0.4.5

What's Changed

• Fix JSON deserialization with preset charges by @mattwthompson in #1274
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #1285
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #1292
• Bump actions/checkout from 4 to 5 by @dependabot[bot] in #1293
• Fix box_shape docstring by @mattwthompson in #1294
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #1303
• Bump OpenEye Toolkits to 2025 line by @mattwthompson in #1305
• Handle NAGLCharges by @j-wags in #1206
• Make padding argument optional, avoid over-specifying inputs by @mattwthompson in #1302
• Finalize 0.4.5 release notes by @mattwthompson in #1307

Full Changelog: v0.4.4...v0.4.5

0.4.4

What's Changed

• Remove obsolete warnings of experimental/unstable status by @mattwthompson in #1259
• Remove importlib_metadata backport when loading plugins by @mattwthompson in #1263
• Skip molecules with zero count in Packmol wrapper by @mattwthompson in #1272
• Implement SLTCAP in solvate_topology by @chapincavender in #1273
• Finalize 0.4.4 release notes by @mattwthompson in #1277

New Contributors

• @chapincavender made their first contribution in #1273

Full Changelog: v0.4.3...v0.4.4

0.4.3

What's Changed

• Make protein-ligand example charge-neutral by @mattwthompson in #1175
• Drop "v0.4 changes" section by @mattwthompson in #1173
• Add smirnoff-plugins back to CI by @mattwthompson in #1176
• Always use openmm.LangevinMiddleIntegrator by @mattwthompson in #1137
• Do not assume molecules are grouped by @mattwthompson in #1186
• Update Interchange.combine warning by @mattwthompson in #1183
• Test on Python 3.13 by @mattwthompson in #1174
• Match toolkit behavior when writing PDB files by @mattwthompson in #1192
• Add CODEOWNERS file by @mattwthompson in #1199
• Fix improper atom ordering in LAMMPS by @mattwthompson in #1200
• LAMMPS improper atom order by @benjamindjensen in #1195
• Add example loading and comparing energy evaluations of prepared SAMPL6 system by @mattwthompson in #1187
• Drop Python 3.10 by @mattwthompson in #1194
• Remove hybrid pair styles by @mattwthompson in #1205
• Add (optional) type labels to LAMMPS export by @mattwthompson in #1216
• LAMMPS type labels by @benjamindjensen in #1208
• Support importing (some) virtual sites in Interchange.from_openmm by @mattwthompson in #1081
• Do not treat topology argument as optional by @mattwthompson in #1215
• Improve errors when parsing GROMACS files by @mattwthompson in #1224
• Treat asterisks as comments in GROMACS topology files by @mattwthompson in #1225
• Document how to control GROMACS molecule names by @mattwthompson in #1241
• Use pyedr instead of panedr by @mattwthompson in #1243
• Improve detailed energy reporting by @mattwthompson in #1229
• Add simple charge array getter by @mattwthompson in #1219
• Allow Interchange.combine when cutoffs differ by tiny amount by @mattwthompson in #1250
• Have get_charge_array fail when virtual sites are present by @mattwthompson in #1255
• Set positions from .gro files by @mattwthompson in #1220
• Finalize release v0.4.3 by @mattwthompson in #1253

New Contributors

• @benjamindjensen made their first contribution in #1195

Full Changelog: v0.4.2...v0.4.3

0.4.2

What's Changed

• Read GROMACS topology files split into .itp files by @mattwthompson in #1120
• Add center-of-mass motion remover in OpenMM export by @mattwthompson in #1133
• Cache some charge increment calculations by @mattwthompson in #1126
• Handle OpenMM version parsing in regression tests by @mattwthompson in #1140
• Document why tolerance is removed from box edges by @mattwthompson in #1159
• Document sharp edge of charges and Interchange.combine by @mattwthompson in #1155
• Error when non-bonded 1-4 scaling factors differ significantly by @mattwthompson in #1153
• Fixing some packmol interface docs. by @IAlibay in #1163
• Update experimental tag on examples, tests, experimental docs by @mattwthompson in #1150
• Finalize 0.4.2 release notes by @mattwthompson in #1171

New Contributors

• @IAlibay made their first contribution in #1163

Full Changelog: v0.4.1...v0.4.2

0.4.1

What's Changed

• Log charge assignment by @mattwthompson in #1053
• Handle some edge cases with preset charges by @mattwthompson in #1070
• Switch CI to use macos-latest by @mattwthompson in #1092
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1094
• Constrain openmm =8.1.2 in tests by @mattwthompson in #1100
• Switch version handling to to versioningit by @mattwthompson in #1097
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1099
• Fix RTD build by @Yoshanuikabundi in #1103
• Defer some third-party imports for quicker high-level imports by @mattwthompson in #1085
• Allow HMR with virtual sites in OpenMM by @mattwthompson in #1080
• Bump codecov/codecov-action from 4 to 5 by @dependabot in #1108
• Revert "Bump codecov/codecov-action from 4 to 5" by @mattwthompson in #1112
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1113
• Discard other conformers when packing by @mattwthompson in #1111
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1116
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1117
• Document Pydantic/Pint helpers by @mattwthompson in #1105
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1121
• Bump mamba-org/setup-micromamba from 1 to 2 by @dependabot in #1072
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1128
• Test JSON roundtrip after Interchange.from_openmm by @mattwthompson in #1089
• Update CI by @mattwthompson in #1123
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1129
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1130
• Update beta workflow by @mattwthompson in #1131
• Optionally write GROMACS topologies as multiple .itp files by @mattwthompson in #1119
• Create blank collections when importing only water by @mattwthompson in #1134
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1138
• Improve testing of GROMACS import by @mattwthompson in #1118
• More consistently use existing charge caching by @mattwthompson in #1115
• Improve performance of Interchange.from_smirnoff on polymers by @mattwthompson in #1122
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1147
• Consolidate Python config files by @mattwthompson in #1104
• Finalize 0.4.1 release notes by @mattwthompson in #1148

Full Changelog: v0.4.0...v0.4.1

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.

---

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.