Added

• Inverse map (label to type ID) in LabelMap.
• Type hints.
• Support for Python 3.14.
• Tutorial on initializing an atomistic simulation.
• Tutorial on using NumPy and Numba to accelerate calculations.

Fixed

• Jupyter notebooks for tutorials execute as scripts.
• Mass section of data file is written in the same spot as by LAMMPS.

Removed

• Support for Python 3.9.

Added

• Complete sphinx documentation is hosted on Read the Docs.
• Unit tests that run against LAMMPS.
• Convenience methods for working with boxes: to/from a matrix and to/from a HOOMD box definition.

Fixed

• Lists of known/unknown headers and bodies for DataFile are now current.
• Particle positions are now correctly recentered when converting a Snapshot to a GSD Frame if the Box is not centered at the origin.

Added

• Initial support for type labels of particle and topology data through the
  LabelMap object.
• Interconversion of topology data with GSD Frame.
• Support for Python 3.13.
• Copying of topology data from an existing Snapshot when reading a dump file.

Fixed

• Only GSD properties that have been assigned are converted to a Snapshot.
• Issues with writing topology information to data files.
• Deduction of atom type from information in Snapshot.

Removed

• Support for Python 3.8.

Added

• Backwards compatible support for NumPy 2.0.

Fixed

• Test dependencies for Python 3.8.

Added

• Support for reading and writing dump files with zstd compression.

Fixed

• Reading and writing dump files with triclinic boxes.
• Validation of image in user-specified dump schema.

Added

• Basic support for molecular topology data. These data are exposed as Bonds, Angles, Dihedrals and Impropers objects that can be included in a Snapshot and read/written to a DataFile. Some features are not yet fully supported, such as conversion to/from GSD format and as an option to copy_from for a DumpFile.
• Testing for Python 3.12.

Changed

• Bumped license year to 2024.

Added

• lammpsio is available for download on conda-forge. Installation directions
  have been updated to include this option.

Fixed

• Compatibility with GSD 3.

Added

• Snapshot can be created from and converted to a GSD HOOMD frame.
• Package version is embedded in __version__.

Changed

• Python 3.11 is supported and tested.
• Code style is enforced using black and flake8. Developers should install
  requirements-dev.txt and configure pre-commit.
• Classes are broken into modules for readability. The user API does not change.
• NumPy arrays use float and int as data types instead of specified precision.

Added

• Dump file defaults to reading schema from atoms header.

Fixed

• Dump file now reads/writes box bounds header correctly.

Added

• Snapshots store particle IDs. Files can contain noncompact particle ID ranges.
• Dump file can copy fields from another snapshot during reading.