Scine-database

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Changes (DB schema changing)
- Remove `MODEL_TRANSFORMATION` elementary step type

Additions (backwards compatible):
- 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.).

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Changes (DB schema changing):
- 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

Additions (backwards compatible):
- 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`
- `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.

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Changes (backwards compatible):
- `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.

Important Technical Changes:
- Increase pickle support of Python bindings.

Bugfixes:
- Corrected the 1.0.0 to 1.1.0 update script.
- Corrected case sensitivity in model completion.
- Corrected temperature setting completion for `none` case.

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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)

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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