One test fails with pandas 3.0 dev version #3291
Description
In the GMT Dev tests workflow, one test fails (see https://github.com/GenericMappingTools/pygmt/actions/runs/9540235948/job/26291686710).
__________________________ test_compute_bins_outfile ___________________________
[gw1] linux -- Python 3.12.3 /home/runner/micromamba/envs/pygmt/bin/python
grid = <xarray.DataArray 'z' (lat: 14, lon: 8)> Size: 448B
array([[347.5, 344.5, 386. , 640.5, 617. , 579. , 646.5, 671. ],
...3.5 -22.5 -21.5 -20.5 ... -12.5 -11.5 -10.5
Attributes:
long_name: elevation (m)
actual_range: [190. 981.]
expected_df = start stop bin_id
0 345.5 519.5 0
1 519.5 726.5 1
region = [-52, -48, -22, -18]
def test_compute_bins_outfile(grid, expected_df, region):
"""
Test grdhisteq.compute_bins with ``outfile``.
"""
with GMTTempFile(suffix=".txt") as tmpfile:
with pytest.warns(RuntimeWarning) as record:
result = grdhisteq.compute_bins(
grid=grid,
divisions=2,
region=region,
outfile=tmpfile.name,
)
assert len(record) == 1 # check that only one warning was raised
assert result is None # return value is None
assert Path(tmpfile.name).stat().st_size > 0
temp_df = pd.read_csv(
filepath_or_buffer=tmpfile.name,
sep="\t",
header=None,
names=["start", "stop", "bin_id"],
dtype={"start": np.float32, "stop": np.float32, "bin_id": np.uint32},
index_col="bin_id",
)
> pd.testing.assert_frame_equal(
left=temp_df, right=expected_df.set_index("bin_id")
)
../pygmt/tests/test_grdhisteq.py:130:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
left = RangeIndex(start=0, stop=2, step=1, name='bin_id')
right = Index([0, 1], dtype='uint32', name='bin_id'), obj = 'DataFrame.index'
def _check_types(left, right, obj: str = "Index") -> None:
if not exact:
return
assert_class_equal(left, right, exact=exact, obj=obj)
assert_attr_equal("inferred_type", left, right, obj=obj)
# Skip exact dtype checking when `check_categorical` is False
if isinstance(left.dtype, CategoricalDtype) and isinstance(
right.dtype, CategoricalDtype
):
if check_categorical:
assert_attr_equal("dtype", left, right, obj=obj)
assert_index_equal(left.categories, right.categories, exact=exact)
return
> assert_attr_equal("dtype", left, right, obj=obj)
E AssertionError: DataFrame.index are different
E
E Attribute "dtype" are different
E [left]: int64
E [right]: uint32
The fail is likely due to changes/bugs in pandas dev version (3.x). To reproduce the issue:
>>> import numpy as np
>>> import pandas as pd
>>> df = pd.read_csv("text.dat", sep=r"\s+",
... header=None,
... names=["start", "stop", "bin_id"],
... dtype={"start": np.float32, "stop": np.float32, "bin_id": np.uint32},
... index_col="bin_id")
>>> df.index.dtype
pandas 2.x returns dtype('uint32') but pandas 3.x returns dtype('int64').
The test data is:
345.5 519.5 0
519.5 726.5 1
Need to read the pandas documentation to understand if it's a desired feature or an upstream bug.