Release 1.4.0

Changes:

• Remove MODEL_TRANSFORMATION elementary step type
• Exact type of stored integers in the database is checked before retrieval in case fields have been manipulated with other MongoDB applications
• Projection options are added to almost all internal database queries to reduce the bandwidth requirements.
• Added support for list-of-lists of integers as elements in value collections (calculation settings etc.).

Release 1.3.0

Changes:

• Add restart_information field to Calculation
• Add pressure to Model
• Add MODEL_TRANSFORMATION elementary step type
• Change DB version to 1.2.0 and provide update script
• Add additional structure labels for intermediate structures of calculations
• Python package now includes pure Python code for more complex query utilities. This code is added in the modules
  queries, energy_query_functions, compound_and_flask_creation, concentration_query_functions, and insert_concentration.
  All of them are top level modules (import scine_database.energy_query_functions)
• Added the possibility to configure the connection based on a custom URI instead of credentials.

Release 1.2.0

Changes:

• getAggregate per default recursively looks up the original structure
  in case the method calling Structure instance is a duplicate.
  This avoids adding duplicates to aggregates.
• The methods related to duplicates were renamed, the old method calls
  are now deprecated.
• Increase pickle support of Python bindings.
• Corrected the 1.0.0 to 1.1.0 update script.
• Corrected case sensitivity in model completion.
• Corrected temperature setting completion for none case.

Release 1.1.0

Changes (require updates):

• Structures are now sorted into aggregates which can be Compounds
  or Flasks
• Update Reactions to connect Flasks and/or Compounds
  • lhs and rhs are expanded with a type attribute

Additions (backwards compatible):

• Add atom index maps to elementary steps
• Add Flasks, a new type of aggregate for stable non-bonded complexes
• Add collection for Flasks
• Add aggregate related functions to the Structure class

Deprecated:

• All Compound related functions of the Structure class are now deprecated
  (they point to the new aggregate fields)

Release 1.0.0

Initial features:

• Connection manager for MongoDB servers
• Definition of specialized classes for data objects that
  encode chemical reaction networks
• All functionalities present in C++ and Python3 bindings

Initial classes:

• Structure
• Compound (aggregate of Structures)
• ElementaryStep
• Reaction (aggregate of ElementarySteps)
• Property (Data class attached to Structures)
  • BoolProperty (bool/bool)
  • NumberProperty (double/float)
  • StringProperty (string/str)
  • VectorProperty (Eigen::VectorXd/numpy.ndarray)
  • DenseMatrixProperty (Eigen::MatrixXd/numpy.ndarray)
  • SparseMatrixProperty (Eigen::SparseMatrix/scipy.sparse.csr_matrix)
• Calculation

Initial collections:

• structures
• compounds
• elementary_steps
• reactions
• properties
• calculations