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bugSomething isn't workingSomething isn't workingsmall thing/optimizationMinor change or marginal benefit (but would be nice)Minor change or marginal benefit (but would be nice)
Description
There was another recent build failure that i discovered to be caused by the latest pandas release (i think it happened today). i fixed the issue by pinning our pandas installation in the build-deploy github workflow to 2.2.3.
RespiLens should work with latest pandas.
https://github.com/ACCIDDA/RespiLens/actions/runs/21220830841/job/61054808766 (but will get deleted so copy paste
INFO:__main__:Collecting data from FluSight repo...
/home/runner/work/RespiLens/RespiLens/scripts/helper.py:66: UserWarning: Could not infer format, so each element will be parsed individually, falling back to `dateutil`. To ensure parsing is consistent and as-expected, please specify a format.
date_output_ids = pd.to_datetime(df['output_type_id'], errors='coerce')
Traceback (most recent call last):
File "/home/runner/work/RespiLens/RespiLens/scripts/process_RespiLens_data.py", line 157, in <module>
main()
File "/home/runner/work/RespiLens/RespiLens/scripts/process_RespiLens_data.py", line 61, in main
flu_hubverse_df = clean_nan_values(hubverse_df_preprocessor(df=flu_hub_conn.get_dataset().to_table().to_pandas(), filter_nowcasts=True))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/RespiLens/RespiLens/scripts/helper.py", line 72, in hubverse_df_preprocessor
df.loc[quantile_mask, 'output_type_id'] = df.loc[quantile_mask, 'output_type_id'].astype(float)
~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.14/x64/lib/python3.11/site-packages/pandas/core/indexing.py", line 938, in __setitem__
iloc._setitem_with_indexer(indexer, value, self.name)
File "/opt/hostedtoolcache/Python/3.11.14/x64/lib/python3.11/site-packages/pandas/core/indexing.py", line 1953, in _setitem_with_indexer
self._setitem_with_indexer_split_path(indexer, value, name)
File "/opt/hostedtoolcache/Python/3.11.14/x64/lib/python3.11/site-packages/pandas/core/indexing.py", line 1997, in _setitem_with_indexer_split_path
self._setitem_single_column(ilocs[0], value, pi)
File "/opt/hostedtoolcache/Python/3.11.14/x64/lib/python3.11/site-packages/pandas/core/indexing.py", line 2181, in _setitem_single_column
self.obj._mgr.column_setitem(loc, plane_indexer, value)
File "/opt/hostedtoolcache/Python/3.11.14/x64/lib/python3.11/site-packages/pandas/core/internals/managers.py", line 1503, in column_setitem
new_mgr = col_mgr.setitem((idx,), value)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.14/x64/lib/python3.11/site-packages/pandas/core/internals/managers.py", line 604, in setitem
return self.apply("setitem", indexer=indexer, value=value)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.14/x64/lib/python3.11/site-packages/pandas/core/internals/managers.py", line 442, in apply
applied = getattr(b, f)(**kwargs)
^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.14/x64/lib/python3.11/site-packages/pandas/core/internals/blocks.py", line 1667, in setitem
values[indexer] = value
~~~~~~^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.14/x64/lib/python3.11/site-packages/pandas/core/arrays/arrow/array.py", line 2221, in __setitem__
value = self._maybe_convert_setitem_value(value)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.14/x64/lib/python3.11/site-packages/pandas/core/arrays/string_arrow.py", line 293, in _maybe_convert_setitem_value
raise TypeError(
TypeError: Invalid value for dtype 'str'. Value should be a string or missing value (or array of those).
Error: Process completed with exit code 1.
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bugSomething isn't workingSomething isn't workingsmall thing/optimizationMinor change or marginal benefit (but would be nice)Minor change or marginal benefit (but would be nice)