0.4.0

This release includes several new features, bug fixes, documentation improvements, and some behavior changes. Some features previously tagged as experimental are now, with some limitations, in the public API.

For more, see the 0.4.0 release notes, installation instructions, or full documentation.

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What's Changed

• Migrate to Pydantic v2 by @mattwthompson in #964
• Make Interchange.topology a required field by @mattwthompson in #995
• Collection ergonomics by @Yoshanuikabundi in #990
• Improve documentation of from_openmm and related features by @mattwthompson in #1008
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1025
• Simplify access to Pydantic v1 API by @mattwthompson in #1026
• Migrate formatting to ruff by @mattwthompson in #1032
• Convenience methods for producing run input files by @Yoshanuikabundi in #1027
• Do not write vacuum simulations to GROMACS files by @mattwthompson in #1034
• API cleanup by @mattwthompson in #1043
• Add amber example by @mattwthompson in #1046
• Add to_amber convenience method by @mattwthompson in #1041
• Fix default .charges by @mattwthompson in #1066
• Use update instead of assignment to set _charges by @ntBre in #1069
• Log packing failures by @mattwthompson in #1067
• Error if HMR results in negative particle mass by @mattwthompson in #1065
• Clarify to_openmm_simulation docstring and rename to_lammps(file_path) arg to prefix by @Yoshanuikabundi in #1042
• Fix regression tests by @mattwthompson in #1073
• Add high-level positions getter, exclude virtual sites by default by @mattwthompson in #1074
• Export positions with virtual sites by default by @mattwthompson in #1078
• Decrease default density in Packmol wrappers by @mattwthompson in #1068
• Update topology/system particle bookkeeping in OpenMM by @mattwthompson in #1051
• Document that topology charges are ignored by @mattwthompson in #1064

New Contributors

• @ntBre made their first contribution in #1069

Full Changelog: v0.3.29...v0.4.0rc1