Update dependency mdtraj to v1.11.2

[renovate]

This PR contains the following updates:

Package	Update	Change
mdtraj (source)	patch	1.11.1 → 1.11.2

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Release Notes

mdtraj/mdtraj (mdtraj)

v1.11.2

Compare Source

1.11.2 (October 5, 2026)

• Fix PyPI upload GitHub Action Process by @​jeremyleung521 in #​2124
• Cache some tests with pytest-recording by @​jeremyleung521 in #​2127
• Move most project config from setup.py to pyproject.toml by @​jeremyleung521 in #​2130
• Fix max_face_to_face_centroid_distance value by @​bagheeera in #​2131
• Fix Topology.copy bond remapping and PDBxFile pathlib support by @​YuuuXie in #​2135
• Implement RMSF for residues by @​CharlieLaughton in #​2133
• Support Pandas 3 by @​janash in #​2134
• Drop Python 3.11 testing and support by @​jeremyleung521 in #​2139
• Ensure topology.join retains chain ID information by @​CharlieLaughton in #​2141
• Fix for libnetcdf4 >= 4.10.0 by @​jeremyleung521 in #​2143
• Throw error in superpose if overflow/underflow error by @​jeremyleung521 in #​2147
• Take care when PDB files mix unit cell information by @​jeremyleung521 in #​2137
• Optimize call to box_vector_length_angle in compute_distances_core by @​rjdirisio in #​2153
• Guard against empty atom indices producing NaNs in superpose by @​badisa in #​2159
• Add bridge_anchors option to image_molecules by @​jgullingsrud in #​2172
• Numpy 2.5 compatibility fix with eigen-calcs by @​jeremyleung521 in #​2189

A total of 7 people contributed to this release.
People with a "+" by their names contributed to MDTraj for the first time.

• Jeremy Leung
• Jessica A. Nash
• Charlie Laughton
• bagheeera +
• Yu Xie +
• badisa +
• Justin Gullingsrud

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