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

0.4.0rc1

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

0.4.0beta2

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

New Contributors

• @ntBre made their first contribution in #1069

Full Changelog: v0.3.29...v0.4.0beta2

0.4.0beta1

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
• 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 changes by @mattwthompson in #1043
• Remove openff-models dependency in d35a4b5

Full Changelog: v0.3.29...v0.4.0beta1

0.3.29

0.3.29 GROMACS export performance improvements and bugfixes

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

0.3.28

0.3.28 Interoperability bugfixes

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

0.3.27

0.3.27 Interoperability improvements and bugfixes

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

0.3.26

0.3.26 Interoperability and documentation improvements

This release drops support for Python 3.9, updates some notebooks, and some experimental features

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

0.3.25

0.3.25 Virtual site improvements

This release updates two example notebooks and fixes a bug in which virtual site parameters sometimes clashed and.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

0.3.24

0.3.24 Interoperability improvements

This release fixes two bugs adjacent to Interchange.from_openmm and improves testing with it and Interchange.combine.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.