Bump mdanalysis from 2.5.0 to 2.6.0

[dependabot]

Bumps mdanalysis from 2.5.0 to 2.6.0.

Release notes

Sourced from mdanalysis's releases.

Release 2.6.0 of MDAnalysis

This a minor release of MDAnalysis.

This release of MDAnalysis is packaged under a GPLv3+ license, additionally all contributions made from commit 44733fc214dcfdcc2b7cb3e3705258781bb491bd onwards are made under the LGPLv2.1+ license. More details about these license changes will be provided in an upcoming blog post.

The minimum supported NumPy version has been raised to 1.22.3 as per NEP29. Please note that package builds are now made with NumPy 1.25+ which offer backwards runtime compatibility with NEP29 supported versions of NumPy.

Supported Python versions:

• 3.9, 3.10, 3.11

Major changes:

See the CHANGELOG and our release blog post for more details.

Fixes:

• The -ffast-math compiler flag is no longer used by default at build time, avoiding inconsistent (although still scientifically correct) results seen in Intel MacOS systems when calling `AtomGroup.center_of_charge(..., unwrap=True). This also avoids potentially incorrect floating point results as detailed here. (MDAnalysis/mdanalysis#4220)
• DATAWriter, CRD, PQR, and PDBQT files can now be correctly written to compressed files. Before this change, any attempt to write to a compressed format (gzip or bzip2) would lead to writing out an uncompressed file. (MDAnalysis/mdanalysis#4163)
• Prevent accidental merging of bond/angle/dihedral types when they are defined as LAMMPS style string integers instead of tuples. This was leading to an incorrect number of bond/angle/dihedral types being written to lammps data files. (MDAnalysis/mdanalysis#4003)

Enhancements:

• An exclude_same argument has been added to InterRDF allowing pairs of atoms that share the same residue, segment or chain to be excluded from the calculation. (MDAnalysis/mdanalysis#4161)
• LAMMPS reader now supports the continuous ChainReader option. (MDAnalysis/mdanalysis#4170)
• AtomGroup representation now returns atom indices in the same order as they are stored in the AtomGroup. (MDAnalysis/mdanalysis#4191)

Changes:

• Package builds now use NumPy 1.25 or higher instead of the lowest supported NumPy version. (MDAnalysis/mdanalysis#4198)
• As per NEP29, the minimum supported runtime version of NumPy has been increased to 1.22.3. (MDAnalysis/mdanalysis#4160)
• The GSD package is now an optional dependency. (MDAnalysis/mdanalysis#4174)
• The MDAnalysis package now only supports GSD versions 3.0.1 or above. (MDAnalysis/mdanalysis#4153)
• MDAnalysis no longer officially supports 32 bit installations. (they are no longer tested in our continuous integration pipelines). Note: no code changes have been made to disable 32 bit, although it is known that new versions of most MDAnalysis core dependencies no longer release 32 bit compatible versions. (MDAnalysis/mdanalysis#4176)
• The package license has been updated to GPLv3+ to better reflect the compatibility of GPLv2+ with Apache and GPLv3 licensed codes. Additionally all new contributions from commit 44733fc214dcfdcc2b7cb3e3705258781bb491bd onwards are made under the LGPLv2.1+ license. (MDAnalysis/mdanalysis#4219)

Deprecations:

• The misspelt Boltzman_constant entry in MDAnalysis.units is now deprecated in favour the correctly spelt Boltzmann_constant. (MDAnalysis/mdanalysis#4230 and MDAnalysis/mdanalysis#4214)
• MDAnalysis.analysis.hole2 is now deprecated in favour of a new HOLE2 MDAKit. (MDAnalysis/mdanalysis#4200)

New Contributors

• @​MohitKumar020291 made their first contribution in MDAnalysis/mdanalysis#4182
• @​Shubx10 made their first contribution in MDAnalysis/mdanalysis#4184
• @​ztimol made their first contribution in MDAnalysis/mdanalysis#4191

Commits

• 76c931d Add Cython 3.0.0 generated files (#4243)
• a603475 Pre release 2.6.0 (#4241)
• fa0fb82 Build wheels with numpy 1.25+ (#4198)
• b21478f deal with leftover master references (#4235)
• 6e80c28 fix error message for XDR readers (#4231)
• 1eca655 TST: test_streamplot_2D faster (#4221)
• bd3c14c Enable old Boltzmann key with DeprecationWarning (#4230)
• d33cc3a Corrected environment varaible for duecredit in docs (#4226)
• 072209f update numpy in pyproject.toml (#4227)
• 2bf55dd Remove -ffast-math compiler flag (#4220)
• Additional commits viewable in compare view

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