Pr/1.4.5

[mpvanderschelling]

This pull request will update the main code to version 1.4.5

Major updates

Domain and Parameter classes

• All Parameter classes are now private. The suggested way to add parameters to a Domain will be with the public add_float, add_int, add_category and add_constant methods.
• Change the behaviour of the public Domain.add method to require the type and arguments of the (private) parameter to construct, instead of requiring the private Parameter object

ExperimentData class

• Added a method that extracts all ExperimentSample objects or a selection of ExperimentSample objects from an ExperimentData object
• Removed the .filename attribute in ExperimentData: the name of the stored objects are hardcoded
• Refactored the .path attribute to the .project_dir attribute. When storing the ExperimentData object with the .store() method, a subdirectory (/experiment_data/) will be created and the input data, output data, domain and jobs will be stored there.

Optimizer class

• Added functionality to select different strategies to determine the initial points ($x_0$) before optimization.

_Data class

• Decoupled the headers of the _Data class to a separate private _Columns class. This makes it more flexible for future development on the generalization of different back-ends (currently pandas) for _Data
• Removed dependency of Domain to _Data class

Storing output data

• Output that is stored to disk will no longer have the path_ prefix before the parameter. This information is stored within the _Columns object
• The ExperimentSample.output_data will, if applicable, load the output parameters from disk automatically
• The attribute ExperimentSample.output_data_with_references will give you the paths of the references
• Added backwards compatibility for ExperimentSample.output_data_loaded (will redirect to ExperimentSample.output_data

Documentation

• Made private methods of public objects visible in sphinx documentation API

Bessa Group Coding Guidelines

• Restored the original .flake8 file of the BRG coding guidelines; the maximum linewidth is now 79 instead of 119.

Miscellaneous

• Represent all private attributes and methods with an underscore (_).

Closed issues

• Make the parameter classes private #224
• Make factory methods in experimentdata.py file private #206
• Change instantiation of Domain object with hydra config #225
• Adding a __repr__ method to the ExperimentData object #227
• this function is incompatible with a 1D design #61
• this function is incompatible with a 1D design #62
• Best input parameters ?  #73
• Parameter errors display blank information #129
• Change the names of the private attributes of ExperimentData to start with an underscore #202

[BernardoFerreira]

Good job with this new release version, a lot of major updates that will significantly improve f3dasm functionality for sure! Please review the few comments that I left before approval.

Thank you for the less "functionality" improvements such as the compliance with the BRG guidelines and the private leading _ convention. Nonetheless, I point out that there are some modules that still don't have the correct BRG header format and several functions/methods/classes that don't have docstrings (namely private ones). These should be fixed for the next CRW (December 5).