## What's Changed ### Features * Update equation_compare.py by @bc118 in https://github.com/mosdef-hub/gmso/pull/834 * Handlers for template potentials that are different forms of the same equation. by @CalCraven in https://github.com/mosdef-hub/gmso/pull/855 * Add settles_tag by @CalCraven in https://github.com/mosdef-hub/gmso/pull/872 * Sympy Numpy expressions by @CalCraven in https://github.com/mosdef-hub/gmso/pull/881 * Virtual site class by @Zeerakkhan47 in https://github.com/mosdef-hub/gmso/pull/876 * Add support for writing rigid bodies when converting to HOOMD formats. by @chrisjonesBSU in https://github.com/mosdef-hub/gmso/pull/850 * create virtual site test and pass tip4p finding types by @CalCraven in https://github.com/mosdef-hub/gmso/pull/890 ### Bug fixes * Fix `__repr__` method in `abstract_site.Molecule` and `abstract_site.Residue` by @chrisjonesBSU in https://github.com/mosdef-hub/gmso/pull/851 * Fix invalid options in the docstrings for `ignore_params` in `apply()` by @chrisjonesBSU in https://github.com/mosdef-hub/gmso/pull/895 ### Maintenance * [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/gmso/pull/829, https://github.com/mosdef-hub/gmso/pull/830, https://github.com/mosdef-hub/gmso/pull/832, https://github.com/mosdef-hub/gmso/pull/833, https://github.com/mosdef-hub/gmso/pull/835, https://github.com/mosdef-hub/gmso/pull/836, https://github.com/mosdef-hub/gmso/pull/838, https://github.com/mosdef-hub/gmso/pull/840, https://github.com/mosdef-hub/gmso/pull/842, https://github.com/mosdef-hub/gmso/pull/843, https://github.com/mosdef-hub/gmso/pull/844, https://github.com/mosdef-hub/gmso/pull/849, https://github.com/mosdef-hub/gmso/pull/852, https://github.com/mosdef-hub/gmso/pull/854, https://github.com/mosdef-hub/gmso/pull/858, https://github.com/mosdef-hub/gmso/pull/860, https://github.com/mosdef-hub/gmso/pull/867, https://github.com/mosdef-hub/gmso/pull/868, https://github.com/mosdef-hub/gmso/pull/871, https://github.com/mosdef-hub/gmso/pull/873, https://github.com/mosdef-hub/gmso/pull/875, https://github.com/mosdef-hub/gmso/pull/877, https://github.com/mosdef-hub/gmso/pull/878, https://github.com/mosdef-hub/gmso/pull/882, https://github.com/mosdef-hub/gmso/pull/883, https://github.com/mosdef-hub/gmso/pull/884, https://github.com/mosdef-hub/gmso/pull/880, https://github.com/mosdef-hub/gmso/pull/885, https://github.com/mosdef-hub/gmso/pull/889, https://github.com/mosdef-hub/gmso/pull/891, https://github.com/mosdef-hub/gmso/pull/892, https://github.com/mosdef-hub/gmso/pull/894, https://github.com/mosdef-hub/gmso/pull/897 * Reduce tests in CI workflow by @chrisjonesBSU in https://github.com/mosdef-hub/gmso/pull/831 * add dmref acknowledgement by @CalCraven in https://github.com/mosdef-hub/gmso/pull/839 * Remove all references to mbuild loaders so tests begin to work by @CalCraven in https://github.com/mosdef-hub/gmso/pull/862 * Add templates for PR and Issues by @CalCraven in https://github.com/mosdef-hub/gmso/pull/861 * Replace `setup.py` with `pyproject.toml`, update actions to latest versions by @chrisjonesBSU in https://github.com/mosdef-hub/gmso/pull/865 * Update docker file by @chrisjonesBSU in https://github.com/mosdef-hub/gmso/pull/870 * Drop support for hoomd 3, include Hoomd 5 in environment by @chrisjonesBSU in https://github.com/mosdef-hub/gmso/pull/879 * Drop `importlib_resources` dependency by @mattwthompson in https://github.com/mosdef-hub/gmso/pull/893 ## New Contributors * @Zeerakkhan47 made their first contribution in https://github.com/mosdef-hub/gmso/pull/876 **Full Changelog**: https://github.com/mosdef-hub/gmso/compare/0.12.4...0.13.0

## What's Changed * Fix hoomd version handling in `convert_hoomd.py` by @chrisjonesBSU in https://github.com/mosdef-hub/gmso/pull/828 **Full Changelog**: https://github.com/mosdef-hub/gmso/compare/0.12.2...0.12.4

## What's Changed * Update README graphic by @daico007 in https://github.com/mosdef-hub/gmso/pull/813 * Fix failing LAMMPS writer test by @daico007 in https://github.com/mosdef-hub/gmso/pull/815 * Add Ruff to pre-commit by @CalCraven in https://github.com/mosdef-hub/gmso/pull/819 * [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/gmso/pull/816 * [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/gmso/pull/820 * [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/gmso/pull/821 * Add support for `hoomd.md.improper.Periodic` in `to_hoomd_forcefield` by @chrisjonesBSU in https://github.com/mosdef-hub/gmso/pull/807 * Add python 3.12 to CI workflow and environment files by @chrisjonesBSU in https://github.com/mosdef-hub/gmso/pull/822 * [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/gmso/pull/823 * [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/gmso/pull/824 * Write out rigid water for GROMACS top file by @daico007 in https://github.com/mosdef-hub/gmso/pull/771 **Full Changelog**: https://github.com/mosdef-hub/gmso/compare/0.12.1...0.12.2 ## What's Changed * Update README graphic by @daico007 in https://github.com/mosdef-hub/gmso/pull/813 * Fix failing LAMMPS writer test by @daico007 in https://github.com/mosdef-hub/gmso/pull/815 * Add Ruff to pre-commit by @CalCraven in https://github.com/mosdef-hub/gmso/pull/819 * [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/gmso/pull/816 * [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/gmso/pull/820 * [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/gmso/pull/821 * Add support for `hoomd.md.improper.Periodic` in `to_hoomd_forcefield` by @chrisjonesBSU in https://github.com/mosdef-hub/gmso/pull/807 * Add python 3.12 to CI workflow and environment files by @chrisjonesBSU in https://github.com/mosdef-hub/gmso/pull/822 * [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/gmso/pull/823 * [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/gmso/pull/824 * Write out rigid water for GROMACS top file by @daico007 in https://github.com/mosdef-hub/gmso/pull/771 **Full Changelog**: https://github.com/mosdef-hub/gmso/compare/0.12.1...0.12.2

## Features * Edits for JOSS paper by @CalCraven in https://github.com/mosdef-hub/gmso/pull/799 * Update docs landing page by @daico007 in https://github.com/mosdef-hub/gmso/pull/803 * Update connection members during parameterization by @CalCraven in https://github.com/mosdef-hub/gmso/pull/808 * Add TOC for GMSO paper by @daico007 in https://github.com/mosdef-hub/gmso/pull/809 ## Bug fixes * Fix order of matching when atomtyping by @daico007 in https://github.com/mosdef-hub/gmso/pull/802 * Fix docs to work with pyndatic v2 by @daico007 in https://github.com/mosdef-hub/gmso/pull/805 ## Maintenance * [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #804, #811 * Remove old Ar example by @daico007 in https://github.com/mosdef-hub/gmso/pull/812 **Full Changelog**: https://github.com/mosdef-hub/gmso/compare/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 https://github.com/mosdef-hub/gmso/pull/770 * Add `to_xml` method to Topology by @chrisjonesBSU in https://github.com/mosdef-hub/gmso/pull/782 * Update GMSO to work with pydantic 2.0 by @daico007 in https://github.com/mosdef-hub/gmso/pull/745 * Sorting of improper types by @CalCraven in https://github.com/mosdef-hub/gmso/pull/796 * Write charge in elementary charge unit (XML writer) by @daico007 in https://github.com/mosdef-hub/gmso/pull/794 * Support Lammps charmm dihedrals by @CalCraven in https://github.com/mosdef-hub/gmso/pull/787 ## Bug fixes * Fix to bug in handling charge loading for JSON serialization by @CalCraven in https://github.com/mosdef-hub/gmso/pull/793 * Fix bug in GRO reader by @daico007 in https://github.com/mosdef-hub/gmso/pull/775 ## Maintenance * [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #772, #779, #784, #790, #791, #800 https://github.com/mosdef-hub/gmso/pull/772 * Drop support/testing for py3.8 by @daico007 in https://github.com/mosdef-hub/gmso/pull/781 * Update Dockerfile by @daico007 in https://github.com/mosdef-hub/gmso/pull/789 **Full Changelog**: https://github.com/mosdef-hub/gmso/compare/0.11.2...0.12.0

## Features * Add shift_coord for gro writer by @daico007 in https://github.com/mosdef-hub/gmso/pull/730 * Turn off identify_connected_components default by @daico007 in https://github.com/mosdef-hub/gmso/pull/760 * Remove convert_foyer_xml and replace with using foyer as the backend by @CalCraven in https://github.com/mosdef-hub/gmso/pull/749 * Add functionality to remove sites and connections from a topology by @chrisjonesBSU in https://github.com/mosdef-hub/gmso/pull/761 * Speedup `to_parmed` conversion by @daico007 in https://github.com/mosdef-hub/gmso/pull/768 * Improve Cassandra support by @emarinri in https://github.com/mosdef-hub/gmso/pull/756 * Sort indices in `Frame.bond.group` by @chrisjonesBSU in https://github.com/mosdef-hub/gmso/pull/769 ## Bug fixes * Replace `unyt.amu` with `Unit("amu")` to preserve mass values from mBuild by @chrisjonesBSU in https://github.com/mosdef-hub/gmso/pull/759 * Fix HOOMD issues with GAFF ForceField by @CalCraven in https://github.com/mosdef-hub/gmso/pull/765 ## Maintenance * [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/gmso/pull/763 * Attempt to unpin some of our dependencies by @daico007 in https://github.com/mosdef-hub/gmso/pull/764 ## New Contributors * @emarinri made their first contribution in https://github.com/mosdef-hub/gmso/pull/756 **Full Changelog**: https://github.com/mosdef-hub/gmso/compare/0.11.1...0.11.2

## Features * Initial centralization of topology’s unit conversions (by unit systems) by @CalCraven in https://github.com/mosdef-hub/gmso/pull/747 ## Bug Fixes * Fix return statement in `_parse_coulombic` by @chrisjonesBSU in https://github.com/mosdef-hub/gmso/pull/744 * Fix mass type in convert_parmed by @marjanAlbouye in https://github.com/mosdef-hub/gmso/pull/754 ## Maintenance * [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/gmso/pull/746 * Reconcile conflict with pydantic 2.0 by @mattwthompson in https://github.com/mosdef-hub/gmso/pull/752 and by @daico007 in https://github.com/mosdef-hub/gmso/pull/751 **Full Changelog**: https://github.com/mosdef-hub/gmso/compare/0.11.0...0.11.1

## Features * Add verbose options for mol2 and element by @daico007 in https://github.com/mosdef-hub/gmso/pull/729 * Support GSD 3 by @chrisjonesBSU in https://github.com/mosdef-hub/gmso/pull/739 * Speedup identify_connections by @daico007 in https://github.com/mosdef-hub/gmso/pull/741 * Lammps Writer Changes For Updated Topology Class by @CalCraven in https://github.com/mosdef-hub/gmso/pull/701 ## Bug fixes * Small fix to mass in convert_parmed by @chrisjonesBSU in https://github.com/mosdef-hub/gmso/pull/737 ## Maintenance * Update action/provision and mamba-org/setup-micromamba by @daico007 in https://github.com/mosdef-hub/gmso/pull/732 * Unpin HOOMD by @daico007 in https://github.com/mosdef-hub/gmso/pull/734 * Update test by @daico007 in https://github.com/mosdef-hub/gmso/pull/743 **Full Changelog**: https://github.com/mosdef-hub/gmso/compare/0.10.0...0.11.0