Update numpy to 2.4.0

[jan-janssen]

Summary by CodeRabbit

• Chores
  • Updated numpy dependency to version 2.4.0 across build and development environments.

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[coderabbitai]

📝 Walkthrough

Walkthrough

NumPy dependency updated from version 2.3.5 to 2.4.0 across three environment and project configuration files: .ci_support/environment.yml, .ci_support/environment_mini.yml, and pyproject.toml.

Changes

Cohort / File(s)	Summary
Dependency Version Bump \.ci_support/environment\.yml, \.ci_support/environment_mini\.yml, pyproject\.toml	NumPy version constraint bumped from 2.3.5 to 2.4.0 across all three dependency specification files. No structural or logical changes.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~3 minutes

Possibly related PRs

• Update numpy to 2.3.5 #422 — Sequential version-bump PR that updates the same numpy dependency in identical configuration files
• Remove Numpy restriction #392 — Related PR modifying numpy version constraints in the same set of dependency declaration files

Poem

🐰 NumPy marches onward, version two-point-four,
Across three config files, from corner to store,
A hop-skip-update, so simple, so clean,
The newest release in your environment's scene! ✨

Pre-merge checks and finishing touches

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately and clearly describes the main change: updating numpy from 2.3.5 to 2.4.0 across all environment and dependency files.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch numpy

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📜 Recent review details

Configuration used: defaults

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 650188c and 3be684f.

📒 Files selected for processing (3)

• .ci_support/environment.yml
• .ci_support/environment_mini.yml
• pyproject.toml

🔇 Additional comments (3)

pyproject.toml (1)

28-28: Consistent version update across configuration files.

The numpy version is consistently updated to 2.4.0 across all project configuration files. Please refer to the verification request in .ci_support/environment.yml to confirm version availability and security.

.ci_support/environment_mini.yml (1)

6-6: Consistent version update in minimal environment.

The numpy version is consistently updated to 2.4.0 across all environment files. Please refer to the verification request in .ci_support/environment.yml.

.ci_support/environment.yml (1)

12-12: numpy 2.4.0 is available and compatible with this codebase.

numpy 2.4.0 was released December 3, 2025. No CVEs affect this release. The breaking changes in 2.4.0 (round() always returns copy, strides mutation deprecation, arange keyword changes) do not impact this codebase—np.round usage here safely consumes return values, strides are not mutated, and arange is not called with start= keyword.

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[jan-janssen]

======================================================================
ERROR: test_soap_descriptor_per_atom (test_dscribe.Testdscribe.test_soap_descriptor_per_atom)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/structuretoolkit/structuretoolkit/tests/test_dscribe.py", line 26, in test_soap_descriptor_per_atom
    soap = stk.analyse.soap_descriptor_per_atom(
        structure=structure, r_cut=6.0, n_max=8, l_max=6
    )
  File "/home/runner/work/structuretoolkit/structuretoolkit/structuretoolkit/analyse/dscribe.py", line 49, in soap_descriptor_per_atom
    from dscribe.descriptors import SOAP
  File "/home/runner/miniconda3/envs/test/lib/python3.13/site-packages/dscribe/descriptors/__init__.py", line 17, in <module>
    from dscribe.descriptors.acsf import ACSF
  File "/home/runner/miniconda3/envs/test/lib/python3.13/site-packages/dscribe/descriptors/acsf.py", line 20, in <module>
    from dscribe.descriptors.descriptorlocal import DescriptorLocal
  File "/home/runner/miniconda3/envs/test/lib/python3.13/site-packages/dscribe/descriptors/descriptorlocal.py", line 17, in <module>
    from dscribe.descriptors.descriptor import Descriptor
  File "/home/runner/miniconda3/envs/test/lib/python3.13/site-packages/dscribe/descriptors/descriptor.py", line 21, in <module>
    import sparse as sp
  File "/home/runner/miniconda3/envs/test/lib/python3.13/site-packages/sparse/__init__.py", line 1, in <module>
    from .coo import COO, elemwise, tensordot, concatenate, stack, dot, triu, tril, where, \
        nansum, nanprod, nanmin, nanmax
  File "/home/runner/miniconda3/envs/test/lib/python3.13/site-packages/sparse/coo.py", line 4, in <module>
    from collections import Iterable, defaultdict, deque
ImportError: cannot import name 'Iterable' from 'collections' (/home/runner/miniconda3/envs/test/lib/python3.13/collections/__init__.py)

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