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Replace PyYAML with ruamel.yaml in test_common_io.py #1418

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Merged
rly merged 1 commit into from
Mar 5, 2026
Merged

Replace PyYAML with ruamel.yaml in test_common_io.py #1418

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5 changes: 5 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,10 @@
# HDMF Changelog

## HDMF 5.0.1 (Upcoming)

### Fixed
- Replaced undeclared `pyyaml` dependency with `ruamel.yaml` (a declared core dependency) in `test_common_io.py`. The test relied on PyYAML being transitively installed by pip's `h5py`, which is not the case in conda environments. @rly [#1418](https://github.com/hdmf-dev/hdmf/pull/1418)

## HDMF 5.0.0 (March 2, 2026)

### Changed
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5 changes: 3 additions & 2 deletions tests/unit/common/test_common_io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
import os

from h5py import File
import yaml
from ruamel.yaml import YAML

from hdmf.backends.hdf5 import HDF5IO
from hdmf.common import Container, get_manager, get_hdf5io
Expand Down Expand Up @@ -70,8 +70,9 @@ def test_write_cache_spec_common_unresolved(self):
cached = json.loads(cached_json)

yaml_path = os.path.join(schema_dir, f'{spec_file}.yaml')
yaml_obj = YAML(typ='safe', pure=True)
with open(yaml_path, 'r') as yaml_file:
original = yaml.safe_load(yaml_file)
original = yaml_obj.load(yaml_file)

# Compare specs recursively (including subspecs)
self._compare_spec_dicts(cached, original, f'{spec_file}.yaml')
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