Merge branch 'main' into use_latest_version_of_ndx_pose

catalystneuro · Jan 14, 2025 · 0636d87 · 0636d87
2 parents 8046d0d + fe5bfb4
commit 0636d87
Show file tree

Hide file tree

Showing 36 changed files with 14 additions and 48 deletions.
diff --git a/.gitignore b/.gitignore
@@ -6,6 +6,13 @@ __pycache__/
 # C extensions
 *.so
 
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+uv.lock
+
 # Distribution / packaging
 .Python
 build/

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,10 +16,12 @@ Small fixes should be here.
 ## Deprecations
 
 ## Bug Fixes
+* Temporary set a ceiling for hdmf to avoid a chunking bug  [PR #1175](https://github.com/catalystneuro/neuroconv/pull/1175)
 
 ## Features
 
 ## Improvements
+* Source validation is no longer performed when initializing interfaces or converters [PR #1168](https://github.com/catalystneuro/neuroconv/pull/1168)
 
 
 # v0.6.6 (December 20, 2024)

diff --git a/docs/conversion_examples_gallery/behavior/lightningpose.rst b/docs/conversion_examples_gallery/behavior/lightningpose.rst
@@ -23,7 +23,6 @@ Convert LightningPose pose estimation data to NWB using :py:class:`~neuroconv.da
     >>> labeled_video_file_path = str(folder_path / "labeled_videos/test_vid_labeled.mp4")
 
     >>> converter = LightningPoseConverter(file_path=file_path, original_video_file_path=original_video_file_path, labeled_video_file_path=labeled_video_file_path, verbose=False)
-    Source data is valid!
     >>> metadata = converter.get_metadata()
     >>> # For data provenance we add the time zone information to the conversion
     >>> session_start_time = metadata["NWBFile"]["session_start_time"]

diff --git a/docs/conversion_examples_gallery/recording/spikeglx.rst b/docs/conversion_examples_gallery/recording/spikeglx.rst
@@ -24,7 +24,6 @@ We can easily convert all data stored in the native SpikeGLX folder structure to
     >>>
     >>> folder_path = f"{ECEPHY_DATA_PATH}/spikeglx/Noise4Sam_g0"
     >>> converter = SpikeGLXConverterPipe(folder_path=folder_path)
-    Source data is valid!
     >>> # Extract what metadata we can from the source files
     >>> metadata = converter.get_metadata()
     >>> # For data provenance we add the time zone information to the conversion

diff --git a/pyproject.toml b/pyproject.toml
@@ -39,7 +39,7 @@ dependencies = [
     "PyYAML>=5.4",
     "scipy>=1.4.1",
     "h5py>=3.9.0",
-    "hdmf>=3.13.0",
+    "hdmf>=3.13.0,<=3.14.5",  # Chunking bug
     "hdmf_zarr>=0.7.0",
     "pynwb>=2.7.0",
     "pydantic>=2.0.0",

diff --git a/src/neuroconv/basedatainterface.py b/src/neuroconv/basedatainterface.py
@@ -68,8 +68,6 @@ def __init__(self, verbose: bool = False, **source_data):
         self.verbose = verbose
         self.source_data = source_data
 
-        self._validate_source_data(source_data=source_data, verbose=verbose)
-
     def get_metadata_schema(self) -> dict:
         """Retrieve JSON schema for metadata."""
         metadata_schema = load_dict_from_file(Path(__file__).parent / "schemas" / "base_metadata_schema.json")

diff --git a/src/neuroconv/datainterfaces/behavior/audio/requirements.txt b/src/neuroconv/datainterfaces/behavior/audio/requirements.txt
diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/requirements.txt b/src/neuroconv/datainterfaces/behavior/deeplabcut/requirements.txt
diff --git a/src/neuroconv/datainterfaces/behavior/fictrac/requirements.txt b/src/neuroconv/datainterfaces/behavior/fictrac/requirements.txt
diff --git a/src/neuroconv/datainterfaces/behavior/lightningpose/requirements.txt b/src/neuroconv/datainterfaces/behavior/lightningpose/requirements.txt
diff --git a/src/neuroconv/datainterfaces/behavior/medpc/requirements.txt b/src/neuroconv/datainterfaces/behavior/medpc/requirements.txt
diff --git a/src/neuroconv/datainterfaces/behavior/miniscope/requirements.txt b/src/neuroconv/datainterfaces/behavior/miniscope/requirements.txt
diff --git a/src/neuroconv/datainterfaces/behavior/sleap/requirements.txt b/src/neuroconv/datainterfaces/behavior/sleap/requirements.txt
diff --git a/src/neuroconv/datainterfaces/behavior/video/requirements.txt b/src/neuroconv/datainterfaces/behavior/video/requirements.txt
diff --git a/src/neuroconv/datainterfaces/ecephys/cellexplorer/requirements.txt b/src/neuroconv/datainterfaces/ecephys/cellexplorer/requirements.txt
diff --git a/src/neuroconv/datainterfaces/ecephys/edf/requirements.txt b/src/neuroconv/datainterfaces/ecephys/edf/requirements.txt
diff --git a/src/neuroconv/datainterfaces/ecephys/intan/requirements.txt b/src/neuroconv/datainterfaces/ecephys/intan/requirements.txt
diff --git a/src/neuroconv/datainterfaces/ecephys/mearec/requirements.txt b/src/neuroconv/datainterfaces/ecephys/mearec/requirements.txt
diff --git a/src/neuroconv/datainterfaces/ecephys/neuralynx/requirements.txt b/src/neuroconv/datainterfaces/ecephys/neuralynx/requirements.txt
diff --git a/src/neuroconv/datainterfaces/ecephys/neuroscope/requirements.txt b/src/neuroconv/datainterfaces/ecephys/neuroscope/requirements.txt
diff --git a/src/neuroconv/datainterfaces/ecephys/openephys/requirements.txt b/src/neuroconv/datainterfaces/ecephys/openephys/requirements.txt
diff --git a/src/neuroconv/datainterfaces/ecephys/plexon/requirements.txt b/src/neuroconv/datainterfaces/ecephys/plexon/requirements.txt
diff --git a/src/neuroconv/datainterfaces/ecephys/requirements.txt b/src/neuroconv/datainterfaces/ecephys/requirements.txt
diff --git a/src/neuroconv/datainterfaces/ecephys/spike2/requirements.txt b/src/neuroconv/datainterfaces/ecephys/spike2/requirements.txt
diff --git a/src/neuroconv/datainterfaces/icephys/abf/requirements.txt b/src/neuroconv/datainterfaces/icephys/abf/requirements.txt
diff --git a/src/neuroconv/datainterfaces/icephys/requirements.txt b/src/neuroconv/datainterfaces/icephys/requirements.txt
diff --git a/src/neuroconv/datainterfaces/ophys/brukertiff/requirements.txt b/src/neuroconv/datainterfaces/ophys/brukertiff/requirements.txt
diff --git a/src/neuroconv/datainterfaces/ophys/micromanagertiff/requirements.txt b/src/neuroconv/datainterfaces/ophys/micromanagertiff/requirements.txt
diff --git a/src/neuroconv/datainterfaces/ophys/miniscope/requirements.txt b/src/neuroconv/datainterfaces/ophys/miniscope/requirements.txt
diff --git a/src/neuroconv/datainterfaces/ophys/requirements.txt b/src/neuroconv/datainterfaces/ophys/requirements.txt
diff --git a/src/neuroconv/datainterfaces/ophys/scanimage/requirements.txt b/src/neuroconv/datainterfaces/ophys/scanimage/requirements.txt
diff --git a/src/neuroconv/datainterfaces/ophys/tdt_fp/requirements.txt b/src/neuroconv/datainterfaces/ophys/tdt_fp/requirements.txt
diff --git a/src/neuroconv/datainterfaces/ophys/tiff/requirements.txt b/src/neuroconv/datainterfaces/ophys/tiff/requirements.txt
diff --git a/src/neuroconv/datainterfaces/text/excel/requirements.txt b/src/neuroconv/datainterfaces/text/excel/requirements.txt
diff --git a/src/neuroconv/nwbconverter.py b/src/neuroconv/nwbconverter.py
@@ -80,7 +80,6 @@ def _validate_source_data(self, source_data: dict[str, dict], verbose: bool = Tr
     def __init__(self, source_data: dict[str, dict], verbose: bool = True):
         """Validate source_data against source_schema and initialize all data interfaces."""
         self.verbose = verbose
-        self._validate_source_data(source_data=source_data, verbose=self.verbose)
         self.data_interface_objects = {
             name: data_interface(**source_data[name])
             for name, data_interface in self.data_interface_classes.items()

diff --git a/tests/test_on_data/setup_paths.py b/tests/test_on_data/setup_paths.py
@@ -10,20 +10,19 @@
 
 
 # Load the configuration for the data tests
-
+project_root_path = Path(__file__).parent.parent.parent
 
 if os.getenv("CI"):
     LOCAL_PATH = Path(".")  # Must be set to "." for CI
     print("Running GIN tests on Github CI!")
 else:
     # Override LOCAL_PATH in the `gin_test_config.json` file to a point on your system that contains the dataset folder
     # Use DANDIHub at hub.dandiarchive.org for open, free use of data found in the /shared/catalystneuro/ directory
-    test_config_path = Path(__file__).parent / "gin_test_config.json"
+    test_config_path = project_root_path / "tests" / "test_on_data" / "gin_test_config.json"
     config_file_exists = test_config_path.exists()
     if not config_file_exists:
 
-        root = test_config_path.parent.parent
-        base_test_config_path = root / "base_gin_test_config.json"
+        base_test_config_path = project_root_path / "base_gin_test_config.json"
 
         test_config_path.parent.mkdir(parents=True, exist_ok=True)
         copy(src=base_test_config_path, dst=test_config_path)
@@ -40,4 +39,4 @@
 ECEPHY_DATA_PATH = LOCAL_PATH / "ephy_testing_data"
 OPHYS_DATA_PATH = LOCAL_PATH / "ophys_testing_data"
 
-TEXT_DATA_PATH = Path(__file__).parent.parent.parent / "tests" / "test_text"
+TEXT_DATA_PATH = project_root_path / "tests" / "test_text"