test_reproject fails on Debian sid

[avalentino]

Code Sample, a copy-pastable example if possible

$ python3 -m pytest -k "not test_clip_geojson__no_drop"

[CUT]
=========================== short test summary info ============================
FAILED test/integration/test_integration_rioxarray.py::test_clip_box__auto_expand[open_rasterio]
FAILED test/integration/test_integration_rioxarray.py::test_clip_box__auto_expand[modis_clip3]
FAILED test/integration/test_integration_rioxarray.py::test_clip_box__auto_expand[modis_clip4]
FAILED test/integration/test_integration_rioxarray.py::test_reproject[modis_reproject2]
FAILED test/integration/test_integration_rioxarray.py::test_reproject__grid_mapping[modis_reproject2]
FAILED test/integration/test_integration_rioxarray.py::test_reproject__masked[modis_reproject2]
FAILED test/integration/test_integration_rioxarray.py::test_reproject__str_resample[modis_reproject2]
FAILED test/integration/test_integration_rioxarray.py::test_reproject__no_transform[modis_reproject2]
FAILED test/integration/test_integration_rioxarray.py::test_reproject__no_nodata[modis_reproject2-None]

[CUT]

FAILED test/integration/test_integration_rioxarray.py::test_reproject__no_nodata[modis_reproject2--9999]
FAILED test/integration/test_integration_rioxarray.py::test_reproject__no_nodata_masked[modis_reproject2]
FAILED test/integration/test_integration_rioxarray.py::test_reproject_match[open_rasterio]
FAILED test/integration/test_integration_rioxarray.py::test_reproject_match[modis_reproject_match3]
FAILED test/integration/test_integration_rioxarray.py::test_reproject_match[modis_reproject_match4]
FAILED test/integration/test_integration_rioxarray.py::test_reproject_match__masked[open_rasterio]
FAILED test/integration/test_integration_rioxarray.py::test_reproject_match__masked[modis_reproject_match3]
FAILED test/integration/test_integration_rioxarray.py::test_reproject_match__masked[modis_reproject_match4]
FAILED test/integration/test_integration_rioxarray.py::test_reproject_match__no_transform_nodata[open_rasterio]
FAILED test/integration/test_integration_rioxarray.py::test_reproject_match__no_transform_nodata[modis_reproject_match_coords3]
FAILED test/integration/test_integration_rioxarray.py::test_reproject_match__pass_nodata[open_rasterio]
FAILED test/integration/test_integration_rioxarray.py::test_reproject_match__pass_nodata[modis_reproject_match__passed_nodata3]
FAILED test/integration/test_integration_rioxarray.py::test_reproject_match__pass_nodata[modis_reproject_match__passed_nodata4]
= 22 failed, 512 passed, 4 skipped, 8 deselected, 2 xfailed, 4 xpassed, 173 warnings in 12.18s =

Problem description

Some tests fail on Debian Sid but not with a clean installation from pip.
The list of failing tests are reported above.
I tried to investigate a bit

test/integration/test_integration_rioxarray.py::test_reproject[modis_reproject2] 

and compared intermediate variables with the clean pip installation.

def test_reproject(modis_reproject):
    mask_args = (
        dict(masked=False, mask_and_scale=False)
        if "rasterio" in str(modis_reproject["open"])
        else dict(mask_and_scale=False)
    )
    print("mask_args:", mask_args)
    print('modis_reproject["open"]:', modis_reproject["open"])
    with (
        modis_reproject["open"](modis_reproject["input"], **mask_args) as mda,
        modis_reproject["open"](modis_reproject["compare"], **mask_args) as mdc,
    ):
        print('modis_reproject["to_proj"]:', modis_reproject["to_proj"])
        mds_repr = mda.rio.reproject(modis_reproject["to_proj"])

        # overwrite test dataset
        # if isinstance(mds_repr, xarray.DataArray):
        #    mds_repr.to_netcdf(modis_reproject["compare"])

        # test
        _assert_xarrays_equal(mds_repr, mdc)
        assert mds_repr.coords[mds_repr.rio.x_dim].attrs == {
            "axis": "X",
            "long_name": "x coordinate of projection",
            "standard_name": "projection_x_coordinate",
            "units": "metre",
        }
        assert mds_repr.coords[mds_repr.rio.y_dim].attrs == {
            "axis": "Y",
            "long_name": "y coordinate of projection",
            "standard_name": "projection_y_coordinate",
            "units": "metre",
        }

Apparently the mdc variable seems to be flipped vertically in the case of the Debian installation (which seems to suggest some link with #650) but for the pip installation everything looks fine.

I collected the following information that could be relevant in this case:

* Debian installation

SCIPY_LT_17: False
SCIPY_INSTALLED: True
scipy.__version__: 1.16.3
GDAL_GE_361: True
rasterio.__gdal_version__: 3.12.3
rasterio.__version__: 1.5.0
MODIS_ARRAY_UTM: /home/antonio/debian/git/python-rioxarray/test/test_data/compare/MODIS_ARRAY_UTM_GDAL361.nc
mask_args: {'masked': False, 'mask_and_scale': False}
modis_reproject["open"]: functools.partial(<function open_dataset at 0x7b8953fa85e0>, engine='rasterio')
modis_reproject["to_proj"]: +datum=WGS84 +no_defs +proj=utm +units=m +zone=15

* pip installation

SCIPY_LT_17: False
SCIPY_INSTALLED: True
scipy.__version__: 1.17.1
GDAL_GE_361: True
rasterio.__gdal_version__: 3.12.1
rasterio.__version__: 1.5.0
MODIS_ARRAY_UTM: /home/antonio/debian/git/python-rioxarray/test/test_data/compare/MODIS_ARRAY_UTM_GDAL361.nc
mask_args: {'masked': False, 'mask_and_scale': False}
modis_reproject["open"]: functools.partial(<function open_dataset at 0x7d575a6713a0>, engine='rasterio')
modis_reproject["to_proj"]: +datum=WGS84 +no_defs +proj=utm +units=m +zone=15

Expected Output

All unittests pass.

Environment Information

Debian installation

rioxarray (0.22.0) deps:
  rasterio: 1.5.0
    xarray: 2026.1.0
      GDAL: 3.12.3
      GEOS: 3.14.1
      PROJ: 9.8.1
 PROJ DATA: ~/.local/share/proj:/usr/share/proj
 GDAL DATA: None

Other python deps:
     scipy: 1.16.3
    pyproj: 3.7.2

System:
    python: 3.13.12 (main, Feb  4 2026, 15:06:39) [GCC 15.2.0]
executable: /usr/bin/python3
   machine: Linux-6.17.0-22-generic-x86_64-with-glibc2.42

Pip installation

rioxarray (0.22.0) deps:
  rasterio: 1.5.0
    xarray: 2026.4.0
      GDAL: 3.12.1
      GEOS: 3.14.1
      PROJ: 9.7.1
 PROJ DATA: ~/debian/git/python-rioxarray/venv/lib/python3.13/site-packages/rasterio/proj_data
 GDAL DATA: ~/debian/git/python-rioxarray/venv/lib/python3.13/site-packages/rasterio/gdal_data

Other python deps:
     scipy: 1.17.1
    pyproj: 3.7.2

System:
    python: 3.13.12 (main, Feb  4 2026, 15:06:39) [GCC 15.2.0]
executable: ~/debian/git/python-rioxarray/venv/bin/python3
   machine: Linux-6.17.0-22-generic-x86_64-with-glibc2.42

Installation method

• installation form debian packages on Debian sid