openforcefield/openff-interchange

📋 What's Changed

• Invalidate OpenMM caches at export time by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1452
• Migrate Pixi config from `pyproject.toml` to `pixi.toml` by @Copilot in https://github.com/openforcefield/openff-interchange/pull/1459
• Fix behavior of `charge_from_molecules` being empty by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1462
• Skip flaky test for now by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1472
• Update charge assignment hierarchy docs for NAGL charges by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1468
• Update citation guidelines by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1470
• Use `openff-packmol` by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1423
• Ensure box vectors are stored with nanometers by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1481
• + 5 more

✨ New Contributors

• @Copilot made their first contribution in https://github.com/openforcefield/openff-interchange/pull/1459
• Full Changelog: https://github.com/openforcefield/openff-interchange/compare/v0.5.2...v0.5.3

📋 What's Changed

• Clear caches when `Collection.set_force_field_parameters` is called by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1434
• Fix 1453 by @j-wags in https://github.com/openforcefield/openff-interchange/pull/1454
• Full Changelog: https://github.com/openforcefield/openff-interchange/compare/v0.5.1...v0.5.2

📋 What's Changed

• Use Sage 2.3.0 in most tests by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1412
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/openforcefield/openff-interchange/pull/1415
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/openforcefield/openff-interchange/pull/1419
• Build(deps): Bump prefix-dev/setup-pixi from 0.9.3 to 0.9.4 by @dependabot[bot] in https://github.com/openforcefield/openff-interchange/pull/1420
• Fix edge case with combination by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1418
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/openforcefield/openff-interchange/pull/1421
• Turn on import sorting by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1424
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/openforcefield/openff-interchange/pull/1425
• + 8 more

📋 What's Changed

• Update Packmol defaults by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1332
• Fix release history by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1373
• Exclude data files from conda/Python packages by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1329
• Bump actions/checkout from 5 to 6 by @dependabot[bot] in https://github.com/openforcefield/openff-interchange/pull/1374
• Make `Interchange.topology` not store positions by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1376
• Fix virtual site key equality definition by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1378
• Update beta workflow by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1381
• Use angstroms in docstrings packing functions by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1383
• + 13 more

📋 What's Changed

• Fix NumPy 2.4 incompatibility by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1404
• Full Changelog: https://github.com/openforcefield/openff-interchange/compare/v0.4.10...v0.4.11

📋 What's Changed

• Fix virtual site key equality definition by @mattwthompson https://github.com/openforcefield/openff-interchange/pull/1378
• Fix charge ordering in Amber files by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1396
• Finalize 0.4.10 release by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1399
• Full Changelog: https://github.com/openforcefield/openff-interchange/compare/v0.4.9...v0.4.10

📋 What's Changed

• Ensure Pydantic 2.12.1+ is not installed in tests by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1351
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/openforcefield/openff-interchange/pull/1350
• Add export benchmarks by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1353
• Add Foyer back to CI by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1354
• Add protein-in-water benchmark by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1355
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/openforcefield/openff-interchange/pull/1356
• Improve unit conversion and OpenMM export runtime by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1352
• Update test dependencies by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1357
• + 8 more

📋 What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/openforcefield/openff-interchange/pull/1326
• Fix beta workflow, type-checking by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1331
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/openforcefield/openff-interchange/pull/1336
• FIx key collision over-correction by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1325
• Skip nonintegral charge logic when not needed by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1328
• Test charge cache after `Interchange.combine` by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1327
• Fix CI by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1343
• Improve Amber energy error reporting by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1334
• + 6 more

📋 What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/openforcefield/openff-interchange/pull/1318
• Treat `openff-nagl` as optional in testing by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1321
• Finalize 0.4.7 release notes by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1323
• Full Changelog: https://github.com/openforcefield/openff-interchange/compare/v0.4.6...v0.4.7

📋 What's Changed

• Do not duplicate type annotations in docstrings by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1297
• Automatically format `pyproject.toml` by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1304
• Fix handling of DoubleExponentialVirtualSites by @fjclark in https://github.com/openforcefield/openff-interchange/pull/1312
• Declare minimum Python version by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1306
• Fix key collisions in `Interchange.combine` by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1315

✨ New Contributors

• @fjclark made their first contribution in https://github.com/openforcefield/openff-interchange/pull/1312
• Full Changelog: https://github.com/openforcefield/openff-interchange/compare/v0.4.5...v0.4.6

📋 What's Changed

• Fix JSON deserialization with preset charges by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1274
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/openforcefield/openff-interchange/pull/1285
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/openforcefield/openff-interchange/pull/1292
• Bump actions/checkout from 4 to 5 by @dependabot[bot] in https://github.com/openforcefield/openff-interchange/pull/1293
• Fix `box_shape` docstring by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1294
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/openforcefield/openff-interchange/pull/1303
• Bump OpenEye Toolkits to 2025 line by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1305
• Handle NAGLCharges by @j-wags in https://github.com/openforcefield/openff-interchange/pull/1206
• + 3 more

📋 What's Changed

• Remove obsolete warnings of experimental/unstable status by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1259
• Remove `importlib_metadata` backport when loading plugins by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1263
• Skip molecules with zero count in Packmol wrapper by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1272
• Implement SLTCAP in `solvate_topology` by @chapincavender in https://github.com/openforcefield/openff-interchange/pull/1273
• Finalize 0.4.4 release notes by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1277

✨ New Contributors

• @chapincavender made their first contribution in https://github.com/openforcefield/openff-interchange/pull/1273
• Full Changelog: https://github.com/openforcefield/openff-interchange/compare/v0.4.3...v0.4.4

📋 What's Changed

• Make protein-ligand example charge-neutral by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1175
• Drop "v0.4 changes" section by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1173
• Add `smirnoff-plugins` back to CI by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1176
• Always use `openmm.LangevinMiddleIntegrator` by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1137
• Do not assume molecules are grouped by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1186
• Update `Interchange.combine` warning by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1183
• Test on Python 3.13 by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1174
• Match toolkit behavior when writing PDB files by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1192
• + 20 more

✨ New Contributors

• @benjamindjensen made their first contribution in https://github.com/openforcefield/openff-interchange/pull/1195
• Full Changelog: https://github.com/openforcefield/openff-interchange/compare/v0.4.2...v0.4.3

📋 What's Changed

• Read GROMACS topology files split into `.itp` files by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1120
• Add center-of-mass motion remover in OpenMM export by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1133
• Cache some charge increment calculations by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1126
• Handle OpenMM version parsing in regression tests by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1140
• Document why `tolerance` is removed from box edges by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1159
• Document sharp edge of charges and `Interchange.combine` by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1155
• Error when non-bonded 1-4 scaling factors differ significantly by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1153
• Fixing some packmol interface docs. by @IAlibay in https://github.com/openforcefield/openff-interchange/pull/1163
• + 2 more

✨ New Contributors

• @IAlibay made their first contribution in https://github.com/openforcefield/openff-interchange/pull/1163
• Full Changelog: https://github.com/openforcefield/openff-interchange/compare/v0.4.1...v0.4.2

📋 What's Changed

• Log charge assignment by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1053
• Handle some edge cases with preset charges by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1070
• Switch CI to use `macos-latest` by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1092
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/openforcefield/openff-interchange/pull/1094
• Constrain `openmm =8.1.2` in tests by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1100
• Switch version handling to to `versioningit` by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1097
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/openforcefield/openff-interchange/pull/1099
• Fix RTD build by @Yoshanuikabundi in https://github.com/openforcefield/openff-interchange/pull/1103
• + 27 more

📋 What's Changed

• Migrate to Pydantic v2 by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/964
• Make `Interchange.topology` a required field by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/995
• Collection ergonomics by @Yoshanuikabundi in https://github.com/openforcefield/openff-interchange/pull/990
• Improve documentation of `from_openmm` and related features by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1008
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/openforcefield/openff-interchange/pull/1025
• Simplify access to Pydantic v1 API by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1026
• Migrate formatting to `ruff` by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1032
• Convenience methods for producing run input files by @Yoshanuikabundi in https://github.com/openforcefield/openff-interchange/pull/1027
• + 15 more

✨ New Contributors

• @ntBre made their first contribution in https://github.com/openforcefield/openff-interchange/pull/1069
• Full Changelog: https://github.com/openforcefield/openff-interchange/compare/v0.3.29...v0.4.0rc1

📋 What's Changed

• Migrate to Pydantic v2 by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/964
• Make `Interchange.topology` a required field by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/995
• Collection ergonomics by @Yoshanuikabundi in https://github.com/openforcefield/openff-interchange/pull/990
• Improve documentation of `from_openmm` and related features by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1008
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/openforcefield/openff-interchange/pull/1025
• Simplify access to Pydantic v1 API by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1026
• Migrate formatting to `ruff` by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1032
• Convenience methods for producing run input files by @Yoshanuikabundi in https://github.com/openforcefield/openff-interchange/pull/1027
• + 15 more

✨ New Contributors

• @ntBre made their first contribution in https://github.com/openforcefield/openff-interchange/pull/1069
• Full Changelog: https://github.com/openforcefield/openff-interchange/compare/v0.3.29...v0.4.0rc1

📋 What's Changed

• Migrate to Pydantic v2 by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/964
• Make `Interchange.topology` a required field by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/995
• Collection ergonomics by @Yoshanuikabundi in https://github.com/openforcefield/openff-interchange/pull/990
• Improve documentation of `from_openmm` and related features by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1008
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/openforcefield/openff-interchange/pull/1025
• Simplify access to Pydantic v1 API by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1026
• Migrate formatting to `ruff` by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1032
• Convenience methods for producing run input files by @Yoshanuikabundi in https://github.com/openforcefield/openff-interchange/pull/1027
• + 11 more

✨ New Contributors

• @ntBre made their first contribution in https://github.com/openforcefield/openff-interchange/pull/1069
• Full Changelog: https://github.com/openforcefield/openff-interchange/compare/v0.3.29...v0.4.0beta2

📋 What's Changed

• Migrate to Pydantic v2 by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/964
• Make `Interchange.topology` a required field by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/995
• Collection ergonomics by @Yoshanuikabundi in https://github.com/openforcefield/openff-interchange/pull/990
• Improve documentation of `from_openmm` and related features by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1008
• Migrate formatting to `ruff` by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1032
• Convenience methods for producing run input files by @Yoshanuikabundi in https://github.com/openforcefield/openff-interchange/pull/1027
• Do not write vacuum simulations to GROMACS files by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1034
• API changes by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1043
• + 2 more