mBuild 0.10.12

Bug Fixes

• Set element to None if it cannot be infered in read_xyz (#821)

Maintenance

• Add python 3.8 support and remove channel mosdef (#823)

mBuild 0.10.11

Features

• Integrate element attribute with object conversions and writers (#790)
• Allow hoomd functions to read in and add to an existing snapshot (#808)

Maintenance

• Fix deprecation warning on 'Iterable' import (#803)
• Remove Travis CI (#812, #817)
• Set ignore_box_warn to True for loading SMILES (#806)
• Add hoomd to testing env (#810)

Bug Fixes

• Fix particles out of box in to_hoomdsnapshot (#815)
• Use correct lattice spacing when reading from cif (#819)

mBuild 0.10.10

Breaking Change

• From this version, mBuild will no longer be distributed on Pypi

Features

• Add sidemax argument for various packing functions (#795)

Bug Fixes

• Fix conversion factor in file header when writing to hoomdxml (#798)
• Fix syntax error in conversion.py (#797)

Maintenance

• Simplify docker behavior (#791)
• Update links in docs/installation.srt (#794)
• Remove Deprecated messages in coordinate_transform.py and compound.py (#763)
• Remove Pypi publish scripts (#801)

mBuild 0.10.9

Announcement

mBuild 0.10.9 will be the last version hosted on Pypi. In the future, all the versions on Pypi will be removed.

Breaking change

• Refactor of mbuild.load() (#721)

Features

• Add element attribute to Compound (#771)

Maintenance

• Add links to github repository in documentation (#777)
• Add OpenBabel as required dependency and pin its version to 0.3.0 (#779, #783)
• Use setup.cfg for coverage, bump2version for versioning (#773)
• Add docker release and pypi publish script (#778)

mBuild 0.10.8

Features

Support entry_point plugins for mbuild package distributed by conda (#754)

Bug fixes

Fix bug when cloning a Compound with Box (#753)
Fix CIF module import statement, add more unit tests (#760)
Include missing transpose of CIF box_matrix (#767)
Fix command typo in packing.py (#761)

Maintenance

Update mBuild document link in README (#757)
Replace instances of manual degree/rad conversion with numpy functions (#764)

mBuild 0.10.7

Features

• Add box attribute to mb.Compound (#742)
• Provide framework to load in .CIF files (#689)
• Improve mass/pair/etc. ordering and improper atomtype comment order in lammps_writer (#673)

Bug Fixes

• Fix MCF fragment identification for more complex ring system (#744)
• Fix a bug with alkane recipe when dealing with n < 3 (#691)

Maintenance

• Drop notebook-specific dependencies from requirements (#687)

mBuild 0.10.6

Feature

• Update element name and atomtype name lengths in MCF writer (#719)
• Automate Docker Image publishing with AZP (#728)
• Add protobuf installation instructions (#738)

Maintenance

• Include Licencse.rst in Manifest.in (#710)
• Drop appveyor CI (#709)
• Include Box and Lattice in Data Structure docs (#714)
• Update conda channel order in one-liner in installation docs (#703)
• Remove nglview as a hard dependency (#713)
• Add documentation for plugin/recipes system (#634)
• Fix conda download URL in Travis CI (#724)
• Reformat docstring for Lattice class (#718)
• Update non-element MOL2 test (unpin mdtraj version) (#733)
• Update documentation to reflect refactoring and remove use of deprecated function (#730)

Bug fixes

• Fix an issue with to_parmed regarding setting box's parameters (#699)
• Fix the factor of 2 error in rmin/2 (#716)
• Setting default of 1-4 interactions to 0.0 when structure.adjusts is empty (#664)
• Typecast float to int to prevent NaNs in np.arange in SpherePattern class (#722)
• Fix MCF charge accuracy issue (#731)

mBuild 0.10.5

Features

• Add internal XYZ writer (#410)
• Add Lennard-Jones unit systems to LAMMPS writer (#646)
• Add a function that returns a populated lattice box (get_populated_box) (#661)
• Add SDF reader/writer (via OpenBabel) (#674)
• Add _BoxArray subclass that allows single box dimensions to be set for mbuild.Box instances (#672, #686)

Bug Fixes

• Update deprecated GSD syntax after v2.0.0 (#682)
• Fix MCF writer for systems with no defined bonds (#662)

Maintenance

• Remove old landscape YAML (#669)
• Add protobuf import message to io.py (#670)
• Migrate mBuild documentation to Read the Docs (#693)

Miscellaneous

• Add recipes links to README (#659)

mBuild 0.10.4

Features

• Add wrap_coords function for wrapping particles into a box (#643)

Bug Fixes

• Don't populate empty lists for hoomd snapshot (#647)

Maintenance

• Add nbval as requirement for tests in conda recpe (#656)
• Remove six and some Python 2 legacy code (#641)
• Remove examples (from this repository) (#658)
• Fix travis by not installing md5sha1sum (#660)
• Add CHANGELOG (#632)

mBuild 0.10.3

Feature

• Add Cassandra MCF writer (#636)
• Add HOOMD snapshot converter (#622)
• Generate mb.Compound from Parmed or MDTraj residues (#526)
• Add **kwargs for write_gsd (#653)

Bug Fixes

• Fix unique naming problem in to_networkx (#583)
• Default the mBuild PAR-writer to use IMPROPER (#648)
• Fix ghost ports attached to removed compound (#593)
• Remove duplicate NP particles in TNP example (#625)
• Only import MCF writer if networkx is installed (#654)

Maintenance

• Add LGTM (#616)
• Add Azure CI testing (#615, #617, #618, #630, #637, #638)
• Update Travis CI (#649)
• Update conda recipe to include nbval (#611, #656)
• Pin nglview to 2.7+ (#651, #655)
• Reduce length of some unit tests (#621)
• Rename AmorphousSilica to be more descriptive (#630)