1.11.0 (June 24, 2025)

• Test on Python 3.13 by @jeremyleung521 in #1973
• Set up cibuildwheel by @mattwthompson in #1980
• Remove scipy import in _lprmsd.pyx to make mdtraj submodules importable without scipy by @rjdirisio in #1988
• Run OpenMM tests on CI by @mikemhenry in #1986
• Add flaky/rerun-failures to tests that require pulling off a PDB by @jeremyleung521 in #1987
• Add logo in SVG by @janash in #1989
• Add type annotation to Topology class by @jchen0506 in #1977
• Remove netCDF4 dependency, set up PyPI build variants by @jeremyleung521 in #2000
• Allow ArcTrajectoryFile to optionally take topology by @jeremyleung521 in #2002
• Add formal charge to the to_dataframe() and from_dataframe() methods by @jchen0506 in #2007
• Fix atom_slice resSeq assignment and add HSD/HSE residue names by @huhlim and @jeremyleung521 in #2013
• Unpin sphinx by @janash in #2016
• Move RNG/ptraj generation for distance tests into fixture by @jeremyleung521 in #1999
• Refactor: remove arbitrary arguments from AST module classes by @RobertArbon in #2009
• Update note on project status by @janash in #2019
• Fix Topology double-loading for HDF5 and MOL2 (+ remove false-positive UserWarning) by @jeremyleung521 in #2012
• Feature: calculate Pi-stacking+T-stacking interactions given aromatic groups by @rjdirisio in #1984
• Sort bonds to avoid make_molecules_whole failures by @eruijsena in #1929
• Test Linux aarch64 by @jeremyleung521 in #1974
• Allow mdtraj.rmsd() to calculate without alignment by @jeremyleung521 in #2011
• Update formatters by @mattwthompson in #2022
• Bugfix: delete_atom_by_index updates bond list by @RobertArbon in #2021
• Preserve chain_id when creating topologies by @k9cdt in #2015
• Add nucleic and is_nucleic atom selection PR by @dwhswenson and @janash in #2023
• Remove header option from PDB writer by @cabb99 in #2034
• Port PDBx/mmCIF Reader/Writer from OpenMM to MDTraj by @cabb99 in #2004
• Add formal charge in missing places on topology by @janash in #2038
• Hotfix for numpy 2.3 by @jeremyleung521 in #2045
• Update dcdplugin.c by @reedharrison and @bennybp in #1771
• Update unitcell.py to check if unitcell is valid by @jeremyleung521 in #2029
• Drop Python 3.10 support by @jeremyleung521 in #2046
• Add py3dmol visualization to pi stacking by @janash in #2020
• Allow HDF5TrajectoryFile().topology = None by @jeremyleung521 in #2042
• Limit warnings in tests by @jeremyleung521 in #2047

A total of 14 people contributed to this release.
People with a "+" by their names contributed to MDTraj for the first time.

• Jeremy Leung
• Matt. W. Thompson
• Ryan DiRisio
• Mike M. Henry +
• Jessica A. Nash
• Jing Chen +
• Lim Heo +
• Lex O'brien +
• Enrico Ruijsenaars +
• Da Teng
• David W.H. Swenson
• Carlos Bueno +
• Reed Harrison +
• Benjamin P. Pritchard +

1.10.3 (February 7, 2025)

• Pin numpy>=1.25 at run time, numpy>=2.0 at build time for numpy C-API #1960
• Fix PDB overflow #1934
• Allow mdtraj.load with top=None #1969
• Preserve chain_ids for to_openmm and from_openmm #1951
• Store and write formal charges from PDB/OpenMM #1967
• Performance enhancement for md.join #1965
• Sorting atom_indices in atom_slice #1938
• Consolidate/update config files #1949
• Mark a few distance tests as flaky #1972

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

• Jeremy Leung
• Matthew W. Thompson
• Jessica A. Nash
• Jan-Oliver Kapp-Joswig +
• Ryan DiRisio +
• Da Teng +
• Pavel Buslaev +

What's Changed

• Add netCDF4 as a dependency in setup.py (#1944)
• Support NumPy 2 (#1928)

Full Changelog: 1.10.1...1.10.2

v1.10.1 (November 4, 2024)

• Update RMSD module for Cython 3.0 (#1917)
• Fix edge case with float rounding in angle computation (#1841)
• Add atom selection via atom_indices to SASA computation (#1844)
• ReadTheDocs migration (#1888)
• Fix netCDF import (#1894)
• Use standard library ast.unparse instead of third-party astunparse (#1898)
• Allow appending to HDF5 files (#1899)
• Remove deprecated oldest-supported-numpy (#1902)
• Remove remaining uses of six (#1908)
• Replace xdrlib with mda_xdrlib (#1911)
• Add mda-xdrlib to setup.py (#1913)
• Set up versioneer (#1909)
• Remove distutils from tests (#1916)
• Remove unused xdrlib import from Python layer (#1919)
• Fix PDB "vmd convention" false-positive (#1904)

A total of 11 people contributed to this release.
People with a "+" by their names contributed a patch for the first time.

• Charlie Laughton
• Guillermo Pérez-Hernández
• Sukrit Singh
• Jeremy Leung
• Sander Roet
• Chris Jones+
• David W.H. Swenson
• Matthew W. Thompson
• Robert Schütz+
• Patrick Kunzmann
• Augustin Zidek+

v1.10.0 (May 30, 2024)

• Remove TNG support (#1875)
• Drop support for long-unsupported upstreams (#1838)
• Drop distutils (#1834)
• Lint codebase (#1874)
• Allow mdtraj.load() to read various non-standard PDB files (#1849)
• Use netCDF4 as default in NetCDFTrajectoryFile, fallback to SciPy implementation (#1878)
• Add dependabot for updating actions (#1865)
• Fix editable mode (#1887)

Jinzhe Zeng+
Matthew W. Thompson
Jeremy Leung
Jessica A. Nash+

v1.10.0rc2 (May 28, 2024)

• Remove TNG support (#1875)
• Drop support for long-unsupported upstreams (#1838)
• Drop distutils (#1834)
• Lint codebase (#1874)
• Allow `mdtraj.load()`` to read various non-standard PDB files (#1849)
• Use netCDF4 as default in NetCDFTrajectoryFile, fallback to SciPy implementation (#1878)
• Add dependabot for updating actions (#1865)
• Fix editable mode (#1887)

Jinzhe Zeng+
Matthew W. Thompson
Jeremy Leung
Jessica A. Nash+

v1.10.0rc1 (May 17, 2024)

• Remove TNG support (#1875)
• Drop support for long-unsupported upstreams (#1838)
• Drop distutils (#1834)
• Lint codebase (#1874)
• Allow `mdtraj.load()`` to read various non-standard PDB files (#1849)
• Use netCDF4 as default in NetCDFTrajectoryFile, fallback to SciPy implementation (#1878)
• Add dependabot for updating actions (#1865)

Jinzhe Zeng+
Matthew W. Thompson
Jeremy Leung
Jessica A. Nash+

v1.9.9 (July 22, 2023)

• Pin Cython~=0.29 in pyproject.toml (#1801)
• Remove "stale" bot (#1758)
• Announce maintainer update (#1795)
• Use oldest-supported-numpy in pyproject.toml (#1751)

A total of 4 people contributed to this release, including three new contributors.
People with a "+" by their names contributed a patch for the first time.

In-Ho Yi+
Sukrit Singh+
Jeremy Leung+
Matthew W. Thompson

v1.9.8 (July 2, 2023)

• Patch util_arm.h for M1 (#1694)
• Avoid side effects in mdtraj.load (#1706)
• Add PDB chainID support (#1715)
• Remove imports from simtk namespace (#1698)
• Implement reading and writing PDBx/mmCIF (#1718)
• Fix compute_inertia_tensor docstring (#1721)
• Fix typo in docs (#1725)
• Adds lower-level compute_distances_core function (#1728)
• Implement generic C code paths for non-accelerated architectures (#1727)
• Add note about project maintinance status (#1738)
• Force new residue when creating new chain (#1740)
• Warn if atom_indices are not monotonically increasing (#1766)
• Delete notes in issue-template by (#1778)
• Fix hashing when unitcell data is not present (#1781)
• Test on Python 3.11 (#1758)
• Constrain GSD to version 2 (#1790)

A total of 10 people contributed to this release.
People with a "+" by their names contributed a patch for the first time.

• Robert T. McGibbon
• Sander Roet
• Peter Eastman
• Charlie Laughton
• Christoph Klein
• Luca Naef +
• Jacob Lumpkins +
• Ray A. Matsumoto
• Matthew W. Thompson
• Moritz Hoffmann +
• German P. Barletta +
• Masataka Yamauchi +
• Samuel Lotz +
• Toni G +
• Bojun Liu +

v1.9.7 (November 12, 2021)

• Replace discourse link with gitter link (904338b)
• Faster load function and more homogenous file parser interface (#1648)
• Reduce memory usage of rdf_t (#1661)
• Update to new OpenMM namespace (#1668)
• Fix compute_contact bug with glycine sidechains (#1674)
• Fix errors in RMSF documentation (#1676)
• Handle path-like objects in place of filenames (#1680)
• Pin NumPy in pyproject.toml for Python 3.10 (#1681)
• Fix compilation errors on M1 Macs (#1684)
• Update Python versions in CI (#1686)
• Fix jupyter runners in CI (#1687)

A total of 10 people contributed to this release.
People with a "+" by their names contributed a patch for the first time.

• Robert T. McGibbon
• Sander Roet
• Charlie Laughton +
• Alexander Matthew Payne +
• Tucker Burgin +
• Maurice Karrenbrock
• Luca Naef +
• Jacob Lumpkins +
• Ray A. Matsumoto
• Matthew W. Thompson