diff --git a/.gitignore b/.gitignore index 04504e9e0..c1e9ea2b8 100644 --- 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 index 1cf788ad9..cfdf7f649 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ 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 diff --git a/pyproject.toml b/pyproject.toml index cd92852ec..9debeb5e9 100644 --- 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/tests/test_on_data/setup_paths.py b/tests/test_on_data/setup_paths.py index 3f7bf4123..939a9d74b 100644 --- a/tests/test_on_data/setup_paths.py +++ b/tests/test_on_data/setup_paths.py @@ -10,7 +10,7 @@ # 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 @@ -18,12 +18,11 @@ 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"