0.15.0

What's Changed

New Features

• GMSOLogger Class by @CalCraven in #904
• Fill out virtual_sites position functionality by @CalCraven in #934
• Bonds and Angles handle wildcards for bonds and sites. by @CalCraven in #928
• Add support for itp file by @askforarun in #896

Bug Fixes

• Update oplsaa.xml file in utils, fix failing CI. by @chrisjonesBSU in #912

Maintenance

• Replace setuptools in GMSO by @CalCraven in #908
• Remove deprecated newshape parameter from some numpy methods. by @chrisjonesBSU in #916
• Replace importlib_resources with built in importlib library by @chrisjonesBSU in #919
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #907, #909, #913, #915, #918, #922, #923, #925, #927, #930, #931, #932, #933, and #935

New Contributors

• @askforarun made their first contribution in #896

Full Changelog: 0.14.0...0.15.0

0.14.0

What's Changed

Features

• mol2 writer by @Zeerakkhan47 and @CalCraven in #869

Bug fixes

Maintenance

• Use numpy 2 in CI testing. Drop python 3.9, add python 3.13 to testing. by @chrisjonesBSU in #901
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #900, #902, #905, #906

Full Changelog: 0.13.0...0.14.0

0.13.0

What's Changed

Features

• Update equation_compare.py by @bc118 in #834
• Handlers for template potentials that are different forms of the same equation. by @CalCraven in #855
• Add settles_tag by @CalCraven in #872
• Sympy Numpy expressions by @CalCraven in #881
• Virtual site class by @Zeerakkhan47 in #876
• Add support for writing rigid bodies when converting to HOOMD formats. by @chrisjonesBSU in #850
• create virtual site test and pass tip4p finding types by @CalCraven in #890

Bug fixes

• Fix __repr__ method in abstract_site.Molecule and abstract_site.Residue by @chrisjonesBSU in #851
• Fix invalid options in the docstrings for ignore_params in apply() by @chrisjonesBSU in #895

Maintenance

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #829, #830, #832, #833, #835, #836, #838, #840, #842, #843, #844, #849, #852, #854, #858, #860, #867, #868, #871, #873, #875, #877, #878, #882, #883, #884, #880, #885, #889, #891, #892, #894, #897
• Reduce tests in CI workflow by @chrisjonesBSU in #831
• add dmref acknowledgement by @CalCraven in #839
• Remove all references to mbuild loaders so tests begin to work by @CalCraven in #862
• Add templates for PR and Issues by @CalCraven in #861
• Replace setup.py with pyproject.toml, update actions to latest versions by @chrisjonesBSU in #865
• Update docker file by @chrisjonesBSU in #870
• Drop support for hoomd 3, include Hoomd 5 in environment by @chrisjonesBSU in #879
• Drop importlib_resources dependency by @mattwthompson in #893

New Contributors

• @Zeerakkhan47 made their first contribution in #876

Full Changelog: 0.12.4...0.13.0

0.12.4

What's Changed

• Fix hoomd version handling in convert_hoomd.py by @chrisjonesBSU in #828

Full Changelog: 0.12.2...0.12.4

GMSO 0.12.2

Features

• Update README graphic by @daico007 in #813
• Add support for hoomd.md.improper.Periodic in to_hoomd_forcefield by @chrisjonesBSU in #807
• Write out rigid water for GROMACS top file by @daico007 in #771

Bug Fixes

• Fix failing LAMMPS writer test by @daico007 in #815

Maintenance

• Add Ruff to pre-commit by @CalCraven in #819
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #816, #820, #821, #823, #824
• Add python 3.12 to CI workflow and environment files by @chrisjonesBSU in #822

Full Changelog: 0.12.1...0.12.2

GMSO 0.12.1

Features

• Edits for JOSS paper by @CalCraven in #799
• Update docs landing page by @daico007 in #803
• Update connection members during parameterization by @CalCraven in #808
• Add TOC for GMSO paper by @daico007 in #809

Bug fixes

• Fix order of matching when atomtyping by @daico007 in #802
• Fix docs to work with pyndatic v2 by @daico007 in #805

Maintenance

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #804, #811
• Remove old Ar example by @daico007 in #812

Full Changelog: 0.12.0...0.12.1

GMSO 0.12.0

Manuscript

• First draft for GMSO paper by @daico007 in #797, #798

Features

• Add position restraints for Site by @daico007 in #770
• Add to_xml method to Topology by @chrisjonesBSU in #782
• Update GMSO to work with pydantic 2.0 by @daico007 in #745
• Sorting of improper types by @CalCraven in #796
• Write charge in elementary charge unit (XML writer) by @daico007 in #794
• Support Lammps charmm dihedrals by @CalCraven in #787

Bug fixes

• Fix to bug in handling charge loading for JSON serialization by @CalCraven in #793
• Fix bug in GRO reader by @daico007 in #775

Maintenance

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #772, #779, #784, #790, #791, #800 #772
• Drop support/testing for py3.8 by @daico007 in #781
• Update Dockerfile by @daico007 in #789

Full Changelog: 0.11.2...0.12.0

GMSO 0.11.2

Features

• Add shift_coord for gro writer by @daico007 in #730
• Turn off identify_connected_components default by @daico007 in #760
• Remove convert_foyer_xml and replace with using foyer as the backend by @CalCraven in #749
• Add functionality to remove sites and connections from a topology by @chrisjonesBSU in #761
• Speedup to_parmed conversion by @daico007 in #768
• Improve Cassandra support by @emarinri in #756
• Sort indices in Frame.bond.group by @chrisjonesBSU in #769

Bug fixes

• Replace unyt.amu with Unit("amu") to preserve mass values from mBuild by @chrisjonesBSU in #759
• Fix HOOMD issues with GAFF ForceField by @CalCraven in #765

Maintenance

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #763
• Attempt to unpin some of our dependencies by @daico007 in #764

New Contributors

• @emarinri made their first contribution in #756

Full Changelog: 0.11.1...0.11.2

GMSO 0.11.1

Features

• Initial centralization of topology’s unit conversions (by unit systems) by @CalCraven in #747

Bug Fixes

• Fix return statement in _parse_coulombic by @chrisjonesBSU in #744
• Fix mass type in convert_parmed by @marjanAlbouye in #754

Maintenance

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #746
• Reconcile conflict with pydantic 2.0 by @mattwthompson in #752 and by @daico007 in #751

Full Changelog: 0.11.0...0.11.1

GMSO 0.11.0

Features

• Add verbose options for mol2 and element by @daico007 in #729
• Support GSD 3 by @chrisjonesBSU in #739
• Speedup identify_connections by @daico007 in #741
• Lammps Writer Changes For Updated Topology Class by @CalCraven in #701

Bug fixes

• Small fix to mass in convert_parmed by @chrisjonesBSU in #737

Maintenance

• Update action/provision and mamba-org/setup-micromamba by @daico007 in #732
• Unpin HOOMD by @daico007 in #734
• Update test by @daico007 in #743

Full Changelog: 0.10.0...0.11.0