Update numpy to 2.3.5

[jan-janssen]

Summary by CodeRabbit

• Chores
  • Bumped core dependencies to latest versions across all environment configurations. Updated packages: numpy, structuretoolkit, pylammpsmpi, pyiron_lammps, and pyiron_vasp. Changes applied to CI, development, notebook, and project configurations.

[coderabbitai]

Walkthrough

This PR updates five package dependencies across all environment configuration files and pyproject.toml: numpy (2.3.4→2.3.5), structuretoolkit (0.0.37→0.0.38), pylammpsmpi (0.3.6→0.3.7), pyiron_lammps (0.4.9→0.4.10), and pyiron_vasp (0.2.15→0.2.16).

Changes

Cohort / File(s)	Change Summary
CI Documentation Environment .ci_support/environment-docs.yml	Version bumps: numpy 2.3.4→2.3.5, structuretoolkit 0.0.37→0.0.38, pylammpsmpi 0.3.6→0.3.7, pyiron_lammps 0.4.9→0.4.10, pyiron_vasp 0.2.15→0.2.16
CI LAMMPS Environments .ci_support/environment-lammps.yml, .ci_support/environment-notebooks.yml	Version bumps: pylammpsmpi 0.3.6→0.3.7, pyiron_lammps 0.4.9→0.4.10
CI Base & Binder Environment .ci_support/environment.yml, binder/environment.yml	Version bumps: numpy 2.3.4→2.3.5, structuretoolkit 0.0.37→0.0.38, pylammpsmpi (0.3.6→0.3.7 or 0.3.2→0.3.7), pyiron_lammps 0.4.9→0.4.10, pyiron_vasp 0.2.15→0.2.16
Project Configuration pyproject.toml	Synchronized version bumps: numpy 2.3.4→2.3.5, structuretoolkit 0.0.37→0.0.38, pylammpsmpi 0.3.6→0.3.7, pyiron_lammps 0.4.9→0.4.10, pyiron_vasp 0.2.15→0.2.16

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~8 minutes

• Verify version consistency across all six modified files—note that binder/environment.yml bumps pylammpsmpi from 0.3.2 (not 0.3.6 like other files) to 0.3.7
• Confirm no unintended version changes were introduced

Possibly related PRs

• Update numpy to 2.3.4 #572: Continues numpy version bumps (previously 2.3.3→2.3.4, now 2.3.4→2.3.5)
• Update LAMMPS to 2024.08.29 #491: Updates pylammpsmpi and pyiron_lammps across LAMMPS environment files
• Update pyiron_vasp to 0.2.10 #530: Updates pyiron_vasp dependency in environment and configuration files

Suggested labels

dependencies

Poem

🐰 Five packages up they hop,
Versions bump from stop to stop,
Docs and LAMMPS, notebooks too,
All synchronized fresh and new! 🌰

Pre-merge checks and finishing touches

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Title check	⚠️ Warning	The title focuses only on numpy version bump but the PR updates multiple dependencies (numpy, structuretoolkit, pylammpsmpi, pyiron_lammps, pyiron_vasp) across multiple files.	Update title to reflect the full scope, such as 'Update multiple dependencies to latest patch versions' or 'Bump numpy and related dependencies to latest versions'.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
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: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 5e2314c and c8a07d1.

📒 Files selected for processing (6)

• .ci_support/environment-docs.yml (1 hunks)
• .ci_support/environment-lammps.yml (1 hunks)
• .ci_support/environment-notebooks.yml (1 hunks)
• .ci_support/environment.yml (1 hunks)
• binder/environment.yml (1 hunks)
• pyproject.toml (3 hunks)

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (1)

• GitHub Check: unittest_old

🔇 Additional comments (7)

.ci_support/environment-notebooks.yml (1)

9-9: Dependency updates are consistent with other environment files.

Version bumps for pylammpsmpi (0.3.7) and pyiron_lammps (0.4.10) align with changes across other configurations.

Also applies to: 12-12

binder/environment.yml (1)

5-5: Verify pylammpsmpi version in binder environment.

Line 14 updates pylammpsmpi from 0.3.2 to 0.3.7, while other environment files (.ci_support/environment-*.yml) bump from 0.3.6 to 0.3.7. Confirm whether the binder environment is intentionally on an older version or if this should be aligned to start from 0.3.6 for consistency.

The numpy (2.3.5), structuretoolkit (0.0.38), pyiron_lammps (0.4.10), and pyiron_vasp (0.2.16) updates are consistent with other files.

Also applies to: 9-9, 14-14, 18-18, 19-19

.ci_support/environment-lammps.yml (1)

6-6: Dependency updates are consistent with other environment configurations.

Version bumps for pylammpsmpi (0.3.7) and pyiron_lammps (0.4.10) align with other environment files.

Also applies to: 10-10

.ci_support/environment.yml (1)

8-8: Dependency updates are consistent across configuration files.

Version bumps for numpy (2.3.5), structuretoolkit (0.0.38), and pyiron_vasp (0.2.16) align with updates in other environment files and pyproject.toml.

Also applies to: 15-15, 18-18

.ci_support/environment-docs.yml (1)

11-11: All dependency updates are consistent with pyproject.toml and other environment files.

The five package version bumps (numpy, structuretoolkit, pylammpsmpi, pyiron_lammps, pyiron_vasp) align across the documentation environment configuration.

Also applies to: 15-15, 19-19, 22-22, 23-23

pyproject.toml (2)

29-29: All dependency versions are pinned consistently and match environment configurations.

The numpy core dependency (line 29) and optional dependencies (structuretoolkit, pylammpsmpi, pyiron_lammps, pyiron_vasp) are correctly updated to match the version strategy across all environment files. Duplicate pins in optional dependency groups (pylammpsmpi, pyiron_lammps in both lammps and lammps_phonons) are correct and consistent.

Also applies to: 44-44, 50-50, 53-53, 56-56, 60-60, 78-78

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1-102: I've confirmed that numpy 2.3.5 contains no breaking changes. Now let me verify the other package updates mentioned in the review:

Confirmed: numpy 2.3.5 is compatible; other package updates require testing.

NumPy 2.3.5 is a patch (bugfix/maintenance) release — no breaking changes listed, and it supports Python 3.11–3.14, which aligns with your project's Python requirement of >=3.9, <3.15.

However, specific release notes for the other four package updates (structuretoolkit 0.0.38, pylammpsmpi 0.3.7, pyiron_lammps 0.4.10, pyiron_vasp 0.2.16) are not publicly documented. Manually test the codebase against these versions to ensure atomistics functionality remains stable, particularly LAMMPS and VASP workflows.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 85.46%. Comparing base (72bec60) to head (c8a07d1).
⚠️ Report is 5 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #588   +/-   ##
=======================================
  Coverage   85.46%   85.46%           
=======================================
  Files          43       43           
  Lines        2545     2545           
=======================================
  Hits         2175     2175           
  Misses        370      370           

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