F3dasm

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

* 224
* 206
* 225
* 227
* 61
* 62
* 73
* 129
* 202

**Full Changelog**: https://github.com/bessagroup/f3dasm/compare/v1.4.4...v1.4.5

Bugfixes and enhancement featured by BernardoFerreira

What's Changed
* Make DataGenerator.run method private by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/197
* Change the default behaviour of the logger so that it doesn't display messages by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/196
* Mpvanderschelling/issue189 by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/199
* ExperimentData.store documentation is not correct by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/203
* Handle similar bounds on add_float to make a constant parameter by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/198
* Get a way to extract input and output data from ExperimentData by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/200
* Fixes 194 by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/204
* Pr/1.4.4 by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/210

Important Note: this release has been recreated to support read-the-docs documentation building.
Now the (static) documentation of this release will be available even when a newer release comes uit

**Full Changelog**: https://github.com/bessagroup/f3dasm/compare/v1.4.3...v1.4.4

This release will have the following additional features:
* Changed source directory structure to have a user API and `_src` folder
* Added `.path` attribute to `ExperimentData` to enable relative paths in disk-stored objects
* Bugfix at RandomSearch optimizer

Release that will be used in the following two student projects:
* ENGN2350 Data-Driven Design and Analysis of Structures and Materials 2023/2024
* TI3165TU Project Capstone Applied AI Project 2023/2024

What's Changed
* Numeric categorical parameters by GuillaumeBroggi in https://github.com/bessagroup/f3dasm/pull/135
* Output-data by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/136
* restructured ExperimentData.from_yaml by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/137
* New-way-of-locking by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/138
* Pr/1.3 by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/139
* Pr/1.3.1 by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/140
* add overwrite run method to function by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/141
* Changed design to ExperimentSample by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/142
* Changed_github_workflows by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/156
* Link in getting started CONTRIBUTING.md is not working by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/157
* Mpvanderschelling/issue69 by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/158
* 147-add-an-empty-machine-learning-stub-to-documentation by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/162
* Fixes 145 by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/161
* add __add__ operator to ExperimentData 163 by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/164
* Add_optimizer_to_experimentdata by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/166
* Mpvanderschelling/issue159 by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/160
* Api-for-importing by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/170
* Remove directory change in abaqus simulator by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/175
* Documentation-update by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/176
* New-sampling-way by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/177
* Optimizer-api by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/178
* Final-update-documentation by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/179
* Pr/1.4 by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/180
* removed ISSUE_TEMPLATE by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/181
* add gh pages push workflow by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/182
* gh pages token by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/183
* bugfixes by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/184
* Pr/1.4.3 by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/185

New Contributors
* GuillaumeBroggi made their first contribution in https://github.com/bessagroup/f3dasm/pull/135

**Full Changelog**: https://github.com/bessagroup/f3dasm/compare/v1.2.0...v1.4.3

- Heavily reduced the number of features and moved it to complementary libraries (`f3dasm_simulate`, `f3dasm_optimize`)
- Added support for Python 3.7
- Big changes on the documentation side

This release covers the following major changes
- Moved the `JobQueue` object as a private attribute in the new `ExperimentData` class
- Added parallelization decorators
- Added hydra `to_yaml` methods to base classes

old_version
This release is the "development" code developed until 2020 before Martin took over the main responsibilities of the f3dasm project
The purpose of this release is to make sure that the original code is not lost, and users may download this legacy code to reproduce their experiments.

pre-release
This release is the "master branch" code developed until 2020 before Martin took over the main responsibilities of the f3dasm project
The purpose of this release is to make sure that the original code is not lost, and users may download this legacy code to reproduce their experiments.