test: add comprehensive coverage for Experiment class and data generation utilities

Author: BitForge95

.github/workflows/docs.yml

@@ -7,15 +7,13 @@ on:
   pull_request:
     branches:
       - '**'
-  workflow_dispatch:
 
 jobs:
   build-docs:
     name: Build Sphinx Docs
     runs-on: ubuntu-latest
     if: |
       github.event_name == 'push' ||
-      github.event_name == 'workflow_dispatch' ||
       (
         github.event_name == 'pull_request' &&
         github.repository != github.event.pull_request.head.repo.full_name

.github/workflows/ruff.yml

@@ -7,15 +7,13 @@ on:
   pull_request:
     branches:
       - '**'
-  workflow_dispatch:
 
 jobs:
   ruff:
     name: Ruff Linting
     runs-on: ubuntu-latest
     if: |
       github.event_name == 'push' ||
-      github.event_name == 'workflow_dispatch' ||
       (
         github.event_name == 'pull_request' &&
         github.repository != github.event.pull_request.head.repo.full_name

.github/workflows/test.yml

@@ -7,15 +7,13 @@ on:
   pull_request:
     branches:
       - '**'
-  workflow_dispatch:
 
 jobs:
   test:
     name: Run Tests
     runs-on: ubuntu-latest
     if: |
       github.event_name == 'push' ||
-      github.event_name == 'workflow_dispatch' ||
       (
         github.event_name == 'pull_request' &&
         github.repository != github.event.pull_request.head.repo.full_name
@@ -49,7 +47,6 @@ jobs:
     runs-on: ubuntu-latest
     if: |
       github.event_name == 'push' ||
-      github.event_name == 'workflow_dispatch' ||
       (
         github.event_name == 'pull_request' &&
         github.repository != github.event.pull_request.head.repo.full_name
@@ -67,25 +64,25 @@ jobs:
       - name: Install tools
         run: |
           python -m pip install --upgrade pip
-          pip install -e ".[dev]"
+          pip install "black[jupyter]==25.1.0" isort==6.0.1
 
       - name: Run Black and Isort
         run: |
           if [[ "${{ github.event_name }}" == "push" && "${{ github.repository }}" == "${{ github.event.repository.full_name }}" ]]; then
             echo "Push event in same repo: Running black and isort with auto-format and commit"
             black .
             isort .
-            git config user.name "github-actions[bot]"
-            git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+            git config user.name "github-actions"
+            git config user.email "github-actions@github.com"
             if ! git diff --quiet; then
               git commit -am "style: auto-format with black and isort"
               git push
             else
               echo "No formatting changes to commit."
             fi
 
-          elif [[ "${{ github.event_name }}" == "pull_request" || "${{ github.event_name }}" == "workflow_dispatch" ]]; then
-            echo "PR or manual run: Running black and isort in check mode"
+          elif [[ "${{ github.event_name }}" == "pull_request" ]]; then
+            echo "PR from fork: Running black and isort in check mode"
             black --check . || { echo "Black formatting issues found. Run 'black .' to fix."; exit 1; }
             isort --check-only . || { echo "isort import order issues found. Run 'isort .' to fix."; exit 1; }
 
@@ -98,7 +95,6 @@ jobs:
     runs-on: ubuntu-latest
     if: |
       github.event_name == 'push' ||
-      github.event_name == 'workflow_dispatch' ||
       (
         github.event_name == 'pull_request' &&
         github.repository != github.event.pull_request.head.repo.full_name

.readthedocs.yml

@@ -4,7 +4,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.12"
+    python: "3.9"
 
 python:
   install:

docs/source/conf.py

@@ -13,7 +13,7 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = "Experanto"
+project = "experanto"
 copyright = f"{datetime.today().strftime('%Y')}, sinzlab"
 author = "sinzlab"
 release = "0.1"
@@ -83,8 +83,6 @@
     "optree",
     "rootutils",
     "numba",
-    "numpy",
-    "yaml",
 ]
 
 # -- Intersphinx settings (cross-references to external docs) ----------------

experanto/experiment.py

@@ -1,10 +1,13 @@
 from __future__ import annotations
 
 import logging
+import re
 import warnings
+from collections.abc import Sequence
 from pathlib import Path
 
 import numpy as np
+
 from hydra.utils import instantiate
 from omegaconf import DictConfig
 
@@ -76,7 +79,7 @@ def __init__(
     def _load_devices(self) -> None:
         # Populate devices by going through subfolders
         # Assumption: blocks are sorted by start time
-        device_folders = [d for d in self.root_folder.iterdir() if (d.is_dir())]
+        device_folders = [d for d in self.root_folder.iterdir() if d.is_dir()]
 
         for d in device_folders:
             if d.name not in self.modality_config:
@@ -95,14 +98,14 @@ def _load_devices(self) -> None:
                 dev = instantiate(
                     interp_conf, root_folder=d, cache_data=self.cache_data
                 )
+
                 # Check if instantiated object is proper Interpolator
                 if not isinstance(dev, Interpolator):
                     raise ValueError(
-                        "Please provide an Interpolator which inherits from experantos Interpolator class."
+                        "Instantiated object must inherit from Interpolator class."
                     )
 
             elif isinstance(interp_conf, Interpolator):
-                # Already instantiated Interpolator
                 dev = interp_conf
 
             else:
@@ -207,26 +210,22 @@ def interpolate(
         dict_keys(['screen', 'responses', 'eye_tracker'])
         """
         if device is None:
-            values = {}
-            valid = {}
+            values, valid = {}, {}
             for d, interp in self.devices.items():
                 res = interp.interpolate(times, return_valid=return_valid)
                 if return_valid:
                     vals, vlds = res
-                    values[d] = vals
-                    valid[d] = vlds
+                    values[d], valid[d] = vals, vlds
                 else:
                     values[d] = res
-            if return_valid:
-                return values, valid
-            else:
-                return values
+            return (values, valid) if return_valid else values
+
         elif isinstance(device, str):
-            assert device in self.devices, f"Unknown device '{device}'"
-            res = self.devices[device].interpolate(times, return_valid=return_valid)
-            return res
-        else:
-            raise ValueError(f"Unsupported device type: {type(device)}")
+            if device not in self.devices:
+                raise KeyError(f"Unknown device '{device}'")
+            return self.devices[device].interpolate(times, return_valid=return_valid)
+
+        raise ValueError(f"Unsupported device type: {type(device)}")
 
     def get_valid_range(self, device_name: str) -> tuple[float, float]:
         """Get the valid time range for a specific device.
@@ -239,7 +238,7 @@ def get_valid_range(self, device_name: str) -> tuple[float, float]:
         Returns
         -------
         tuple
-            A tuple ``(start_time, end_time)`` representing the valid
+            A tuple `(start_time, end_time)` representing the valid
             time interval in seconds.
         """
         return tuple(self.devices[device_name].valid_interval)

experanto/interpolators.py

@@ -84,7 +84,9 @@ def __exit__(self, *exc):
         self.close()
 
     @staticmethod
-    def create(root_folder: str, cache_data: bool = False, **kwargs) -> Interpolator:
+    def create(
+        root_folder: str | Path, cache_data: bool = False, **kwargs
+    ) -> "Interpolator":
         """Factory method to create the appropriate interpolator for a modality.
 
         Reads the ``meta.yml`` file in the folder to determine the modality type
@@ -109,35 +111,24 @@ def create(root_folder: str, cache_data: bool = False, **kwargs) -> Interpolator
         ValueError
             If the modality type is not supported.
         """
+        root_folder = str(root_folder)
         with open(Path(root_folder) / "meta.yml") as file:
             meta_data = yaml.safe_load(file)
         modality = meta_data.get("modality")
 
         if modality == "sequence":
             if meta_data.get("phase_shift_per_signal", False):
                 return PhaseShiftedSequenceInterpolator(
-                    root_folder, cache_data=cache_data, **kwargs
+                    root_folder, cache_data, **kwargs
                 )
             else:
-                return SequenceInterpolator(
-                    root_folder, cache_data=cache_data, **kwargs
-                )
+                return SequenceInterpolator(root_folder, cache_data, **kwargs)
         elif modality == "screen":
-            use_stimuli_names = kwargs.pop(
-                "use_stimuli_names", meta_data.get("use_stimuli_names", False)
-            )
-            return ScreenInterpolator(
-                root_folder,
-                cache_data=cache_data,
-                use_stimuli_names=use_stimuli_names,
-                **kwargs,
-            )
+            return ScreenInterpolator(root_folder, cache_data, **kwargs)
         elif modality == "time_interval":
-            return TimeIntervalInterpolator(
-                root_folder, cache_data=cache_data, **kwargs
-            )
+            return TimeIntervalInterpolator(root_folder, cache_data, **kwargs)
         elif modality == "spikes":
-            return SpikeInterpolator(root_folder, cache_data=cache_data, **kwargs)
+            return SpikeInterpolator(root_folder, cache_data, **kwargs)
         else:
             raise ValueError(
                 f"There is no interpolator for {modality}. Please use 'sequence', 'screen', 'time_interval' as modality or provide a custom interpolator."
@@ -497,8 +488,6 @@ class ScreenInterpolator(Interpolator):
         native image size from metadata.
     normalize : bool, default=False
         If True, normalizes frames using stored mean/std statistics.
-    use_stimuli_names : bool, default=False
-        If True, uses ``stimulus_name`` from metadata to locate data files instead of trial keys.
     **kwargs
         Additional keyword arguments (ignored).
 
@@ -519,11 +508,10 @@ class ScreenInterpolator(Interpolator):
     def __init__(
         self,
         root_folder: str,
-        cache_data: bool = False,
+        cache_data: bool = False,  # New parameter
         rescale: bool = False,
         rescale_size: tuple[int, int] | None = None,
         normalize: bool = False,
-        use_stimuli_names: bool = False,
         **kwargs,
     ) -> None:
         super().__init__(root_folder)
@@ -533,7 +521,6 @@ def __init__(
         self.valid_interval = TimeInterval(self.start_time, self.end_time)
         self.rescale = rescale
         self.cache_trials = cache_data  # Store the cache preference
-        self.use_stimuli_names = use_stimuli_names
         self._parse_trials()
 
         # create mapping from image index to file index
@@ -618,14 +605,8 @@ def _parse_trials(self) -> None:
         metadatas, keys = self.read_combined_meta()
 
         for key, metadata in zip(keys, metadatas, strict=True):
-            if self.use_stimuli_names:
-                stimulus_name = metadata.get("stimulus_name")
-                assert (
-                    stimulus_name is not None
-                ), f"stimulus_name is required in metadata when use_stimuli_names is True, but not found for key: {key}"
-                data_file_name = self.root_folder / "data" / f"{stimulus_name}.npy"
-            else:
-                data_file_name = self.root_folder / "data" / f"{key}.npy"
+            data_file_name = self.root_folder / "data" / f"{key}.npy"
+            # Pass the cache_trials parameter when creating trials
             self.trials.append(
                 ScreenTrial.create(
                     data_file_name, metadata, cache_data=self.cache_trials

pyproject.toml

@@ -4,7 +4,6 @@ version = "0.1"
 description = "Python package to interpolate recordings and stimuli of neuroscience experiments"
 readme = "README.md"
 requires-python = ">=3.9"
-# When adding or removing dependencies, also update autodoc_mock_imports in docs/source/conf.py if necessary.
 dependencies = [
     "scipy>=1.13.1",
     "jaxtyping>=0.2.30",
@@ -22,9 +21,7 @@ dependencies = [
 dev = [
     "pytest==8.3.5",
     "pytest-cov>=7.0.0",
-    "pyright==1.1.408",
-    "black[jupyter]==25.1.0",
-    "isort==6.0.1",
+    "pyright",
     "hypothesis>=6.0",
     "ruff==0.15.6",
 ]