1.2.1

What's Changed

Features

Bug fixes

• Fix sidemax test in test_packing.py by using a more reasonable length by @chrisjonesBSU in #1256

Maintenance

• Use numpy 2 in CI testing. Drop python 3.9, add python 3.13 to testing, remove openbabel from enviroment-dev.yml by @chrisjonesBSU in #1252
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #1251, #1253, #1254, #1255,

Full Changelog: 1.2.0...1.2.1

1.2.0

What's Changed

Features

• Add method to Compound that checks for overlapping particles by @chrisjonesBSU in #1225
• Add option for periodic boundaries when using PACKMOL. by @chrisjonesBSU in #1223

Bugfixes

• Fix show ports by @chrisiacovella in #1233

Maintenance

• Fix and update Dockerfile by @chrisjonesBSU in #1220
• Remove windows tesitng, add separate WSL test, update readthedocs environment and remove documentation of deprecated modules. by @chrisjonesBSU in #1227
• Drop importlib.resources backport by @mattwthompson in #1246
• Add py3Dmol to dev env file by @chrisjonesBSU in #1248
• Remove experimental feature tag for freud generate_bonds by @CalCraven in #1249
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1221 #1222 #1224 #1228 #1229 #1230 #1234 #1235 #1238 #1239 #1240 #1242 #1243 #1244 #1245 #1247 #1250

Full Changelog: 1.1.1...1.2.0

1.1.1

What's Changed

Features

• Add Ruff to pre-commit hooks by @chrisjonesBSU in #1207
• Reformat loaders for different smiles paths by @CalCraven in #1211
• Replace setup.py with pyproject.toml, update actions to latest versions by @chrisjonesBSU in #1217
• Update 1.1.1 by @CalCraven in #1219

Bugfixes

• fix label handling during flatten by @CalCraven in #1208

Maintenance

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1209 #1210 #1213 #1214 #1215 #1216 #1218

Full Changelog: 1.0.0...1.1.1

1.1.0

What's Changed

Bugfixes

• fix label handling during flatten by @CalCraven in #1208
• Reformat loaders for different smiles paths by @CalCraven in #1211

Maintenance

• Add Ruff to pre-commit hooks by @chrisjonesBSU in #1207
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1209, #1210, #1213

Full Changelog: 1.0.0...1.1.0

mBuild 1.0 stable release

mBuild 1.0 Announcement

mBuild has reached a relatively feature complete stage. The core functionality of building up a wide array of systems is very stable and generalizeable through custom recipes. As GMSO has continued to inherit the workload of functionality, including being the nexus of conversion to other python objects and file readers and writers, many methods of mBuild have been exported. This leaves mBuild as a more focused package on handling diverse simulation configurations. Continued development will shift towards more complicated initialization utilities, such as energy minimization steps, quick and dirty Monte Carlo methods for thermodynamic configurations, polymer crosslinking, protein folding, and potentially more coarse grain accessibility and backmapping. We hope to continue to work with others who have developed these methods for their own research, and make them available to the community through mBuild routines.

What's Changed just in the last patch.

• improve speedup of large lattice by @CalCraven in #1198
• Remove deprecated formats, update reader and writer backends by @chrisjonesBSU in #1191
• Remove rigid body data structure from Compound by @chrisjonesBSU in #1203
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1201

Full Changelog: 0.18.0...1.0.0

0.18.0

What's Changed

Features

• Add packmol_args parameter to packing fucntions. Allows user to give additional commands to PACKMOL. by @chrisjonesBSU in #787
• Add cap hydrogens to head and tail compounds in the polymer builder by @chrisjonesBSU in #1196

Bugfixes

• reset_labels kwarg to force_overlap, new method reset_labels by @jaclark5 in #1195

Maintenance

• Fix failing tests with latest version of packmol by @CalCraven in #1189
• Add warnings for deprecated file formats (protobuf, hoomdxml, Hoomd-Blue and LAMMPS simulation writers) by @chrisjonesBSU in #1188
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1193
• Fix deprecation warnig in packing.py and replace .format() with f-strings where possible. by @chrisjonesBSU in #1192

Full Changelog: 0.17.1...0.18.0

0.17.1

What's Changed

Features

• Update README graphic by @daico007 in #1178
• Add option to reset child labels in Compound.remove() by @jaclark5 in #1173
• Periodic polymer by @jaclark5 in #1170

Bugfixes

• Attempt to fix docs build by @daico007 in #1169
• Fix failing doc build by @daico007 in #1177

Maintenance

• Bump to python 3.12 by @CalCraven in #1180
• [pre-commit.ci] pre-commit autoupdate by https://github.com/pre-commit-ci in #1167, #1176, #1181, #1183, #1184
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1184

Full Changelog: 0.17.0...0.17.1

mBuild 0.17.0

Features

• Add export to RDKIT to allow for chemdraw style visualization. by @chrisiacovella in #1137
• Add check_box_size option for add method in Compound.add() by @daico007 in #1149
• Add new default option for combining_rule in Compound.save() by @daico007 in #1153
• Added ability to adjust bead_size by @jaclark5 in #1158
• Speed up json loader by @daico007 in #1163

Bug fixes

• fixed the tree print issue by @GuiLingfeng in #1155

Maintenance

• Fix Docker build by @daico007 in #1147
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1148, #1151, #1154, #1161, #1164, #1165
• Update deprecated syntax in CI.yml by @daico007 in #1160

New Contributors

• @GuiLingfeng made their first contribution in #1155

Full Changelog: 0.16.4...0.17.0

mBuild 0.16.4

Features

• Revised load_xyz function by @chrisiacovella in #1140
• Add new option for packing.solvate by @daico007 in #1144

Bug fixes

• Fix Treelib test by @daico007 in #1142

Maintenance

• Added extensions to savers doc string by @CalCraven in #1146

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1136, #1145

Full Changelog: 0.16.3...0.16.4

mBuild 0.16.3

What's Changed

Features

• Support GSD >= 2.9 by @chrisjonesBSU in #1131
• Turn off infer_residues for when converting to parmed by @daico007 in (#1129, #1134, #1135)

Full Changelog: 0.16.2...0.16.3