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.}

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 6b936f3c-338c-443a-a5ba-e12af9789f1a

📥 Commits

Reviewing files that changed from the base of the PR and between 854e18b and c40b0b3.

📒 Files selected for processing (3)

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

📝 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.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch numpy

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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

[jan-janssen]

======================================================================
ERROR: test_sqs_structures_no_stats (test_sqs.SQSTestCase.test_sqs_structures_no_stats)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/structuretoolkit/structuretoolkit/tests/test_sqs.py", line 21, in test_sqs_structures_no_stats
    structures_lst = stk.build.sqs_structures(
        structure=bulk("Au", cubic=True).repeat([2, 2, 2]),
    ...<15 lines>...
        return_statistics=False,
    )
  File "/home/runner/miniconda3/envs/test/lib/python3.13/site-packages/structuretoolkit/build/sqs.py", line 205, in sqs_structures
    from sqsgenerator import sqs_optimize
ImportError: cannot import name 'sqs_optimize' from 'sqsgenerator' (/home/runner/miniconda3/envs/test/lib/python3.13/site-packages/sqsgenerator/__init__.py)
======================================================================
ERROR: test_sqs_structures_with_stats (test_sqs.SQSTestCase.test_sqs_structures_with_stats)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/structuretoolkit/structuretoolkit/tests/test_sqs.py", line 49, in test_sqs_structures_with_stats
    stk.build.sqs_structures(
    ~~~~~~~~~~~~~~~~~~~~~~~~^
        structure=bulk("Au", cubic=True).repeat([2, 2, 2]),
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    ...<15 lines>...
        return_statistics=True,
        ^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/runner/miniconda3/envs/test/lib/python3.13/site-packages/structuretoolkit/build/sqs.py", line 205, in sqs_structures
    from sqsgenerator import sqs_optimize
ImportError: cannot import name 'sqs_optimize' from 'sqsgenerator' (/home/runner/miniconda3/envs/test/lib/python3.13/site-packages/sqsgenerator/__init__.py)
----------------------------------------------------------------------

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 82.69%. Comparing base (684c115) to head (c40b0b3).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #438   +/-   ##
=======================================
  Coverage   82.69%   82.69%           
=======================================
  Files          25       25           
  Lines        1832     1832           
=======================================
  Hits         1515     1515           
  Misses        317      317           

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[Copilot]

Pull request overview

This PR updates the project’s NumPy pin across Python packaging metadata and conda environment specs to standardize the version used in builds/dev/CI.

Changes:

• Bumped numpy in pyproject.toml to 2.4.3.
• Bumped numpy in conda environment specs (.ci_support/environment*.yml) to 2.4.3.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.

File	Description
pyproject.toml	Updates the runtime dependency pin for NumPy.
.ci_support/environment_mini.yml	Updates the minimal conda environment NumPy pin.
.ci_support/environment.yml	Updates the full conda environment NumPy pin.

---

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[Copilot]

PR title/description says updating NumPy to 2.4.0 (and mentions adding sparse), but the actual pin here is 2.4.3 and there’s no sparse change in this PR. Please align the PR title/description with the actual changes (or adjust the pin if 2.4.0 is the intended target).