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fix: Numpy 2 compatibility #905

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Merged
merged 3 commits into from
Nov 21, 2024
Merged

fix: Numpy 2 compatibility #905

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c5f1bb0
fix(doctest): Set legacy printoptions
effigies Nov 21, 2024
fabaa47
fix: Numpy stopped accepting b-strings as savetxt fmt args
effigies Nov 21, 2024
3f308c7
fix(np2): Replace np.NaN with np.nan
effigies Nov 21, 2024
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8 changes: 8 additions & 0 deletions niworkflows/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,14 @@ def find_resource_or_skip(resource):
return pathlike


@pytest.fixture(scope="session", autouse=True)
def legacy_printoptions():
from packaging.version import Version

if Version(np.__version__) >= Version("1.22"):
np.set_printoptions(legacy="1.21")


@pytest.fixture(autouse=True)
def add_np(doctest_namespace):
from .utils.bids import collect_data
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2 changes: 1 addition & 1 deletion niworkflows/interfaces/images.py
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Expand Up @@ -749,6 +749,6 @@ def _run_interface(self, runtime):

output = np.vstack((self.inputs.class_labels, series.astype(str)))
self._results["out_file"] = os.path.join(runtime.cwd, self.inputs.out_file)
np.savetxt(self._results["out_file"], output, fmt=b"%s", delimiter="\t")
np.savetxt(self._results["out_file"], output, fmt="%s", delimiter="\t")

return runtime
22 changes: 11 additions & 11 deletions niworkflows/tests/test_confounds.py
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Expand Up @@ -98,15 +98,15 @@ def test_expansion_derivatives_and_powers():
{
"a": [-1, -2, -3, -4, -5],
"a_power2": [1, 4, 9, 16, 25],
"a_derivative1": [np.NaN, -1, -1, -1, -1],
"a_derivative1_power2": [np.NaN, 1, 1, 1, 1],
"b_derivative1": [np.NaN, 0, 0, 0, 0],
"b_derivative1_power2": [np.NaN, 0, 0, 0, 0],
"c_power2_derivative1": [np.NaN, 1, -1, 1, -1],
"c_power2_derivative2": [np.NaN, np.NaN, -2, 2, -2],
"a_derivative1": [np.nan, -1, -1, -1, -1],
"a_derivative1_power2": [np.nan, 1, 1, 1, 1],
"b_derivative1": [np.nan, 0, 0, 0, 0],
"b_derivative1_power2": [np.nan, 0, 0, 0, 0],
"c_power2_derivative1": [np.nan, 1, -1, 1, -1],
"c_power2_derivative2": [np.nan, np.nan, -2, 2, -2],
"d": [9, 7, 5, 3, 1],
"e": [0, 0, 0, 0, 0],
"f": [np.NaN, 6, 4, 2, 0],
"f": [np.nan, 6, 4, 2, 0],
}
)
exp_data = _expand_test(model_formula)
Expand All @@ -122,10 +122,10 @@ def test_expansion_na_robustness():
model_formula = "(dd1(f))^^2"
expected_data = pd.DataFrame(
{
"f": [np.NaN, 6, 4, 2, 0],
"f_power2": [np.NaN, 36, 16, 4, 0],
"f_derivative1": [np.NaN, np.NaN, -2, -2, -2],
"f_derivative1_power2": [np.NaN, np.NaN, 4, 4, 4],
"f": [np.nan, 6, 4, 2, 0],
"f_power2": [np.nan, 36, 16, 4, 0],
"f_derivative1": [np.nan, np.nan, -2, -2, -2],
"f_derivative1_power2": [np.nan, np.nan, 4, 4, 4],
}
)
exp_data = _expand_test(model_formula)
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