⬆️ Bump numpy from 1.26.4 to 2.0.1 (#1523)

* Bump numpy from 1.26.4 to 2.1.0

Bumps [numpy](https://github.com/numpy/numpy) from 1.26.4 to 2.1.0.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v1.26.4...v2.1.0)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* 🩹 Fix repr issue with numpy>2 str values

This caused the following test error:
```py
FAILED glotaran/utils/test/test_io.py::test_create_clp_guide_dataset_errors - assert "Unknown clp_...'species_3')]" == "Unknown clp_... 'species_3']"

  Skipping 49 identical leading characters in diff, use -v to show
    ls are:
  -  ['species_1', 'species_2', 'species_3']
  +  [np.str_('species_1'), np.str_('species_2'), np.str_('species_3')]
```

* ⬆️ Correct minor version of numpy

numpy 2.1 is not yet supported be e.g. numba

* Use .to_numpy instead of .values

* 🩹 Use add_svd_to_dataset instead of duplication with error

This way we can reuse code and fixes and don't have the extra duplication and maintenance burden

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: s-weigand <s.weigand.phy@gmail.com>
Co-authored-by: Joris Snellenburg <jsnel@users.noreply.github.com>

glotaran/optimization/objective.py

@@ -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
@@ -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

glotaran/utils/io.py

@@ -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(

pyproject.toml

@@ -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",

requirements_pinned.txt

@@ -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