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Python Freethreading in future Python versions (3.13+)

dependenciesPull requests that update a dependency filePull requests that update a dependency file

prio-high

Status: Open.

Feature

#2063 In mdtraj/mdtraj;

· jeremyleung521 opened on Jul 25, 2025

Incomplete hash methods in <code>Topology</code> class

Status: Open.

#2039 In mdtraj/mdtraj;

· janash opened on Jun 3, 2025

<code>Topology.delete_atom_by_index</code> can create inconsistency between topology and trajectory data

Status: Open.

#2025 In mdtraj/mdtraj;

· janash opened on May 17, 2025

Revival of the "within" keyword for atom selection

apiFor changes to the way the user interacts with the codebaseFor changes to the way the user interacts with the codebase

wishlist

Status: Open.

Feature

#2024 In mdtraj/mdtraj;

· jeremyleung521 opened on May 16, 2025

Memory not released when reusing Trajectory variable – possible cyclic references or missing explicit cleanup

Status: Open.

#2005 In mdtraj/mdtraj;

· turcinv opened on Mar 22, 2025

Performance enhancements for <code>_geometry.pyx</code>

geometryFor changes or updates to the way geometric values are calculatedFor changes or updates to the way geometric values are calculated

Status: Open.

#1975 In mdtraj/mdtraj;

· jeremyleung521 opened on Feb 6, 2025

Precentered is ignored when atom_indices != None

Status: Open.

#1966 In mdtraj/mdtraj;

· d-beltran opened on Jan 8, 2025

Including additional arrays in H5MD trajectory files?

Status: Open.

#1955 In mdtraj/mdtraj;

· orionarcher opened on Dec 2, 2024

_ZSt28__throw_bad_array_new_lengthv

Status: Open.

#1954 In mdtraj/mdtraj;

· weigcdsb opened on Nov 29, 2024

UnicodeEncodeError: 'ascii' codec can't encode characters in position 12-16: ordinal not in range(128)

Status: Open.

#1953 In mdtraj/mdtraj;

· AthenACHY opened on Nov 29, 2024

Type annotations

Status: Open.

#1950 In mdtraj/mdtraj;

· mattwthompson opened on Nov 21, 2024

Issues with wernet_nilsson hbond counting in trajectory

Status: Open.

#1948 In mdtraj/mdtraj;

· PowersPope opened on Nov 15, 2024