Update numpy to 2.4.0

[jan-janssen]

Summary by CodeRabbit

• Chores
  • Updated numpy to 2.4.0 across build, development, and project configuration to standardize environments.
  • Added sparse (0.17.0) to the full environment specification.
  • No functional, public API, or behavioral changes introduced.

_{✏️ Tip: You can customize this high-level summary in your review settings.}

[coderabbitai]

📝 Walkthrough

Walkthrough

NumPy version updated from 2.3.5 → 2.4.0 in three dependency files; sparse (0.17.0) was added to .ci_support/environment.yml. No code, control-flow, or exported/public-API changes.

Changes

Cohort / File(s)	Summary
Dependency spec files .ci_support/environment.yml, .ci_support/environment_mini.yml, pyproject.toml	NumPy bumped from 2.3.5 → 2.4.0 across all three files. In addition, sparse==0.17.0 was added to .ci_support/environment.yml. No other edits to code or public APIs.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• Update numpy to 2.3.5 #422 — Edited the same numpy entries in .ci_support/environment.yml, .ci_support/environment_mini.yml, and pyproject.toml.
• Remove Numpy restriction #392 — Also modified numpy version constraints across the same dependency declaration files.

Poem

🐰 I nibbled at versions, a tiny delight,
NumPy hopped up to shine a bit bright,
A sparse friend joined the YAML parade,
Three files updated, a tidy crusade,
Hooray for small hops that keep builds light!

Pre-merge checks

✅ 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 'Update numpy to 2.4.0' directly and clearly describes the main change—a numpy version upgrade from 2.3.5 to 2.4.0 across multiple configuration files.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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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 210cb76 and 854e18b.

📒 Files selected for processing (1)

• .ci_support/environment.yml

🔇 Additional comments (2)

.ci_support/environment.yml (2)

12-12: No issues found. numpy 2.4.0 is a stable release (December 2025) and is available via pip.

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20-20: sparse 0.17.0 is compatible with Python 3.13.

PyPI metadata confirms that sparse 0.17.0 (the latest release, uploaded May 20, 2025) was built with CPython 3.13.3 and explicitly supports Python 3.13. If the earlier test failure referenced an ImportError about collections.Iterable, the source is not sparse 0.17.0 itself—it may be another dependency or an outdated version reference. No action required for the sparse version specified.

Likely an incorrect or invalid review comment.

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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)

----------------------------------------------------------------------

[jan-janssen]

└─ numba >=0.49 * with the potential options
            ├─ numba [0.56.2|0.56.3|0.56.4] would require
            │  └─ numpy >=1.18,(!=1.22.0,(!=1.22.1,(!=1.22.2,<1.24))) *, which conflicts with any installable versions previously reported;
            ├─ numba [0.57.0|0.57.1] would require
            │  └─ numpy >=1.21,(!=1.22.0,(!=1.22.1,(!=1.22.2,<1.25))) *, which conflicts with any installable versions previously reported;
            ├─ numba [0.58.1|0.59.0|0.59.1] would require
            │  └─ numpy >=1.22.3,<1.27 *, which conflicts with any installable versions previously reported;
            ├─ numba 0.60.0 would require
            │  └─ numpy >=1.22.3,<2.1 *, which conflicts with any installable versions previously reported;
            ├─ numba 0.61.0 would require
            │  └─ numpy >=1.24,<2.2 *, which conflicts with any installable versions previously reported;
            ├─ numba 0.61.2 would require
            │  └─ numpy [>=1.24,<2.3 *|>=1.24,<2.3.0a0 *], which conflicts with any installable versions previously reported;
            ├─ numba [0.62.0|0.62.1] would require
            │  └─ numpy >=1.24,<2.4 * with the potential options
            │     ├─ numpy [1.24.0|1.24.1|...|2.0.2] conflicts with any installable versions previously reported;
            │     ├─ numpy [2.1.0|2.1.1|2.1.2|2.1.3] conflicts with any installable versions previously reported;
            │     ├─ numpy [2.2.0|2.2.1|...|2.2.6] conflicts with any installable versions previously reported;
            │     ├─ numpy [2.3.0|2.3.1|...|2.3.5] conflicts with any installable versions previously reported;
            │     └─ numpy [2.3.2|2.3.3|2.3.4|2.3.5|2.4.0], which can be installed (as previously explained);
            ├─ numba [0.63.0|0.63.1] would require
            │  └─ numpy >=1.22.3,<2.4 * with the potential options
            │     ├─ numpy [1.22.3|1.22.4|...|1.23.5] conflicts with any installable versions previously reported;
            │     ├─ numpy [1.24.0|1.24.1|...|2.0.2] conflicts with any installable versions previously reported;
            │     ├─ numpy [2.1.0|2.1.1|2.1.2|2.1.3] conflicts with any installable versions previously reported;
            │     ├─ numpy [2.2.0|2.2.1|...|2.2.6] conflicts with any installable versions previously reported;
            │     ├─ numpy [2.3.0|2.3.1|...|2.3.5] conflicts with any installable versions previously reported;
            │     └─ numpy [2.3.2|2.3.3|2.3.4|2.3.5|2.4.0], which can be installed (as previously explained);
            ├─ numba [0.63.0|0.63.1] would require
            │  └─ python_abi =3.14 *_cp314, which can be installed (as previously explained);
            ├─ numba [0.49.0|0.49.1] would require
            │  └─ numpy >=1.14.6,<1.18.0 *, which conflicts with any installable versions previously reported;
            ├─ numba 0.50.1 would require
            │  └─ numpy >=1.14.6,<1.21.0a0 *, which conflicts with any installable versions previously reported;
            ├─ numba [0.51.0|0.51.1|0.51.2|0.52.0] would require
            │  └─ numpy >=1.16.5,<1.21.0a0 *, which conflicts with any installable versions previously reported;
            ├─ numba 0.53.0 would require
            │  └─ numpy >=1.16.6,<1.21.0a0 *, which conflicts with any installable versions previously reported;
            ├─ numba [0.53.0|0.53.1] would require
            │  └─ numpy >=1.19.5,<1.21.0a0 *, which conflicts with any installable versions previously reported;
            ├─ numba 0.53.1 would require
            │  └─ numpy >=1.17.5,<1.21.0a0 *, which conflicts with any in