F3dasm

Features

- Added storage method for matplotlib figures
- Added GridSearch sampler*
- Added helper functions for datageneration with hydra configuration files
- Added overwrite function to `ExperimentData`
- Added callback functionality for optimizers
- Allow addition of Domains
- Add differentiable tag to benchmark functions and optimizers
- Added `cluster_parallel` mode to `ExperimentData.evaluate()

_* only working for categorical or discrete variables!_


Bugfixes

- Fixes 248
- Fixes 250
- Fixes 252
- Fixes 253
- Fixes 259
- Fixes 89
- Fixes 230
- Fixes 223
- Fixes 218

What's Changed
* Fixes 248 by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/249
* Mpvanderschelling/issue250 by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/255
* Improving usability by implementing helper function to convert arbitrary functions to DataGenerators by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/254
* Documentation is both hosted by GitHub Pages and ReadTheDocs by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/256
* Implement new x0_selection strategy and add select_all_finished functionality by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/260
* RETRY: refactoring optimization iterate and iterate_scipy by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/262
* Pr/1.4.7 by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/263


**Full Changelog**: https://github.com/bessagroup/f3dasm/compare/v1.4.6...v1.4.7

Major changes

* Added documentation on SLURM job scheduler. Added sphinx-tabs as dependency when building documentation.
* WIP: New back-end of `_Data` that relies on lists instead of pd.DataFrame. *This has not yet replaced the pandas back-end but tests are passing with the new `_newdata.py` module.*
* Removed unused method `Domain.from_yaml`.
* Removed unused `_Data.fill_output` method
* Output of benchmark functions is now a `float` instead of `np.ndarray[float]`. Necessary to pass tests for new back-end, won't affect pandas back-end.

Minor changes

* Refactoring parts of the `ExperimentSample` code to be more robust to changes in the back-end
* Moving factory methods to appropriate modules
* Removed `try_import`; import checks are moved to extension packages
* Added `__version__.py` file
* Updated docstrings to remove leading spaces

Bugfixes

* Correct equality operator of `Domain` to also compare for `output_space` attribute
* Closes 241
* Closes 191
* Closes 240
* Closes 243

What's Changed
* Newdata by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/245
* Pr/1.4.6 by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/246


**Full Changelog**: https://github.com/bessagroup/f3dasm/compare/v1.4.5...v1.4.6

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