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

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merged 5 commits into from
Jan 14, 2025
Merged

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

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46ddd4e
test fix
h-mayorquin Jan 8, 2025
44ddacc
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 8, 2025
07a8063
pep 508 compliant
h-mayorquin Jan 8, 2025
ec7d012
setup paths fix
h-mayorquin Jan 8, 2025
8cf6cbc
changelog
h-mayorquin Jan 13, 2025
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7 changes: 7 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,13 @@ __pycache__/
# C extensions
*.so


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I have been using uv on my mac and I would like to add uv to our gitignore.

This is in line with what github is doing now, see:
github/gitignore#4545

For the same change "upstream".

# 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/
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -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

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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -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",
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9 changes: 4 additions & 5 deletions tests/test_on_data/setup_paths.py
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This was failing to create the file for me on mac when using uv. I guess the problem is that uv uses a different base directory.

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I also tested this on a conda base installation on my linux system and it correctly moves the file.

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Why was this failing? Could it not find the base_gin_test_config.json file when you were using uv?

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I can't remember right now. Either source or destination was incorrect during the copy.

Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand All @@ -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"
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