v1.4.0 #157
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v1.4.0 #157
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* Made pygam an optional dependency that can be installed with `pip install palantir[gam]` or `pip install palantir[full]` * Added proper conditional imports and improved error handling for pygam * Enhanced `run_magic_imputation` to return appropriate data types for different inputs * For numpy arrays or csr_matrix inputs, returns sparse matrices by default (sparse=True) * For pandas DataFrames, returns pandas DataFrames * For AnnData objects, stores results in the object and returns sparse matrices by default * Maintained sparse=True as the default for run_magic_imputation for backward compatibility * Added better support for both sparse and dense output formats in `run_magic_imputation` * Fixed circular import issues between modules * Updated code to use direct AnnData imports for newer compatibility * Improved version detection using importlib.metadata with graceful fallbacks * Fixed Series indexing deprecation warnings in early cell detection functions * Standardized documentation with NumPy-style docstrings throughout the codebase * Added comprehensive type hints to improve code quality and IDE support
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This merges all the changes for v1.4.0 including:
pip install palantir[gam]orpip install palantir[full]run_magic_imputationto return appropriate data types for different inputsimportlib.metadatawith graceful fallbacks_methods from scanpy for plotting.