Update Dependency Compatibility #2716
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mikejhuang
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morriscb
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Aug 11, 2023
| @@ -164,7 +164,7 @@ def json_handler(obj): | |||
| return float(obj) | |||
| elif isinstance(obj, np.integer): | |||
| return int(obj) | |||
| elif (isinstance(obj, np.bool) or | |||
| elif (isinstance(obj, bool) or | |||
| isinstance(obj, np.bool_)): | |||
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Wanted to make sure this one shouldn't also be changed to bool_ as interval_unionize/data_utilities.py was switched from np.bool_ to bool_.
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Include Python 3.11 compatibility, unpeg all dependencies and fix breaking changes from updated packages or downgrade packages.
Steps
1.Unpin requirements.txt
2. Use poetry to setup supported python version range into pyproject.toml
4. Add requirements.txt dependencies with poetry and resolve Python version compatibility issues
5. xarray, scipy, and numpy versions adjusted to meet python version requirements
6. Run tests by creating virtualenv with 3.8, 3.9, 3.10, 3.11
7. For failing tests, either fix code or revert package version
Final explicitly defined requirements
8. Remove poetry created files (pyproject.toml, poetry.lock)
Fixes for compatibility
Int64Indexdeprecated DEPR: Remove Int64Index, UInt64Index, Float64Index and Index._is_backward_compat_public_numeric_index pandas-dev/pandas#42717pd.Series.str.replacemust specifyregex=Trueif regex is used.pd.Series.reindexwith aMultiIndexcan no longer take in single integer Index as an inputcheck_less_preciseis a deprecated parameter inpd.testing.assert_series_equal. This is replaced withr_tolanda_tolReverting versions instead of fixing
VisualBehaviorProjectCache.get_ophys_session_table( index_column="ophys_experiment_id").indexis type'object', expectedint64All the values in this index are int64 so I'm not sure why it was loaded as an object type.