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SPEC 0: Bump minimum supported version to NumPy 2.0 and Xarray 2024.5 #4090

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Merged
merged 12 commits into from
Oct 15, 2025
Merged

SPEC 0: Bump minimum supported version to NumPy 2.0 and Xarray 2024.5 #4090

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1abd1f2
SPEC 0: Bump minimum supported versions to NumPy 2.0
seisman Sep 16, 2025
d1d79d2
Remove workarounds for NumPy < 2.0
seisman Sep 16, 2025
5ce69a2
Fix two tests due to the removal of conftest.py
seisman Sep 16, 2025
88adf9a
Merge branch 'main' into spec0/numpy
seisman Sep 17, 2025
f0753eb
Merge branch 'main' into spec0/numpy
seisman Oct 8, 2025
1b97f25
Bump to xarray 2024.5
seisman Oct 8, 2025
5c7e25c
Merge branch 'main' into spec0/numpy
seisman Oct 9, 2025
7d3c1d1
Update to xarray repr for xarray>=2024.02
seisman Oct 9, 2025
e1a0e4e
Fix doctests
seisman Oct 9, 2025
0bc407b
Fix int to int64, but it may not work on Windows
seisman Oct 9, 2025
69e5417
Merge branch 'main' into spec0/numpy
seisman Oct 12, 2025
14c53bb
Merge branch 'main' into spec0/numpy
seisman Oct 14, 2025
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4 changes: 2 additions & 2 deletions .github/workflows/ci_tests.yaml
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Expand Up @@ -72,9 +72,9 @@ jobs:
include:
# Python 3.11 + core packages (minimum supported versions) + optional packages (minimum supported versions if any)
- python-version: '3.11'
numpy-version: '1.26'
numpy-version: '2.0'
pandas-version: '=2.2'
xarray-version: '=2023.10'
xarray-version: '=2024.5'
optional-packages: ' contextily geopandas ipython pyarrow-core rioxarray netCDF4 sphinx-gallery'
# Python 3.13 + core packages (latest versions) + optional packages
- python-version: '3.13'
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4 changes: 2 additions & 2 deletions .github/workflows/ci_tests_legacy.yaml
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Expand Up @@ -61,9 +61,9 @@ jobs:
python=3.11
gmt=${{ matrix.gmt_version }}
ghostscript
numpy=1.26
numpy=2.0
pandas=2.2
xarray=2023.10
xarray=2024.5
packaging=24.2
contextily=1.5
geopandas=1.0
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4 changes: 2 additions & 2 deletions environment.yml
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Expand Up @@ -7,9 +7,9 @@ dependencies:
# Required dependencies
- gmt=6.6.0
- ghostscript=10.06.0
- numpy>=1.26
- numpy>=2.0
- pandas>=2.2
- xarray>=2023.10
- xarray>=2024.5
- packaging>=24.2
# Optional dependencies
- contextily>=1.5
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11 changes: 0 additions & 11 deletions pygmt/conftest.py
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This file was deleted.

10 changes: 5 additions & 5 deletions pygmt/datasets/tile_map.py
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Expand Up @@ -122,12 +122,12 @@ def load_tile_map(
... )
>>> raster.sizes
Frozen({'band': 3, 'y': 256, 'x': 512})
>>> raster.coords # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
>>> raster.coords
Coordinates:
* band (band) uint8... 1 2 3
* y (y) float64... -7.081e-10 -7.858e+04 ... -1.996e+07 -2.004e+07
* x (x) float64... -2.004e+07 -1.996e+07 ... 1.996e+07 2.004e+07
spatial_ref int... 0
* band (band) uint8 3B 1 2 3
* y (y) float64 2kB -7.081e-10 -7.858e+04 ... -1.996e+07 -2.004e+07
* x (x) float64 4kB -2.004e+07 -1.996e+07 ... 1.996e+07 2.004e+07
spatial_ref int64 8B 0
>>> # CRS is set only if rioxarray is available
>>> if hasattr(raster, "rio"):
... raster.rio.crs.to_string()
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22 changes: 11 additions & 11 deletions pygmt/datatypes/grid.py
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Expand Up @@ -114,8 +114,8 @@ def to_xarray(self) -> xr.DataArray:
... grid = lib.read_virtualfile(voutgrd, kind="grid")
... # Convert to xarray.DataArray and use it later
... da = grid.contents.to_xarray()
>>> da # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
<xarray.DataArray 'z' (lat: 14, lon: 8)>...
>>> da
<xarray.DataArray 'z' (lat: 14, lon: 8)> Size: 448B
array([[347.5, 344.5, 386. , 640.5, 617. , 579. , 646.5, 671. ],
[383. , 284.5, 344.5, 394. , 491. , 556.5, 578.5, 618.5],
[373. , 367.5, 349. , 352.5, 419.5, 428. , 570. , 667.5],
Expand All @@ -132,32 +132,32 @@ def to_xarray(self) -> xr.DataArray:
[347.5, 331.5, 309. , 282. , 190. , 208. , 299.5, 348. ]],
dtype=float32)
Coordinates:
* lat (lat) float64... -23.5 -22.5 -21.5 -20.5 ... -12.5 -11.5 -10.5
* lon (lon) float64... -54.5 -53.5 -52.5 -51.5 -50.5 -49.5 -48.5 -47.5
* lat (lat) float64 112B -23.5 -22.5 -21.5 -20.5 ... -12.5 -11.5 -10.5
* lon (lon) float64 64B -54.5 -53.5 -52.5 -51.5 -50.5 -49.5 -48.5 -47.5
Attributes:
Conventions: CF-1.7
title: Produced by grdcut
history: grdcut @earth_relief_01d_p -R-55/-47/-24/-10 -Gstatic_ea...
description: Reduced by Gaussian Cartesian filtering (111.2 km fullwi...
actual_range: [190. 981.]
long_name: elevation (m)
>>> da.coords["lon"] # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
<xarray.DataArray 'lon' (lon: 8)>...
>>> da.coords["lon"]
<xarray.DataArray 'lon' (lon: 8)> Size: 64B
array([-54.5, -53.5, -52.5, -51.5, -50.5, -49.5, -48.5, -47.5])
Coordinates:
* lon (lon) float64... -54.5 -53.5 -52.5 -51.5 -50.5 -49.5 -48.5 -47.5
* lon (lon) float64 64B -54.5 -53.5 -52.5 -51.5 -50.5 -49.5 -48.5 -47.5
Attributes:
long_name: longitude
units: degrees_east
standard_name: longitude
axis: X
actual_range: [-55. -47.]
>>> da.coords["lat"] # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
<xarray.DataArray 'lat' (lat: 14)>...
>>> da.coords["lat"]
<xarray.DataArray 'lat' (lat: 14)> Size: 112B
array([-23.5, -22.5, -21.5, -20.5, -19.5, -18.5, -17.5, -16.5, -15.5, -14.5,
-13.5, -12.5, -11.5, -10.5])
-13.5, -12.5, -11.5, -10.5])
Coordinates:
* lat (lat) float64... -23.5 -22.5 -21.5 -20.5 ... -12.5 -11.5 -10.5
* lat (lat) float64 112B -23.5 -22.5 -21.5 -20.5 ... -12.5 -11.5 -10.5
Attributes:
long_name: latitude
units: degrees_north
Expand Down
17 changes: 9 additions & 8 deletions pygmt/datatypes/image.py
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Expand Up @@ -67,16 +67,16 @@ class _GMT_IMAGE(ctp.Structure): # noqa: N801
[2, 2, 2, 2]
b'BRPa' 0.5
1 0
>>> x # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
>>> x
array([-179.5, -178.5, ..., 178.5, 179.5])
>>> y # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
>>> y
array([ 89.5, 88.5, ..., -88.5, -89.5])
>>> data.dtype
dtype('uint8')
>>> data.shape
(180, 360, 3)
>>> data.min(), data.max()
(10, 255)
(np.uint8(10), np.uint8(255))
"""

_fields_: ClassVar = [
Expand Down Expand Up @@ -121,7 +121,7 @@ def to_xarray(self) -> xr.DataArray:
... image = lib.read_virtualfile(voutimg, kind="image")
... # Convert to xarray.DataArray and use it later
... da = image.contents.to_xarray()
>>> da # doctest: +NORMALIZE_WHITESPACE
>>> da
<xarray.DataArray 'z' (band: 3, y: 180, x: 360)> Size: 194kB
array([[[ 10, 10, 10, ..., 10, 10, 10],
[ 10, 10, 10, ..., 10, 10, 10],
Expand All @@ -145,24 +145,25 @@ def to_xarray(self) -> xr.DataArray:
...,
[177, 179, 179, ..., 178, 177, 177],
[185, 187, 187, ..., 187, 186, 185],
[189, 191, 191, ..., 191, 191, 189]]], dtype=uint8)
[189, 191, 191, ..., 191, 191, 189]]],
shape=(3, 180, 360), dtype=uint8)
Coordinates:
* band (band) uint8 3B 1 2 3
* y (y) float64 1kB 89.5 88.5 87.5 86.5 ... -86.5 -87.5 -88.5 -89.5
* x (x) float64 3kB -179.5 -178.5 -177.5 -176.5 ... 177.5 178.5 179.5
Attributes:
long_name: z

>>> da.coords["x"] # doctest: +NORMALIZE_WHITESPACE
>>> da.coords["x"]
<xarray.DataArray 'x' (x: 360)> Size: 3kB
array([-179.5, -178.5, -177.5, ..., 177.5, 178.5, 179.5])
array([-179.5, -178.5, -177.5, ..., 177.5, 178.5, 179.5], shape=(360,))
Coordinates:
* x (x) float64 3kB -179.5 -178.5 -177.5 -176.5 ... 177.5 178.5 179.5
Attributes:
long_name: x
axis: X
actual_range: [-180. 180.]
>>> da.coords["y"] # doctest: +NORMALIZE_WHITESPACE
>>> da.coords["y"]
<xarray.DataArray 'y' (y: 180)> Size: 1kB
array([ 89.5, 88.5, 87.5, 86.5, ..., -87.5, -88.5, -89.5])
Coordinates:
Expand Down
4 changes: 1 addition & 3 deletions pygmt/helpers/decorators.py
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Expand Up @@ -514,9 +514,7 @@ def use_alias(**aliases):
R = bla J = meh
>>> my_module(region="bla", projection="meh")
R = bla J = meh
>>> my_module(
... region="bla", projection="meh", J="bla"
... ) # doctest: +NORMALIZE_WHITESPACE
>>> my_module(region="bla", projection="meh", J="bla")
Traceback (most recent call last):
...
pygmt.exceptions.GMTInvalidInput:
Expand Down
10 changes: 1 addition & 9 deletions pygmt/tests/test_clib_to_numpy.py
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Expand Up @@ -3,7 +3,6 @@
"""

import datetime
import sys

import numpy as np
import numpy.testing as npt
Expand Down Expand Up @@ -52,14 +51,7 @@ def _check_result(result, expected_dtype):
@pytest.mark.parametrize(
("data", "expected_dtype"),
[
# TODO(NumPy>=2.0): Remove the if-else statement after NumPy>=2.0.
pytest.param(
[1, 2, 3],
np.int32
if sys.platform == "win32" and Version(np.__version__) < Version("2.0")
else np.int64,
id="int",
),
pytest.param([1, 2, 3], np.int64, id="int"),
pytest.param([1.0, 2.0, 3.0], np.float64, id="float"),
pytest.param(
[complex(+1), complex(-2j), complex("-Infinity+NaNj")],
Expand Down
16 changes: 8 additions & 8 deletions pygmt/xarray/backend.py
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Expand Up @@ -50,13 +50,13 @@ class GMTBackendEntrypoint(BackendEntrypoint):
>>> da_grid = xr.open_dataarray(
... "@static_earth_relief.nc", engine="gmt", raster_kind="grid"
... )
>>> da_grid # doctest: +NORMALIZE_WHITESPACE
>>> da_grid
<xarray.DataArray 'z' (lat: 14, lon: 8)> Size: 448B
[112 values with dtype=float32]
Coordinates:
* lat (lat) float64 112B -23.5 -22.5 -21.5 -20.5 ... -12.5 -11.5 -10.5
* lon (lon) float64 64B -54.5 -53.5 -52.5 -51.5 -50.5 -49.5 -48.5 -47.5
Attributes:...
Attributes:
Conventions: CF-1.7
title: Produced by grdcut
history: grdcut @earth_relief_01d_p -R-55/-47/-24/-10 -Gstatic_eart...
Expand All @@ -69,14 +69,14 @@ class GMTBackendEntrypoint(BackendEntrypoint):
>>> da_image = xr.open_dataarray(
... "@earth_night_01d", engine="gmt", raster_kind="image"
... )
>>> da_image # doctest: +NORMALIZE_WHITESPACE
>>> da_image
<xarray.DataArray 'z' (band: 3, y: 180, x: 360)> Size: 194kB
[194400 values with dtype=uint8]
Coordinates:
* band (band) uint8... 1 2 3
* y (y) float64... 89.5 88.5 87.5 86.5 ... -86.5 -87.5 -88.5 -89.5
* x (x) float64... -179.5 -178.5 -177.5 -176.5 ... 177.5 178.5 179.5
Attributes:...
* band (band) uint8 3B 1 2 3
* y (y) float64 1kB 89.5 88.5 87.5 86.5 ... -86.5 -87.5 -88.5 -89.5
* x (x) float64 3kB -179.5 -178.5 -177.5 -176.5 ... 177.5 178.5 179.5
Attributes:
long_name: z

Load a single-band netCDF file using ``raster_kind="grid"`` over a bounding box
Expand All @@ -95,7 +95,7 @@ class GMTBackendEntrypoint(BackendEntrypoint):
Coordinates:
* lat (lat) float64 104B 32.0 32.08 32.17 32.25 ... 32.83 32.92 33.0
* lon (lon) float64 200B -64.0 -63.92 -63.83 ... -62.17 -62.08 -62.0
Attributes:...
Attributes:
Conventions: CF-1.7
title: ETOPO5 global topography
history: grdreformat -fg bermuda.grd bermuda.nc=ns
Expand Down
4 changes: 2 additions & 2 deletions pyproject.toml
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Expand Up @@ -35,9 +35,9 @@ classifiers = [
"Programming Language :: Python :: 3.13",
]
dependencies = [
"numpy>=1.26",
"numpy>=2.0",
"pandas>=2.2",
"xarray>=2023.10",
"xarray>=2024.5",
"packaging>=24.2",
]
dynamic = ["version"]
Expand Down
4 changes: 2 additions & 2 deletions requirements.txt
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We can probably delete this requirements.txt file (in a separate PR). This was kept during the transition to pyproject.toml (#812 (comment)), and also because the view at https://github.com/GenericMappingTools/pygmt/network/dependencies didn't support pyproject.toml before, but now it does.

Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# Required packages
numpy>=1.26
numpy>=2.0
pandas>=2.2
xarray>=2023.10
xarray>=2024.5
packaging>=24.2