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

GMSO 0.7.3

What's Changed

Bugfixes

• Fix XML unit conversion by @daico007 in #614
• Fix bug in convert foyer XML by @daico007 in #622
• Change scaling factors terminology in gmso.Topology by @daico007 in #619
• Fix get_potential bugs by @daico007 in #623

Maintenance

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #626
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #612
• Pin pydantic to versions less than 1.9 by @justinGilmer in #627

Full Changelog: 0.7.2...0.7.3

GMSO 0.7.2

Features

• Update readers/writers to use the registry format introduced for JSON (#578)

Bug fixes

• Fixed epsilon parameter name when converting Foyer XML to GMSO XML (#610

Maintenance

• Pre-commit auto updates (#605, #607, #608)
• Use proper code-blocks section in installation.rst docs (#606)
• Update formats/__init__.py to include new loader and writer methods (#611)

GMSO 0.7.1

This is a patch release for gmso to resolve an issue with Potentials not being populated with their tags.

Bug fixes

• Ensure Potentials objects properly populate their tags from **kwargs. (#601)

Features

• Change warnings to conditional warnings during element search. (#599)

Maintenance

• Ignore setup.cfg in pre-commit trailing whitespace. (#602)

GMSO 0.7.0

Features

• Add methods to serialize and deserialize Topology and related objects (#462, #567)
• Switch to using unyt.elementary_charge for clarity (#559)
• Add PairPotentialType object (#484)
• Add is_fully_typed and get_untyped methods for Topology (#545)
• Add index_only option in identify_connection (#588)
• Optimize Forcefield XML parsing (#589)
• Extend Site to store residue information (#554)
• Update __repr__ method for Potential objects (#591)
• Add mol2 parser (#562)
• Add member_classes attribute to parametric potentials (#549)

Bug Fixes

• Strip white space when parsing atomtype overrides (#553)
• Fix default expression for PairPotentialType (#572)
• Update/fix bug when converting mbuild Compounds (#571, #584)
• Fix bug in _get_improper_type in ForceField (#593)
• Properly exclude **kwargs consolidation in ParametricPotential.dict (#596)

Maintenance

• Pre-commit enhancement and autoupdate(#547, #556, #550, #568, #576, #580, #592)
• Update MoSDeF graphic in README (#574)
• Use mamba instead of conda for installation instructions (#579)
• Refactor OpenMM import in utils/conversion modules (#586)
• Update docker image and re-add anaconda user (#594)
• Use codecov uploader for uploading coverage reports (#598)

GMSO 0.6.0

Features

• Use ele’s json to build element information (#536)
• Add visualizations for networkx representation of Topology object (#492)

Bug Fixes

• Fix nonbonded expression and charge unit in foyer XML conversion (#542)
• Update syntax for new mbuild.Box and pin mBuild version (#546)

Maintenance

• Use conda environment yml files for requirements installation (#532)
• Fix azure build (#534)
• Simplify Docker image (#537)
• Update README (#538)
• Use conda environment for RTD builds (#544)
• Add pre-commit (#543)

GMSO 0.5.0

Features

• Addition of a Mixin class to add tagged data to Potential class (#501)
• Add PeriodicImproperPotential class (#515)
• Enhanced __repr__ and __str__ methods to core classes (#517)
• Addition of scaling factors to the Topology class (#516)
• Add overrides section when converting a foyer XML (#525)
• Access Potentials and parameters from GMSO ForceField with wildcard support (#519)

Bug Fixes

• Fix error in mbuild conversion when compound.name is empty (#504)
• Fix bug with MetadataMixin.add_tag when overwrite=False (#518)

Maintenance

• Remove autodoc warning (#502)
• Fix typo in PeriodicTorsionPotential (#514)
• Change element’s __repr__ to report mass in amu (#512)
• Use potential_expression as hash for AtomType (#528)

GMSO 0.4.0

Features

• Allow creation of ForceField from etree.ElementTree (#440)
• Add group potentials in forcefield.py (#466)
• Add atomclass attribute to atomtype (#478)
• Add conversion to and from NetworkX (#472, #488, #491)
• Add conversion from Foyer XML (#438, #500)
• Make checking atom types optional in ForceField creation (#498)

Optimization

• Cached unit conversions when hashing unyt quantities (#469)

Maintenance

• Add python 3.8 support and remove channel mosdef (#490)

GMSO 0.3.1

This is a hotfix release to ensure compatibility with Pydantic v1.7

Optimization

• Improve performance of conversion from mBuild Compounds (#470)

Maintenance

• Update README (#483)

Bug Fix

• Use default_factory in abstract_site position field to ensure compatibility with Pydantic v1.7 (#482)