Bump phonopy from 2.39.0 to 2.40.0

[dependabot]

Bumps phonopy from 2.39.0 to 2.40.0.

Changelog

Sourced from phonopy's changelog.

Jun-15-2025: Version 2.40.0

• --rd-auto-factor command option (RD_NUMBER_ESTIMATION_FACTOR tag) was added.

Commits

• 268f5fb Merge branch 'develop'
• b19bdd3 Merge pull request #577 from phonopy/release
• c66694a Set version 2.40.0
• a0f677d Merge pull request #576 from phonopy/rd-auto-factor
• e74f652 Add command option --rd-auto-factor
• 0970b17 Minor update
• 3bbb8c3 Add number_estimation_factor parameter in settings
• a81b4c0 Merge pull request #575 from dmt4/qlm
• 17daee1 Fix test_qlm.py for windows py v3.9
• See full diff in compare view

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 85.27%. Comparing base (1b73caf) to head (b8b46e2).
Report is 5 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #481   +/-   ##
=======================================
  Coverage   85.27%   85.27%           
=======================================
  Files          43       43           
  Lines        2581     2581           
=======================================
  Hits         2201     2201           
  Misses        380      380           

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