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The dependency check passed a list to importlib.metadata.version(), which expects a single distribution name. It always raised TypeError, was swallowed by the blanket except, and left ElementTree unbound, so sleep_staging_shhs_fn could never parse SHHS labels. ElementTree is the standard library and the only XML API the function uses; elementpath was never referenced and is not a declared dependency. Import ElementTree at module top and drop the check.
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Title: Fix SHHS sleep staging dependency check leaving XML parser undefined
Fixes #1282.
sleep_staging_shhs_fninpyhealth/tasks/sleep_staging.pycould not parse SHHS labels. Its dependency check passed a list toimportlib.metadata.version(), which takes one distribution name, so it always raisedTypeError. The bareexceptswallowed that,import xml.etree.ElementTree as ETnever ran, andET.fromstringraisedUnboundLocalError.The check guarded
elementpath, which the function never uses and the package does not declare. This PR removes the check and imports ElementTree at module level.Changes
pyhealth/tasks/sleep_staging.py: remove the dependency check and importxml.etree.ElementTreeat the top of the module.tests/core/test_sleep_staging_shhs.py: new tests. One checks thatETis bound at module level. One runssleep_staging_shhs_fnend to end with a stubbed EDF read and an SHHS-shaped XML annotation file, and checks the labels and saved epochs.docs/api/tasks/pyhealth.tasks.sleep_staging.rst: note that SHHS annotation parsing needs only the standard library.examples/eeg/sleep_staging/sleep_staging_shhs_contrawr.py: remove the unusedContraWRimport.The issue offers two fixes: call
version("elementpath"), or remove the check. I removed it, because a repaired check would either ask users to install a package the function does not need or add a new hard dependency. If you prefer to keep a check, I can restore it.Both new tests fail on the current code and pass with this change.