Parmed

What's Changed
* Fixed Improper Method Call: Replaced `mktemp` by fazledyn-or in https://github.com/ParmEd/ParmEd/pull/1328
* Add support for 12-6-4 models. by swails in https://github.com/ParmEd/ParmEd/pull/1346
* Fix wildcard sorting when writing Amber parameter sets (fixes 1347) by murfalo in https://github.com/ParmEd/ParmEd/pull/1348
* Match tleap by ensuring parm{10|99|15}.dat are loaded no more than once by murfalo in https://github.com/ParmEd/ParmEd/pull/1353
* Ignore TURN comments in PDBs by slochower in https://github.com/ParmEd/ParmEd/pull/1351
* fix `SyntaxWarning: invalid escape sequence` by njzjz in https://github.com/ParmEd/ParmEd/pull/1350
* Fix output of changeLJSingleType by swails in https://github.com/ParmEd/ParmEd/pull/1355
* Bugfixed AtomType equality operator by murfalo in https://github.com/ParmEd/ParmEd/pull/1360
* Fix the build wrt RDKit package issues by swails in https://github.com/ParmEd/ParmEd/pull/1370
* Fixed compatibility with NumPy 2.0+ by vedranmiletic in https://github.com/ParmEd/ParmEd/pull/1374
* Fix serialization of structure with bond type attributes and add test by swails in https://github.com/ParmEd/ParmEd/pull/1376
* Ensure PBC box vectors are in reduced form for OpenMM by nffaruk in https://github.com/ParmEd/ParmEd/pull/1368
* Improve mdin parsing to not split restraintmask fields using '=' wildcard char by nffaruk in https://github.com/ParmEd/ParmEd/pull/1369
* Fix velocity unit scale for existing vels passed to OpenMM by nffaruk in https://github.com/ParmEd/ParmEd/pull/1367
* Switch to non-deprecated miniforge by swails in https://github.com/ParmEd/ParmEd/pull/1378

New Contributors
* fazledyn-or made their first contribution in https://github.com/ParmEd/ParmEd/pull/1328
* murfalo made their first contribution in https://github.com/ParmEd/ParmEd/pull/1348
* slochower made their first contribution in https://github.com/ParmEd/ParmEd/pull/1351
* vedranmiletic made their first contribution in https://github.com/ParmEd/ParmEd/pull/1374

**Full Changelog**: https://github.com/ParmEd/ParmEd/compare/4.2.2...4.3.0

What's Changed
* Fix setup.py by swails in https://github.com/ParmEd/ParmEd/pull/1327


**Full Changelog**: https://github.com/ParmEd/ParmEd/compare/4.2.1...4.2.2

What's Changed
* Support Python 3.12 by mattwthompson in https://github.com/ParmEd/ParmEd/pull/1325
* Fix usage of lru_cache for cache in py38 by swails in https://github.com/ParmEd/ParmEd/pull/1326


**Full Changelog**: https://github.com/ParmEd/ParmEd/compare/4.2.0...4.2.1

What's Changed
* Added 3D-RISM and GBNSR6 to mdin configuration by Valdes-Tresanco-MS in https://github.com/ParmEd/ParmEd/pull/1305
* Basic routines for internal to cartesian coordinate conversion by bradakta in https://github.com/ParmEd/ParmEd/pull/1311
* Transfer chain IDs to OpenMM topology. by jpthompson17 in https://github.com/ParmEd/ParmEd/pull/1310
* Add a library of all CCD residues separate from modified amino/nucleic acids by swails in https://github.com/ParmEd/ParmEd/pull/1315
* Fix Python 3.8 support by swails in https://github.com/ParmEd/ParmEd/pull/1319
* Preserve residue IDs, insertion codes, and bond orders in OpenMM topology conversions by jpthompson17 in https://github.com/ParmEd/ParmEd/pull/1316

New Contributors
* bradakta made their first contribution in https://github.com/ParmEd/ParmEd/pull/1311

**Full Changelog**: https://github.com/ParmEd/ParmEd/compare/4.1.0...4.2.0

What's Changed
* set `python_requires` to `>=3.8` by njzjz in https://github.com/ParmEd/ParmEd/pull/1285
* switch out copy with deepcopy for structure.copy() method by daico007 in https://github.com/ParmEd/ParmEd/pull/1290
* Drude psf where NUMANISO is zero by florianjoerg in https://github.com/ParmEd/ParmEd/pull/1274
* lonepair refinement by JohannesKarwou in https://github.com/ParmEd/ParmEd/pull/1266
* Set atomic number when applying a patch by peastman in https://github.com/ParmEd/ParmEd/pull/1275
* Prefer patch versions that replace external bonds by peastman in https://github.com/ParmEd/ParmEd/pull/1278
* Enable changing C4 terms in LJ pairs individually by KevinMei-Github in https://github.com/ParmEd/ParmEd/pull/1277
* Fix an error with mdin changing by swails in https://github.com/ParmEd/ParmEd/pull/1299
* Fix bug with adding positional restraints for OpenMM (ParmEd1301) by nffaruk in https://github.com/ParmEd/ParmEd/pull/1302
* Fix bug with restart reporter for OpenMM minimization by nffaruk in https://github.com/ParmEd/ParmEd/pull/1303
* Preserve formal charges from PDB and CIF files if present over templates by swails in https://github.com/ParmEd/ParmEd/pull/1304

New Contributors
* njzjz made their first contribution in https://github.com/ParmEd/ParmEd/pull/1285
* daico007 made their first contribution in https://github.com/ParmEd/ParmEd/pull/1290
* florianjoerg made their first contribution in https://github.com/ParmEd/ParmEd/pull/1274
* JohannesKarwou made their first contribution in https://github.com/ParmEd/ParmEd/pull/1266
* KevinMei-Github made their first contribution in https://github.com/ParmEd/ParmEd/pull/1277
* nffaruk made their first contribution in https://github.com/ParmEd/ParmEd/pull/1302

**Full Changelog**: https://github.com/ParmEd/ParmEd/compare/4.0.0...4.1.0