Set ceiling for HDMF to avoid failures with the latest release (#1175)

catalystneuro · Jan 14, 2025 · cd7764e · cd7764e
1 parent cb70df3
commit cd7764e
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Showing 4 changed files with 13 additions and 6 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
@@ -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
@@ -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
@@ -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"