Mark test_binstats_quantile as xfail in the GMT Legacy Tests workflow

[weiji14]

Description of proposed changes

The test_binstats_quantile test (introduced in #3012) is failing on the legacy CI tests. Trying to see if it's due to xarray/pandas/numpy or using old version of GMT 6.4 Edit: seems to be that GMT 6.4 gives different results to GMT 6.5+, most likely due to changes in GenericMappingTools/gmt#8243

Traceback from https://github.com/GenericMappingTools/pygmt/actions/runs/16895808645/job/47865247702#step:6:1098

___________________________ test_binstats_quantile ____________________________
deftest_binstats_quantile():
"""
Test binstats quantile statistic functionality.
"""
temp_grid = binstats(
data="@capitals.gmt",
spacing=5,
statistic="quantile",
quantile_value=75,
search_radius="1000k",
aspatial="2=population",
region="g",
)
assert temp_grid.dims == ("y", "x")
assert temp_grid.gmt.gtype is GridType.CARTESIANassert temp_grid.gmt.registration is GridRegistration.GRIDLINE
npt.assert_allclose(temp_grid.max(), 15047685)
> npt.assert_allclose(temp_grid.min(), 53)
..\pygmt\tests\test_binstats.py:71: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
args = (<function assert_allclose.<locals>.compare at 0x000001D761A02E80>, array(0., dtype=float32), array(53))
kwds = {'equal_nan': True, 'err_msg': '', 'header': 'Not equal to tolerance rtol=1e-07, atol=0', 'verbose': True}
@wraps(func)
definner(*args, **kwds):
withself._recreate_cm():
> return func(*args, **kwds)
E AssertionError: E Not equal to tolerance rtol=1e-07, atol=0
E E Mismatched elements: 1 / 1 (100%)
E Max absolute difference: 53.
E Max relative difference: 1.
E x: array(0., dtype=float32)
E y: array(53)
C:\hostedtoolcache\windows\Python\3.11.9\x64\Lib\contextlib.py:81: AssertionError

Output of pygmt.show_versions() from CI:

PyGMT information:
version: v0.17.0.dev39+g354b50a0f
System information:
python: 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:36:13) [GCC 12.3.0]
executable: /home/runner/micromamba/envs/pygmt/bin/python
machine: Linux-6.8.0-1031-azure-x86_64-with-glibc2.35
Dependency information:
numpy: 1.26.4
pandas: 2.3.1
xarray: 2025.7.1
packaging: 24.2
contextily: 1.5.2
geopandas: 1.0.1
IPython: 9.4.0
pyarrow: 16.1.0
rioxarray: 0.19.0
gdal: 3.8.5
ghostscript: 9.56.1
GMT library information:
version: 6.4.0
padding: 2
share dir: /home/runner/micromamba/envs/pygmt/share/gmt
plugin dir: /home/runner/micromamba/envs/pygmt/lib/gmt/plugins
library path: /home/runner/micromamba/envs/pygmt/lib/libgmt.so
cores: 4
grid layout: rows
image layout: binary version: 6.4.0

Patches #3012

Preview:

Reminders

• Run make format and make check to make sure the code follows the style guide.
• Add tests for new features or tests that would have caught the bug that you're fixing.
• Add new public functions/methods/classes to doc/api/index.rst.
• Write detailed docstrings for all functions/methods.
• If wrapping a new module, open a 'Wrap new GMT module' issue and submit reasonably-sized PRs.
• If adding new functionality, add an example to docstrings or tutorials.

Slash Commands

You can write slash commands (/command) in the first line of a comment to perform
specific operations. Supported slash command is:

• /format: automatically format and lint the code

[weiji14]

This PR probably won't be needed if #4017 goes ahead, depends on whether we can get #4018 to work before the next release.

[weiji14]

Unsure which values are the correct ones. Do we want to check in upstream GMT on what might have changed binstat from GMT 6.4 to 6.5?

[seisman]

Likely related to GenericMappingTools/gmt#8243.

[weiji14]

Thanks for the reminder, forgot about that thread! Have changed to an xfail in commit 1dc2e42