Update dependencies

[jan-janssen]

Summary by CodeRabbit

• Chores
  • Updated dependencies to latest versions: ase (3.28.0), h5py (3.16.0), numpy (2.4.3), and scipy (1.17.1).

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 4cdef34b-71c3-42ac-bb60-0dab732159f8

📥 Commits

Reviewing files that changed from the base of the PR and between f531a39 and 3bdf8a9.

📒 Files selected for processing (3)

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

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📝 Walkthrough

Walkthrough

Updated Conda and Python package dependency versions across three configuration files: ase (3.27.0→3.28.0), h5py (3.15.1→3.16.0), numpy (2.4.2→2.4.3), and scipy (1.17.0→1.17.1).

Changes

Cohort / File(s)	Summary
Dependency Version Updates .ci_support/environment.yml, binder/environment.yml, pyproject.toml	Bumped pinned versions: ase (3.27.0→3.28.0), h5py (3.15.1→3.16.0), numpy (2.4.2→2.4.3), scipy (1.17.0→1.17.1).

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~3 minutes

Poem

🐰 Our dependencies bloom anew,
With versions fresh and code on cue,
From ase to h5py, numpy true,
Scipy climbs and libraries grew,
The garden's tools all shiny through!

🚥 Pre-merge checks | ✅ 3

✅ 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 dependencies' directly and accurately describes the main change: updating pinned versions of multiple dependencies (ase, h5py, numpy, scipy) across three configuration files.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

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

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 82.36%. Comparing base (cb3a215) to head (3bdf8a9).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #321   +/-   ##
=======================================
  Coverage   82.36%   82.36%           
=======================================
  Files          11       11           
  Lines        1157     1157           
=======================================
  Hits          953      953           
  Misses        204      204           

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[Copilot]

Pull request overview

This PR updates pinned dependency versions across the Python package metadata and the conda environments used for CI and Binder to keep the project’s runtime stack in sync.

Changes:

• Bump core runtime dependencies: ase, numpy, and scipy to newer patch releases.
• Bump optional h5md extra (h5py) to a newer patch release.
• Mirror the same version bumps in Binder and CI conda environment definitions.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated no comments.

File	Description
pyproject.toml	Updates pinned runtime deps and the h5md optional extra to newer patch versions.
binder/environment.yml	Aligns Binder conda environment package versions with updated pins.
.ci_support/environment.yml	Aligns CI conda environment package versions with updated pins.

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