fix: restore project files accidentally overwritten during rebase

Author: BitForge95

.github/workflows/docs.yml

@@ -7,13 +7,15 @@ 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

@@ -7,13 +7,15 @@ 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

@@ -7,13 +7,15 @@ 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
@@ -47,6 +49,7 @@ 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
@@ -64,25 +67,25 @@ jobs:
       - name: Install tools
         run: |
           python -m pip install --upgrade pip
-          pip install "black[jupyter]==25.1.0" isort==6.0.1
+          pip install -e ".[dev]"
 
       - 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"
-            git config user.email "github-actions@github.com"
+            git config user.name "github-actions[bot]"
+            git config user.email "41898282+github-actions[bot]@users.noreply.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 [[ "${{ github.event_name }}" == "pull_request" ]]; then
-            echo "PR from fork: Running black and isort in check mode"
+          elif [[ "${{ github.event_name }}" == "pull_request" || "${{ github.event_name }}" == "workflow_dispatch" ]]; then
+            echo "PR or manual run: 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; }
 
@@ -95,6 +98,7 @@ 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

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"
@@ -83,6 +83,8 @@
     "optree",
     "rootutils",
     "numba",
+    "numpy",
+    "yaml",
 ]
 
 # -- Intersphinx settings (cross-references to external docs) ----------------

experanto/interpolators.py

@@ -84,9 +84,7 @@ def __exit__(self, *exc):
         self.close()
 
     @staticmethod
-    def create(
-        root_folder: str | Path, cache_data: bool = False, **kwargs
-    ) -> "Interpolator":
+    def create(root_folder: str, 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
@@ -111,24 +109,35 @@ def create(
         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, **kwargs
+                    root_folder, cache_data=cache_data, **kwargs
                 )
             else:
-                return SequenceInterpolator(root_folder, cache_data, **kwargs)
+                return SequenceInterpolator(
+                    root_folder, cache_data=cache_data, **kwargs
+                )
         elif modality == "screen":
-            return ScreenInterpolator(root_folder, cache_data, **kwargs)
+            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,
+            )
         elif modality == "time_interval":
-            return TimeIntervalInterpolator(root_folder, cache_data, **kwargs)
+            return TimeIntervalInterpolator(
+                root_folder, cache_data=cache_data, **kwargs
+            )
         elif modality == "spikes":
-            return SpikeInterpolator(root_folder, cache_data, **kwargs)
+            return SpikeInterpolator(root_folder, cache_data=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."
@@ -488,6 +497,8 @@ 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).
 
@@ -508,10 +519,11 @@ class ScreenInterpolator(Interpolator):
     def __init__(
         self,
         root_folder: str,
-        cache_data: bool = False,  # New parameter
+        cache_data: bool = False,
         rescale: bool = False,
         rescale_size: tuple[int, int] | None = None,
         normalize: bool = False,
+        use_stimuli_names: bool = False,
         **kwargs,
     ) -> None:
         super().__init__(root_folder)
@@ -521,6 +533,7 @@ 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
@@ -605,8 +618,14 @@ def _parse_trials(self) -> None:
         metadatas, keys = self.read_combined_meta()
 
         for key, metadata in zip(keys, metadatas, strict=True):
-            data_file_name = self.root_folder / "data" / f"{key}.npy"
-            # Pass the cache_trials parameter when creating trials
+            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"
             self.trials.append(
                 ScreenTrial.create(
                     data_file_name, metadata, cache_data=self.cache_trials

pyproject.toml

@@ -4,6 +4,7 @@ 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",
@@ -21,7 +22,9 @@ dependencies = [
 dev = [
     "pytest==8.3.5",
     "pytest-cov>=7.0.0",
-    "pyright",
+    "pyright==1.1.408",
+    "black[jupyter]==25.1.0",
+    "isort==6.0.1",
     "hypothesis>=6.0",
     "ruff==0.15.6",
 ]