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Eliminate deprecation warnings from scipy and pandas (#2951)

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Paul Romano 2024-06-11 21:56:31 -05:00 • committed by GitHub
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3 changed files with 23 additions and 14 deletions
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12
openmc/data/photon.py
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@ -124,7 +124,7 @@ class AtomicRelaxation(EqualityMixin):
Dictionary indicating the number of electrons in a subshell when neutral
(values) for given subshells (keys). The subshells should be given as
strings, e.g., 'K', 'L1', 'L2', etc.
transitions : pandas.DataFrame
transitions : dict of str to pandas.DataFrame
Dictionary indicating allowed transitions and their probabilities
(values) for given subshells (keys). The subshells should be given as
strings, e.g., 'K', 'L1', 'L2', etc. The transitions are represented as
@ -363,8 +363,9 @@ class AtomicRelaxation(EqualityMixin):
df = pd.DataFrame(sub_group['transitions'][()],
columns=columns)
# Replace float indexes back to subshell strings
df[columns[:2]] = df[columns[:2]].replace(
np.arange(float(len(_SUBSHELLS))), _SUBSHELLS)
with pd.option_context('future.no_silent_downcasting', True):
df[columns[:2]] = df[columns[:2]].replace(
np.arange(float(len(_SUBSHELLS))), _SUBSHELLS)
transitions[shell] = df
return cls(binding_energy, num_electrons, transitions)
@ -387,8 +388,9 @@ class AtomicRelaxation(EqualityMixin):
# Write transition data with replacements
if shell in self.transitions:
df = self.transitions[shell].replace(
_SUBSHELLS, range(len(_SUBSHELLS)))
with pd.option_context('future.no_silent_downcasting', True):
df = self.transitions[shell].replace(
_SUBSHELLS, range(len(_SUBSHELLS)))
group.create_dataset('transitions', data=df.values.astype(float))

18
openmc/mgxs_library.py
View file

@ -3,7 +3,7 @@ from numbers import Real, Integral
import h5py
import numpy as np
from scipy.integrate import simps
import scipy.integrate
from scipy.interpolate import interp1d
from scipy.special import eval_legendre
@ -1823,6 +1823,12 @@ class XSdata:
# Reset and re-generate XSdata.xs_shapes with the new scattering format
xsdata._xs_shapes = None
# scipy 1.11+ prefers 'simpson', whereas older versions use 'simps'
if hasattr(scipy.integrate, 'simpson'):
integrate = scipy.integrate.simpson
else:
integrate = scipy.integrate.simps
for i, temp in enumerate(xsdata.temperatures):
orig_data = self._scatter_matrix[i]
new_shape = orig_data.shape[:-1] + (xsdata.num_orders,)
@ -1860,7 +1866,7 @@ class XSdata:
table_fine[..., imu] += ((l + 0.5)
* eval_legendre(l, mu_fine[imu]) *
orig_data[..., l])
new_data[..., h_bin] = simps(table_fine, mu_fine)
new_data[..., h_bin] = integrate(table_fine, mu_fine)
elif self.scatter_format == SCATTER_TABULAR:
# Calculate the mu points of the current data
@ -1874,7 +1880,7 @@ class XSdata:
for l in range(xsdata.num_orders):
y = (interp1d(mu_self, orig_data)(mu_fine) *
eval_legendre(l, mu_fine))
new_data[..., l] = simps(y, mu_fine)
new_data[..., l] = integrate(y, mu_fine)
elif target_format == SCATTER_TABULAR:
# Simply use an interpolating function to get the new data
@ -1893,7 +1899,7 @@ class XSdata:
interp = interp1d(mu_self, orig_data)
for h_bin in range(xsdata.num_orders):
mu_fine = np.linspace(mu[h_bin], mu[h_bin + 1], _NMU)
new_data[..., h_bin] = simps(interp(mu_fine), mu_fine)
new_data[..., h_bin] = integrate(interp(mu_fine), mu_fine)
elif self.scatter_format == SCATTER_HISTOGRAM:
# The histogram format does not have enough information to
@ -1919,7 +1925,7 @@ class XSdata:
mu_fine = np.linspace(-1, 1, _NMU)
for l in range(xsdata.num_orders):
y = interp(mu_fine) * norm * eval_legendre(l, mu_fine)
new_data[..., l] = simps(y, mu_fine)
new_data[..., l] = integrate(y, mu_fine)
elif target_format == SCATTER_TABULAR:
# Simply use an interpolating function to get the new data
@ -1938,7 +1944,7 @@ class XSdata:
for h_bin in range(xsdata.num_orders):
mu_fine = np.linspace(mu[h_bin], mu[h_bin + 1], _NMU)
new_data[..., h_bin] = \
norm * simps(interp(mu_fine), mu_fine)
norm * integrate(interp(mu_fine), mu_fine)
# Remove small values resulting from numerical precision issues
new_data[..., np.abs(new_data) < 1.E-10] = 0.

7
tests/unit_tests/test_data_photon.py
View file

@ -1,5 +1,3 @@
#!/usr/bin/env python
from collections.abc import Mapping, Callable
import os
from pathlib import Path
@ -123,6 +121,8 @@ def test_reactions(element, reaction):
reactions[18]
# TODO: Remove skip when support is Python 3.9+
@pytest.mark.skipif(not hasattr(pd.options, 'future'), reason='pandas version too old')
@pytest.mark.parametrize('element', ['Pu'], indirect=True)
def test_export_to_hdf5(tmpdir, element):
filename = str(tmpdir.join('tmp.h5'))
@ -146,8 +146,9 @@ def test_export_to_hdf5(tmpdir, element):
# Export to hdf5 again
element2.export_to_hdf5(filename, 'w')
def test_photodat_only(run_in_tmpdir):
endf_dir = Path(os.environ['OPENMC_ENDF_DATA'])
photoatomic_file = endf_dir / 'photoat' / 'photoat-001_H_000.endf'
data = openmc.data.IncidentPhoton.from_endf(photoatomic_file)
data.export_to_hdf5('tmp.h5', 'w')
data.export_to_hdf5('tmp.h5', 'w')