padix-key commented 5 days ago

Currently Biotite requires MDTraj as additional dependency only for reading coordinates from trajectory files. However, MDTraj does not support NumPy 2.0, yet, but Biotite 1.0 will require NumPy 2.0. Therefore we could think about removing the dependency by implementing at least the common trajectory file formats .trr and .xtc. Lowering the number of dependencies would also make Biotite more lightweight.

To resolve this issue,

the TrajectoryFile classes need to be removed,
new trajectory file classes need to be added implementing .trr and .xtc (maybe in structure.io.trr?) and
the consistency tests checking against MDTraj need to be removed (could be solved by checking against a fixed CSV file obtained once from MDTraj).

~Taking verbatim code from https://github.com/mdtraj/mdtraj is not possible due to the incompatible license.~ As the xdrfile C-library is also GPL licensed, the entire Trajectory code would need to go into a separate extension package, if we decide to drop the MDTraj dependency.

padix-key commented 5 days ago

I reached out to the MDTraj developers, asking them about their NumPy 2.0 migration plans: https://github.com/mdtraj/mdtraj/issues/1873#issuecomment-2197294604

padix-key commented 4 days ago

d6ea5069454dbdf2f64b7f49dc0eeb5448889b86

After implementation if this issue, they need to be reenabled.

biotite-dev / biotite

Implementing TRR/XTC support #613

529 temporarily disables trajectory functionalites: https://github.com/biotite-dev/biotite/pull/529/commits/d6ea5069454dbdf2f64b7f49dc0eeb5448889b86