MDTraj 1.10.0

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+

MDTraj 1.10.0rc2

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+

MDTraj 1.10.0rc1

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+

MDTraj 1.9.9

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

MDTraj 1.9.8

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 +

MDTraj 1.9.7

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

MDTraj 1.9.6

v1.9.6

• Fix compatibility with all versions of astunparse (03753d7)
• Rework CI to be simpler and more maintainable
• Fix deployment of the documentation to the website
• Don't use serials for more than 1 chain (#1612)
• Added enforcePeriodicBox option for HDF5Reporter (#1622)
• Add time-dependent distance and RDF functions (#1633)
• Add select option to compute_center_of_mass() (#1640)
• Topology.join() can optionally updates resSeq of new residues (#1639)

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

• Robert T. McGibbon
• Sander Roet
• Ray A. Matsumoto
• Maurice Karrenbrock +
• Kirill Shmilovich
• Heyi Liang +
• Matthew W. Thompson

(Special thank you to Matthew W. Thompson for putting together these release notes)

MDTraj 1.9.5

• Fix memory allocation when opening XTC trajectory on OSX Catalina (#1594)
• Write out serial instead of index in pdbs (#1584)
• Fix residue idx sliced traj (#1586)
• Update shift_wrappers.py (#1579)
• Rsmd atom_indices checks fix (#1571)
• Port to aarch64 (#1562)
• Add compatibility with pandas 1.0

MDTraj 1.9.4

• Update some pandas calls for v1.0 (#1536)
• Fix TRR file offset (#1534)
• Update selection for Python 3.8 compatibility (#1523)
• Ensure bonds exist before using them (#1512, #1513)
• Let compute_displacements handle empty atom_pairs (#1515)
• Add GSD reader and writer (#1494)
• Fix stride parameter for .netcdf files (#1501)
• Ensure that the license file is packaged in the sdist (#1498)
• Right-justify atom symbol when writing PDB files (#1459)
• Add calculations for shape metrics (#1471)
• Fix residue parsing in MOL2 reader (#1490)
• Set up "stale" bot
• Use AZP for CI (#1484, #1536)
• Fix leaving malformed TRR files open (#1482)
• Fix various OpenMP issues (#1476, #1477, #1488, #1508, #1529)
• Add gyration tensor calculation (#1467)
• Fix some type conversions (#1466, #1511)
• Remove bundled dependencies astor and pyparsing (#1452)
• Correct ordering in hoomdxml files (#1453)

1.9.3

• Fix CI (#1416, #1420, #1444)

• Add compute_center_of_geometry (#1405)

• Fix a test failure in test_reporters.py caused by merge of #1431 (#1443)

• Reporters no longer override user request to write unit cell information (#1431)

• Add XTCReporter for OpenMM (#1403)

• Avoid infinite recursion error in mol2 parser (#1426)

• [formats/mol2] add more checks to element parsing (#1407)

• Replace strip() with split() in mol2.py (#1378)

• Use and set resSeq attribute in Topology.to_openmm() and from_openmm() (#1424)

• fix parallel reduction error (#1419)

• Fixes 'Buffer dtype mismatch' error on 64-bit Windows (#1409)

• add RMSF analysis (#1414)

• allow RMSD calls when ref_atom_indices and atom_indices are used (#1392)

• Notebook tests: from __future__ must come first (#1401)

• [setup] do not enforce clang/std++ on osx (#1400)

• silence cython related numpy warnings (#1391)

• Prep py37, some bugfixes (#1388)

• Ensure 'bond_value' is a string (#1382)

• fix typo in docs (#1381)

Authors

• Carlos Hernández
• John Chodera +
• Jack Greisman +
• jgilaber +
• Sunhwan Jo +
• Ray A. Matsumoto +
• Robert T. McGibbon
• João Rodrigues +
• Shyam Saladi
• Martin K. Scherer
• David W.H. Swenson
• Matthew W. Thompson +
• Lee-Ping Wang

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