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Changelog

I'm generally trying to adhere to semver here. This means that in v0.*, assume breaking changes are always possible, even without a major version bump...however, I will try to always note them here if they happen...

Categories to include for each release, if relevant: breaking, added, fixed, removed/deprecated

v0.6.0 [2021-10-2x]

Added

  • actual functioning SpeciesFeatureDescriptor! Including some built-in data to build them using MolecularGraph.jl functions
  • AtomGraph now stores a structure field, giving access to structure representation used to construct graph
  • build AtomGraph from GraphMol objects (from MolecularGraph package)
  • one-hot encoding/one-cold decoding logic now lives in OneHotOneCold codec code
  • new codec type: DirectCodec for storing (scaled) actual (potentially continuous) values of features
  • disambiguate get_value(featuredescriptor, atoms) from encode(featuredescriptor, atoms); "callable" syntax of feature descriptors now calls the former function

Breaking

  • AtomGraph now takes a type parameter and stores a structure field of that type; this allows checking that SpeciesFeatureDescriptor is able to encode since it computes feature values from the original structure
  • disambiguate get_value(featuredescriptor, atoms) from encode(featuredescriptor, atoms); "callable" syntax of feature descriptors now calls the former function

Removed/Deprecated

  • removed encodable_elements(::String) function

v0.5.0 [2021-09-07]

Added

  • Add new FeatureDescriptor - OrbitalFeatureDescriptor
  • Add new module OrbitalFeatureUtils which provides utility functions used by OrbitalFeatureDescriptor
  • Add new simple Codec - SimpleCodec
  • Add a new function - elements, which prints the elements in an Atoms object
  • Make output_shape generic
  • Add a new module - Data which encapsulates all the data and tables required by the package.
  • add pretty printing for GraphNodeFeaturization, FeaturizedAtoms, uniformize spacing via \t across these and AtomGraph
  • [logic] move data/ directory to root of repo
  • [logic] move build_onehot_vec to OneHotOneCold
  • replaced Python ASE dependency with Xtals.jl, allowing AD through graph-building! Can now also pass a Crystal object for graph-building

Fixed

  • export featurize and decode properly for FeaturizedAtoms

Removed/Deprecated

  • ASE deprecation removes compatibility with reading some file formats that ASE supports but Xtals does not

v0.4.2 [2021-07-02]

Added

  • export featurize and decode functions at top-level module

Fixed

  • id is positional rather than keyword argument in AtomGraph constructor so that broadcast works properly, also it defaults to filename sans extension when constructing from file

v0.4.1 [2021-07-01]

Fixed

  • add back wayward semicolon so that keyword arguments work in AtomGraph constructor from file

v0.4.0 [2021-06-30]

Added

  • create FeaturizedAtoms type, remove featurization, encoded_features fields from Atoms objects
  • add docstrings for various things, add section of docs for Codecs

Fixed

  • macOS CI fixed, but possibly not in an ideal way because it seems to result in occasional precompile warnings upon update
  • Docs for stable/tagged versions now build properly

Removed/Deprecated

  • remove encoded features field from AtomGraph type

v0.3.1 [2021-06-18]

Fixed

  • import from submodules before top-level export so that exports actually work, d'oh
  • remove broken dimension check in AtomGraph constructor (doesn't work with generic featurization)
  • fix type assertion of nbins in GraphNodeFeaturization constructor (Vector{<:Integer}, NOT Vector{Integer})

v0.3.0 [2021-06-17]

Major restructure to make extensibility far easier and allow better sharing of elements between featurization schemes! Also streamlined the codebase a lot by organizing things into sensible modules, so technically basically everything is a breaking change because all of the imports are from the submodules now.

Breaking/Added

  • create modules for different functionalities: Atoms, Features, Featurization, Utils, etc.
  • separate out encoding/decoding functionality into a new AbstractCodec type and associated Codec module
  • merged functionality of AtomGraph and WeaveMol into AtomGraph object, with a more generic encoded_features field

v0.2.2 [2021-02-22]

Added

  • updated pretty printing for AtomGraph to include id field

Fixed

  • added some docstrings, updated others

v0.2.1 [2021-02-22]

Breaking

  • rename build_atom_feats to build_featurization to avoid ambiguity with make_feature_vectors

Fixed

  • proper docstrings for more things incl. AtomFeat, AtomGraph, add_features!

v0.2.0 [2021-02-16]

Breaking

  • add id field to AtomGraph (should only be breaking for reading in serialized graphs)
  • build_graphs_batch now returns list of graphs and optionally serializes rather than always serializing and never returning

Added

  • add_features_batch! function
  • AtomGraph constructor directly from adjacency matrix (previously was only from a SimpleWeightedGraph)

Fixed

  • remove deprecated syntax of opening DataFrames from CSV
  • made separate files into modules to avoid redefinition warnings during precompilation

v0.1.1 [2021-02-10]

Fixed

  • add check for NaN values in graph laplacian

v0.1.0 [2020-12-22]

Initial release!

Added

  • Create AtomGraph and AtomFeat types
  • Basic graph visualization functions
  • Graph-building from CIF files via the cgcnn.py "cutoff" method, with support for nonperiodic systems as well