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ValueError: invalid error value specified (Pandas 2.0+ Incompatibility) #89
Description
Description
Crash encountered when using parse() on a .gct file. The code appears to be incompatible with newer versions of Pandas, where the errors='ignore' argument in pd.to_numeric has been deprecated.
Traceback
File ".../site-packages/cmapPy/pandasGEXpress/parse_gct.py", line 139, in parse
(row_metadata, col_metadata, data) = parse_into_3_df(
~~~~~~~~~~~~~~~^
file_path, num_data_rows, num_data_cols,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
num_row_metadata, num_col_metadata, nan_values)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ".../site-packages/cmapPy/pandasGEXpress/parse_gct.py", line 224, in parse_into_3_df
row_metadata = assemble_row_metadata(full_df, num_col_metadata, num_data_rows, num_row_metadata)
File ".../site-packages/cmapPy/pandasGEXpress/parse_gct.py", line 251, in assemble_row_metadata
row_metadata = row_metadata.apply(lambda x: pd.to_numeric(x, errors="ignore"))
File ".../site-packages/pandas/core/frame.py", line 12419, in apply
return op.apply().__finalize__(self, method="apply")
~~~~~~~~^^
File ".../site-packages/pandas/core/apply.py", line 1015, in apply
return self.apply_standard()
~~~~~~~~~~~~~~~~~~~^^
File ".../site-packages/pandas/core/apply.py", line 1167, in apply_standard
results, res_index = self.apply_series_generator()
~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File ".../site-packages/pandas/core/apply.py", line 1183, in apply_series_generator
results[i] = self.func(v, *self.args, **self.kwargs)
~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ".../site-packages/cmapPy/pandasGEXpress/parse_gct.py", line 251, in <lambda>
row_metadata = row_metadata.apply(lambda x: pd.to_numeric(x, errors="ignore"))
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^
File ".../site-packages/pandas/core/tools/numeric.py", line 183, in to_numeric
raise ValueError("invalid error value specified")
ValueError: invalid error value specified
Fix
The following at line 251 can fix the issue locally:
def safe_convert(x):
try:
return pd.to_numeric(x)
except:
return x
row_metadata = row_metadata.apply(safe_convert)
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