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

GMSO 0.10.0

Features

• Restraint support for GROMACS top writer by @daico007 in #685
• Speed up check_compatibility for relevant writer method by @daico007 in #700
• gmso xml equation compare and scaling, and extracting specific data from FFs by @bc118 in #698
• Add HOOMD Supports by @daico007 in #696
• Improve convert to parmed performance by @daico007 in #719
• modified to_mbuild function to improve performance by @chrisiacovella in #723
• Move generate_pairs_lists to utils by @daico007 in #722
• Overhaul parameterized Parmed Conversions by @CalCraven in #721
• Methods for converting to Pandas Dataframes by @CalCraven in #524

Bug fixes

• Fix residue name and atom_type name length, residue id and atom id, for GROMACS .gro writer by @chrisiacovella in #710
• Write out pairs section of top file by @daico007 in #714
• Additional checks when generate pair lists by @daico007 in #720
• Fix HOOMD conversion bug by @daico007 in #725
• Fix geometric mean error in HOOMD forcefield by @marjanAlbouye in #727

Maintenance

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #697, #702, #704, #705, #707. #708, #712, #713, #715
• Add CodeQL workflow for GitHub code scanning by @lgtm-com in #699
• Turn off fail-fast & update readme by @daico007 in #703
• Add testing for py3.10 and 3.11 by @daico007 in #728

New Contributors

• @lgtm-com made their first contribution in #699
• @chrisiacovella made their first contribution in #710
• @marjanAlbouye made their first contribution in #727

Full Changelog: 0.9.1...0.10.0

GMSO 0.9.1

Breaking change

• Stop testing and supporting Python 3.7 by @daico007 in #693

Features

• Support breaking changes from pydantic>=v1.9 by @umesh-timalsina in #691, #689

Maintenance

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #692
• Testing GMSO XML handling and Conversions, Forcefield-utilities backend by @CalCraven in #690
• pin foyer and ffutils version by @daico007 in #694

Full Changelog: 0.9.0...0.9.1

GMSO 0.9.0

Features

• Add cloning support to Potentials by @umesh-timalsina in #642
• Add Kelvin to standard energy converter via unit by @bc118 in #640
• Add non_element_types support for atomtyping by @umesh-timalsina in #648
• Add view classes for handling potentials in a topology by @umesh-timalsina in #649
• Support unyt_array in __eq__/clone for PotentialExpression by @umesh-timalsina in #660
• Expand search for elements when reading mol2 by @umesh-timalsina in #661
• Parmed Conversion Improvement by @CalCraven in #658
• Add expected parameters dimensions to PotentialTemplates by @umesh-timalsina in #657
• Assign proper units when converting from Parmed by @umesh-timalsina in #662
• Expand search for improper_types by @umesh-timalsina in #665
• Atomtype parameterization methods for parameterizing a topology in GMSO. by @CalCraven in #644
• Modify scaling factors to a numpy array by @umesh-timalsina in #669
• Modify mbuild converter to flatten compound hierarchy by @daico007 in #638
• Parse mol2 residue and molecule info for sites. by @CalCraven in #671
• Support list of parameter values in Forcefield XML by @umesh-timalsina in #681
• Populate Group information from mBuild Compounds by @CalCraven in #683
• Populate both member types and classes by @daico007 in #684
• Parse charge and mass in convert mbuild by @daico007 in #687
• Convert mBuild custom group names by @CalCraven in #686
• Fix mass and charge in GSD writer; Add angles and dihedrals to GSD writer by @chrisjonesBSU in #680

Maintenance

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #667
• Resolve conflicts from main by @CalCraven in #675

New Contributors

• @bc118 made their first contribution in #640
• @chrisjonesBSU made their first contribution in #680

Full Changelog: 0.8.1...0.9.0

GMSO 0.8.1

Features

• Infer elements when converting from parmed. Closes #650 by @umesh-timalsina in #651
• Update method to load in mol2 file by @daico007 in #645
• Assign None to charge if not found in mol2 file. Closes #652 by @umesh-timalsina in #653

Bug fixes

• Change strategy for detecting duplicating connection by @daico007 in #654

Maintenance

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in (#639, #643)
• Github Action Setup as Replacement for AzurePipelines by @umesh-timalsina in #646
• Update workflow to reflect default branch name by @umesh-timalsina in #647

Full Changelog: 0.8.0...0.8.1

GMSO 0.8.0

Breaking change

• Stop testing Python 3.6 and add testing for Python 3.9 by @umesh-timalsina in #633

Features

• Add combining rule to ForceField by @umesh-timalsina in #632
• Prevent accidental defaults values while creating Potentials by @umesh-timalsina in #635
• Update parmed converter to use new residue infrastructure by @daico007 in #613

Bug fixes

• Fix bugs in convert_foyer_xml by @daico007 in #629, #636

Maintenance

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #630

Full Changelog: 0.7.3...0.8.0