(start, end, n_samples)
+            data = np.random.rand(n_samples, 5)
+
+            np.save(device_root / "timestamps.npy", timestamps)
+            np.save(device_root / "data.npy", data)
+
+            meta = {
+                "start_time": start,
+                "end_time": end,
+                "modality": "sequence",
+                "sampling_rate": sampling_rate,
+                "phase_shift_per_signal": False,
+                "is_mem_mapped": False,
+                "n_signals": 5,
+                "n_timestamps": n_samples,
+                "dtype": "float64",
+            }
+            with open(device_root / "meta.yml", "w") as f:
+                yaml.safe_dump(meta, f)
+
+        yield EXPERIMENT_ROOT
+
+    finally:
+        shutil.rmtree(EXPERIMENT_ROOT)
+
+
+@contextmanager
+def create_three_device_experiment():
+    """Create a temporary experiment with three sequence devices with different time ranges."""
+    try:
+        for device_name, start, end in [
+            ("device_0", 0.0, 10.0),
+            ("device_1", 1.0, 8.0),
+            ("device_2", 2.0, 9.0),
+        ]:
+            device_root = EXPERIMENT_ROOT / device_name
+            (device_root / "meta").mkdir(parents=True, exist_ok=True)
+
+            sampling_rate = 10.0
+            n_samples = int((end - start) * sampling_rate) + 1
+            timestamps = np.linspace(start, end, n_samples)
+            data = np.random.rand(n_samples, 5)
+
+            np.save(device_root / "timestamps.npy", timestamps)
+            np.save(device_root / "data.npy", data)
+
+            meta = {
+                "start_time": start,
+                "end_time": end,
+                "modality": "sequence",
+                "sampling_rate": sampling_rate,
+                "phase_shift_per_signal": False,
+                "is_mem_mapped": False,
+                "n_signals": 5,
+                "n_timestamps": n_samples,
+                "dtype": "float64",
+            }
+            with open(device_root / "meta.yml", "w") as f:
+                yaml.safe_dump(meta, f)
+
+        yield EXPERIMENT_ROOT
+
+    finally:
+        shutil.rmtree(EXPERIMENT_ROOT)
+
+
+def get_two_device_config():
+    return {
+        "device_0": {"interpolation": {"sampling_rate": 10.0, "offset": 0.0}},
+        "device_1": {"interpolation": {"sampling_rate": 10.0, "offset": 0.0}},
+    }
+
+
+def test_experiment_start_end_time_reflects_union():
+    """
+    Experiment.start_time and end_time should reflect the union
+    of all device time ranges — the earliest start and latest end
+    across all devices, not just the last loaded device.
+    """
+    with create_two_device_experiment(
+        device0_start=1.0,
+        device0_end=8.0,
+        device1_start=0.0,
+        device1_end=10.0,
+    ) as experiment_path:
+        experiment = Experiment(
+            root_folder=experiment_path,
+            modality_config=get_two_device_config(),
+        )
+
+        # Union: start = min(1.0, 0.0) = 0.0, end = max(8.0, 10.0) = 10.0
+        assert experiment.start_time == pytest.approx(0.0), (
+            f"Expected start_time=0.0, got {experiment.start_time}"
+        )
+        assert experiment.end_time == pytest.approx(10.0), (
+            f"Expected end_time=10.0, got {experiment.end_time}"
+        )
+
+
+def test_experiment_single_device_time_range():
+    """With a single device, start_time and end_time should match that device's range."""
+    with create_two_device_experiment(
+        device0_start=2.0,
+        device0_end=9.0,
+    ) as experiment_path:
+        config = {
+            "device_0": {"interpolation": {"sampling_rate": 10.0, "offset": 0.0}}
+        }
+        experiment = Experiment(
+            root_folder=experiment_path,
+            modality_config=config,
+        )
+
+        assert experiment.start_time == pytest.approx(2.0)
+        assert experiment.end_time == pytest.approx(9.0)
+
+
+def test_experiment_start_end_time_three_devices():
+    """With three devices, start_time and end_time should reflect the union of all three —
+    earliest start and latest end across all devices."""
+    with create_three_device_experiment() as experiment_path:
+        config = {
+            "device_0": {"interpolation": {"sampling_rate": 10.0, "offset": 0.0}},
+            "device_1": {"interpolation": {"sampling_rate": 10.0, "offset": 0.0}},
+            "device_2": {"interpolation": {"sampling_rate": 10.0, "offset": 0.0}},
+        }
+        experiment = Experiment(
+            root_folder=experiment_path,
+            modality_config=config,
+        )
+
+        # Union: start = min(0.0, 1.0, 2.0) = 0.0, end = max(10.0, 8.0, 9.0) = 10.0
+        assert experiment.start_time == pytest.approx(0.0)
+        assert experiment.end_time == pytest.approx(10.0)
\ No newline at end of file

From dfe68b5a8364223265ee014fb9c276dc41a667c3 Mon Sep 17 00:00:00 2001
From: github-actions <github-actions@github.com>
Date: Mon, 16 Mar 2026 09:48:27 +0000
Subject: [PATCH 6/6] style: auto-format with black and isort

---
 tests/test_experiment.py | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/tests/test_experiment.py b/tests/test_experiment.py
index a21e8196..e7e846fc 100644
--- a/tests/test_experiment.py
+++ b/tests/test_experiment.py
@@ -120,12 +120,12 @@ def test_experiment_start_end_time_reflects_union():
         )
 
         # Union: start = min(1.0, 0.0) = 0.0, end = max(8.0, 10.0) = 10.0
-        assert experiment.start_time == pytest.approx(0.0), (
-            f"Expected start_time=0.0, got {experiment.start_time}"
-        )
-        assert experiment.end_time == pytest.approx(10.0), (
-            f"Expected end_time=10.0, got {experiment.end_time}"
-        )
+        assert experiment.start_time == pytest.approx(
+            0.0
+        ), f"Expected start_time=0.0, got {experiment.start_time}"
+        assert experiment.end_time == pytest.approx(
+            10.0
+        ), f"Expected end_time=10.0, got {experiment.end_time}"
 
 
 def test_experiment_single_device_time_range():
@@ -134,9 +134,7 @@ def test_experiment_single_device_time_range():
         device0_start=2.0,
         device0_end=9.0,
     ) as experiment_path:
-        config = {
-            "device_0": {"interpolation": {"sampling_rate": 10.0, "offset": 0.0}}
-        }
+        config = {"device_0": {"interpolation": {"sampling_rate": 10.0, "offset": 0.0}}}
         experiment = Experiment(
             root_folder=experiment_path,
             modality_config=config,
@@ -162,4 +160,4 @@ def test_experiment_start_end_time_three_devices():
 
         # Union: start = min(0.0, 1.0, 2.0) = 0.0, end = max(10.0, 8.0, 9.0) = 10.0
         assert experiment.start_time == pytest.approx(0.0)
-        assert experiment.end_time == pytest.approx(10.0)
\ No newline at end of file
+        assert experiment.end_time == pytest.approx(10.0)