2.X enumerators

[bpuchala]

Fixed

• Fixed CASM::config::make_distinct_cluster_sites
• Fixed CASM::config::dof_space_analysis for global DoF with non-primitive unit cell configuration
• Fixed bug in Configuration.from_structure that caused error in resulting occupation

Changed

• Changed libcasm.configuration.Prim.is_atomic, which was returning has_anisotropic_occupants
• Changed libcasm.configuration.is_canonical_configuration arguments for providing a subgroup

Added

• Added prototype and include_subclusters attributes to libcasm.clusterography.IntegralClusterOrbitGenerator
• Added ConfigEnumAllOccupations, ConfigEnumInfo, ConfigEnumMeshGrid, ScelEnum, make_all_distinct_periodic_perturbations, and make_distinct_cluster_sites to libcasm.enumerate
• Added make_all_super_configurations_by_subsets and make_distinct_super_configurations to libcasm.configuration
• Added excluded_species option to Configuration.to_structure and ConfigurationWithProperties.to_structure
• Added with_prim_basis option to Configuration.to_dict and ConfigurationSet.to_dict to allow output of DoF values in the prim basis, along with "basis" tag which is respected on reading from JSON/dict.
• Added set_order_parameters, make_dof_space, order_parameters, order_parameters_contribution, dof_values_vector, and dof_values_vector_contribution methods to libcasm.configuration.Configuration
• Added CASM::config::cluster_from_index_vector and CASM::config::cluster_from_index_set

Removed

• Removed to_canonical_supercell and from_canonical_supercell which can be too easily misinterpreted.

[bpuchala]

Updates:

Changed

• Changed most methods with no arguments that return a value without doing additional work to readonly attributes

Added

• Added libcasm.irreps.IrrepDecomposition and libcasm.irreps.MatrixRepGroup for generic irreducible space decompositions