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Fix the conversion error for pandas.Series with missing values in pandas<=2.1 #3505

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Merged
seisman merged 4 commits into from
Oct 11, 2024
Merged

Fix the conversion error for pandas.Series with missing values in pandas<=2.1 #3505

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5d4bff5
Add workaround for pandas.NA support with pandas<=2.1
seisman Oct 10, 2024
e110015
Remove a blank line
seisman Oct 11, 2024
fd2bf10
Merge branch 'main' into pandas/NA
seisman Oct 11, 2024
aa5d839
Fix a typo [skip ci]
seisman Oct 11, 2024
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22 changes: 20 additions & 2 deletions pygmt/clib/conversion.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,8 @@
from collections.abc import Sequence

import numpy as np
import pandas as pd
from packaging.version import Version
from pygmt.exceptions import GMTInvalidInput


Expand Down Expand Up @@ -178,6 +180,10 @@ def vectors_to_arrays(vectors):
>>> [i.ndim for i in data] # Check that they are 1-D arrays
[1, 1, 1]

>>> series = pd.Series(data=[0, 4, pd.NA, 8, 6], dtype=pd.Int32Dtype())
>>> vectors_to_arrays([series])
[array([ 0., 4., nan, 8., 6.])]

>>> import datetime
>>> import pytest
>>> pa = pytest.importorskip("pyarrow")
Expand Down Expand Up @@ -205,8 +211,20 @@ def vectors_to_arrays(vectors):
}
arrays = []
for vector in vectors:
vec_dtype = str(getattr(vector, "dtype", ""))
arrays.append(np.ascontiguousarray(vector, dtype=dtypes.get(vec_dtype)))
if (
hasattr(vector, "isna")
and vector.isna().any()
and Version(pd.__version__) < Version("2.2")
):
# Workaround for dealing with pd.NA with pandas < 2.2.
# Bug report at: https://github.com/GenericMappingTools/pygmt/issues/2844
# Following SPEC0, pandas 2.1 will be dropped in 2025 Q3, so it's likely
# we can remove the workaround in PyGMT v0.17.0.
array = np.ascontiguousarray(vector.astype(float))
else:
vec_dtype = str(getattr(vector, "dtype", ""))
array = np.ascontiguousarray(vector, dtype=dtypes.get(vec_dtype))
arrays.append(array)
return arrays


Expand Down