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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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Original file line number Diff line number Diff line change
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.

9 changes: 5 additions & 4 deletions pygmt/datatypes/image.py
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Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,7 @@ class _GMT_IMAGE(ctp.Structure): # noqa: N801
>>> data.shape
(180, 360, 3)
>>> data.min(), data.max()
(10, 255)
(np.uint8(10), np.uint8(255))
"""

_fields_: ClassVar = [
Expand Down Expand Up @@ -139,17 +139,18 @@ 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:
* 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
* band (band) uint8... 1 2 3
Attributes:
long_name: z
long_name: z

>>> da.coords["x"] # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
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@weiji14 weiji14 Oct 8, 2025

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The # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS can be removed here

Suggested change
>>> da.coords["x"] # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
>>> da.coords["x"]

Also can remove it at L118 above, and at

pygmt/pygmt/datasets/tile_map.py

Line 125 in f93bae4

>>> raster.coords # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE

Then you'll need to update the repr to include the Size: ?kB. Could maybe use https://github.com/max-sixty/pytest-accept to help automate this a little bit.

<xarray.DataArray 'x' (x: 360)>...
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... -179.5 -178.5 -177.5 -176.5 ... 177.5 178.5 179.5
Attributes:
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
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"]
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4 changes: 2 additions & 2 deletions requirements.txt
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@weiji14 weiji14 Oct 14, 2025

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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
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