GMSO 0.3.0

Breaking Change

• Integrate Pydantic for gmso.abc abstract classes (#431)

Features

• Improve GROMACS top writer (#306, #330, #423)
• Add method to get Site’s index (#343, #365)
• Add Improper Connection and ImproperType Potential (#338)
• Improve LAMMPS writer (#339, #331)
• Add LAMMPS data file reader (#351)
• Add method to convert to and from ParmEd Structure (#334)
• Add a class method in potential.py to create Potential object (#362)
• Add MCF writer (#340)
• Refactor PotentialTemplates (#359)
• Simplify Potential object such that the potential Expression is handled by a separate class (#419)
• Add __hash__ method for Element class (#428)
• Validate site positions and change default to np.nan (#405)
• Extend XML schema to create ConnectionType based on AtomClass (#442)
• Use networkx to enumerate connectivity in Topology (#356)
• Provide ImproperType and group names in Forcefield XML/XSD (#444)
• Ensure duplicate connections are pruned (#460)

Bug Fixes

• Fix element parsing to work with lark parser >0.8.5 (#420)
• Fix bug found in LAMMPS writer (#453)
• Prevent a nondeterministic AssertionError in unit tests (#471)

Maintenance

• Set up CI pipeline (#316, #326, #398, #409, #421)
• Build and update documentation (#322, #328, #353, #391, #429, #457, #468)
• Clean up import statements (#327, #412)
• Update setup.py (#329)
• Include package data in MANIFEST.in (#376)
• Update pytest fixtures in base_test.py (#383, #368)
• Replace allclose with unyt.array.allclose_unit in unit tests (#413)
• Update README (#422)
• Provide Dockerfile for automated image uploads (#401)
• Use bump2version for version management (#434)
• Support docker and pypi publishing from AZP (#437)
• Remove logging functions and configurations (#449)
• Update requirements files (#454, #467)
• Remove Pypi publish script (#476)