F3dasm

Bugfixes and minor improvements

- Change `__eq__` method of `_Data` object to `pd.testing.assert_frame_equal` in order to omit different `float` types
- `Domain.add_output` now has default argument of `to_disk=False`
- Bugfix: `ExperimentSample.from_numpy` now gets the (optional) domain object when constructed
- `ExperimentData.get_input_data` selects now only the input domain and removes the output space
- Removing building JOSS paper workflow (paper has been published and draft is removed from repo)
- (Studies: fragile becomes supercompressible) update scripts config

What's Changed
* [JOSS] Paper by RMeli in https://github.com/bessagroup/f3dasm/pull/277
* Pr/1.5.4 by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/280

New Contributors
* RMeli made their first contribution in https://github.com/bessagroup/f3dasm/pull/277

**Full Changelog**: https://github.com/bessagroup/f3dasm/compare/v1.5.3...v1.5.4

Resolved requests from reviewers JOSS:
- Fixes TOC header sphinx-gallery (274)
- `paper.md`: Added DOI of Optuna reference in paper

What's Changed
* Sphinx Gallery problem with TOC headers by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/275
* update version number to 1.5.3 by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/276


**Full Changelog**: https://github.com/bessagroup/f3dasm/compare/v1.5.2...v1.5.3

Major changes

- Restricted `numpy<2.0.0` from `requirements.txt`
- Minor linting fixes

What's Changed

**Full Changelog**: https://github.com/bessagroup/f3dasm/compare/v1.5.1...v1.5.2

Major changes

- Small bugfixes and typos

What's Changed
* Pr/1.5.1 by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/267


**Full Changelog**: https://github.com/bessagroup/f3dasm/compare/v.1.5.0...v1.5.1

v.1.5.0
Major changes
- Refactoring and removing of legacy code
- Change how hyperparameters are handled; they now need to be given as initialization key-word arguments
- Major rework on optimization functionality
- Rework on JOSS paper draft

What's Changed
* Pr/1.5 by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/266


**Full Changelog**: https://github.com/bessagroup/f3dasm/compare/v.1.4.8...v.1.5.0

v.1.4.8
Major Changes
- Dropped compatibility with Python 3.7
- Added Sphinx Gallery for documentation examples
- added `examples/` folder with code snippets explaining the functionality of `f3dasm`
- added `Experimentdata.join` method
- Change `_Store` class to public: `StorageProtocol`
- Added 2 benchmark studies: Fragile becomes supercompressible and Optimization benchmark

What's Changed
* Pull changes from 1.4.71 to branch 1.pr/4.8 by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/264
* Pr/1.4.8 by mpvanderschelling in https://github.com/bessagroup/f3dasm/pull/265


**Full Changelog**: https://github.com/bessagroup/f3dasm/compare/v.1.4.71...v.1.4.8

v.1.4.71
Bugfix:
- `autosummary` documentation not build because of conflicting submodule name.

**Full Changelog**: https://github.com/bessagroup/f3dasm/compare/v1.4.7...v.1.4.71

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