Update numpy to 2.5.3, scipy to 1.18.0 and structuretoolkit to 0.0.46

[jan-janssen]

No description provided.

[coderabbitai]

Important

• 🔍 Trigger review

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⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Advanced

Run ID: 25f8b169-7ca3-4767-88fb-cafd94937448

✨ Finishing Touches

🧪 Generate unit tests (beta)

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

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[jan-janssen]

Waiting for pyiron/structuretoolkit#529

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.69%. Comparing base (afb27ab) to head (3452fec).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #373   +/-   ##
=======================================
  Coverage   98.69%   98.69%           
=======================================
  Files          13       13           
  Lines        1224     1224           
=======================================
  Hits         1208     1208           
  Misses         16       16           

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