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⬆️ Bump numpy from 1.26.4 to 2.0.1 #1523

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merged 6 commits into from
Aug 25, 2024
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⬆️ Bump numpy from 1.26.4 to 2.0.1 #1523

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6b732ce
Bump numpy from 1.26.4 to 2.1.0
dependabot[bot] Aug 25, 2024
1b42d83
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 25, 2024
36fe5c1
🩹 Fix repr issue with numpy>2 str values
s-weigand Aug 25, 2024
0040b21
⬆️ Correct minor version of numpy
jsnel Aug 25, 2024
70b4085
Use .to_numpy instead of .values
jsnel Aug 25, 2024
8b2c1e5
🩹 Use add_svd_to_dataset instead of duplication with error
s-weigand Aug 25, 2024
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14 changes: 2 additions & 12 deletions glotaran/optimization/objective.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
import numpy as np
import xarray as xr

from glotaran.io.prepare_dataset import add_svd_to_dataset
from glotaran.model.data_model import iterate_data_model_elements
from glotaran.model.data_model import iterate_data_model_global_elements
from glotaran.optimization.data import LinkedOptimizationData
Expand Down Expand Up @@ -256,18 +257,7 @@ def finalize_result_dataset(self, dataset: xr.Dataset, data: OptimizationData, a

if add_svd:
for name in ["data", "residual"]:
if f"{name}_singular_values" in dataset:
continue
lsv, sv, rsv = np.linalg.svd(dataset[name], full_matrices=False)
dataset[f"{name}_left_singular_vectors"] = (
(data.model_dimension, "left_singular_value_index"),
lsv,
)
dataset[f"{name}_singular_values"] = (("singular_value_index"), sv)
dataset[f"{name}_right_singular_vectors"] = (
(data.global_dimension, "right_singular_value_index"),
rsv.T,
)
add_svd_to_dataset(dataset, name, data.model_dimension, data.global_dimension)
for _, model in iterate_data_model_elements(data.model):
model.add_to_result_data( # type:ignore[union-attr]
data.model, dataset, False
Expand Down
2 changes: 1 addition & 1 deletion glotaran/utils/io.py
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Expand Up @@ -442,7 +442,7 @@ def create_clp_guide_dataset(
if clp_label not in dataset.clp_label:
raise ValueError(
f"Unknown clp_label {clp_label!r}. "
f"Known clp_labels are:\n {list(dataset.clp_label.values)}"
f"Known clp_labels are:\n {[str(label) for label in dataset.clp_label.to_numpy()]}"
)
if "model_dimension" not in dataset.attrs:
raise ValueError(
Expand Down
2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -37,7 +37,7 @@ dependencies = [
"asteval!=0.9.28,>=0.9.22",
"netCDF4>=1.5.7",
"numba>=0.55",
"numpy<1.27,>=1.21.2",
"numpy<2.1,>=1.21.2",
"odfpy>=1.4.1",
"openpyxl>=3.0.10",
"pandas>=1.3.4",
Expand Down
2 changes: 1 addition & 1 deletion requirements_pinned.txt
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Expand Up @@ -2,7 +2,7 @@
asteval==1.0.2
netCDF4==1.7.1.post1
numba==0.60.0
numpy==1.26.4
numpy==2.0.1
odfpy==1.4.1
openpyxl==3.1.5
pandas==2.2.2
Expand Down
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