Optimas

What's Changed
* Fix issues with new Ax release by AngelFP in https://github.com/optimas-org/optimas/pull/147
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/optimas-org/optimas/pull/146


**Full Changelog**: https://github.com/optimas-org/optimas/compare/v0.3.0...v0.3.1

What's Changed
* Update readme and documentation by AngelFP in https://github.com/optimas-org/optimas/pull/111
* Run tests daily and with all supported python versions by AngelFP in https://github.com/optimas-org/optimas/pull/113
* Automated typo detection by jmlarson1 in https://github.com/optimas-org/optimas/pull/116
* Typo in documentation by VadimBim in https://github.com/optimas-org/optimas/pull/115
* Allow resuming an exploration and running in substeps by AngelFP in https://github.com/optimas-org/optimas/pull/118
* Allow launching simulations in a different environment by AngelFP in https://github.com/optimas-org/optimas/pull/108
* Implement `ChainEvaluator` by AngelFP in https://github.com/optimas-org/optimas/pull/110
* Install pre-commit by ax3l in https://github.com/optimas-org/optimas/pull/119
* Increase version number to `0.3.0` for next release by AngelFP in https://github.com/optimas-org/optimas/pull/121
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/optimas-org/optimas/pull/122
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/optimas-org/optimas/pull/129
* Fix typo in `MultitaskEvaluator` docstring by AngelFP in https://github.com/optimas-org/optimas/pull/123
* Update installation instructions for Maxwell by AngelFP in https://github.com/optimas-org/optimas/pull/127
* Avoid pydata theme warning by AngelFP in https://github.com/optimas-org/optimas/pull/130
* Change `Exploration` defaults by AngelFP in https://github.com/optimas-org/optimas/pull/125
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/optimas-org/optimas/pull/131
* Disable Ax logs by AngelFP in https://github.com/optimas-org/optimas/pull/126
* Improve multi-objective optimization and add support for fully Bayesian optimization by AngelFP in https://github.com/optimas-org/optimas/pull/124
* Enable manually adding trials and evaluations to `Exploration` by AngelFP in https://github.com/optimas-org/optimas/pull/128
* Fix tests by AngelFP in https://github.com/optimas-org/optimas/pull/136
* Doc: Button to Copy Code Blocks by ax3l in https://github.com/optimas-org/optimas/pull/138
* CI: Blacken-Docs Version w/ Black by ax3l in https://github.com/optimas-org/optimas/pull/139
* Document new features and improve README by AngelFP in https://github.com/optimas-org/optimas/pull/141
* Use new libE save history options by AngelFP in https://github.com/optimas-org/optimas/pull/135
* Reduce number of initialization evaluations if external data is supplied by AngelFP in https://github.com/optimas-org/optimas/pull/137
* Enable local threading communications by AngelFP in https://github.com/optimas-org/optimas/pull/140

New Contributors
* jmlarson1 made their first contribution in https://github.com/optimas-org/optimas/pull/116
* VadimBim made their first contribution in https://github.com/optimas-org/optimas/pull/115
* pre-commit-ci made their first contribution in https://github.com/optimas-org/optimas/pull/122

**Full Changelog**: https://github.com/optimas-org/optimas/compare/v0.2.1...v0.3.0

Minor release with fixes to support the latest Ax version (0.3.4)

What's Changed
* Remove outdated files by AngelFP in https://github.com/optimas-org/optimas/pull/109
* Fix issue with latest Ax release by AngelFP in https://github.com/optimas-org/optimas/pull/112
* Increase version number by AngelFP in https://github.com/optimas-org/optimas/pull/114


**Full Changelog**: https://github.com/optimas-org/optimas/compare/v0.2.0...v0.2.1

This release updates `optimas` to use the latest `libEnsemble` version, introduces a new `Generator`, and greatly expands the documentation.

The main changes can be summarized as follow:
* Update to `libEnsemble` `0.10.2`. This implies:
* Many changes under the hood that should improve resource detection and assignment in HPC environments.
* The output of an `optimas` exploration, including the log files, is now fully contained in a single folder (see the [documentation](https://optimas.readthedocs.io/en/latest/user_guide/basic_usage/analyze_output.html#understanding-the-output-of-optimas) for details).
* The `n_procs` argument of the `TemplateEvaluator` is now functional. Therefore, you can now specify the number of MPI processes that your simulation needs (previously, the number of processes was always equal to the number of GPUs given in `n_gpus`).
* The default number of GPUs assigned to a `TemplateEvaluator` is now 0 (i.e., `n_gpus=0`).
* An exploration will now fail to start if the workers require more resources than available in the system (e.g., require more workers than CPU cores, or more GPUs than available).
* A new `AxClientGenerator` has been implemented. This generator allows the user to provide fully-customized `AxClient`, thus allowing for a higher control of the optimization. Basically, you can now use `optimas` as a platform to launch an `Ax` optimization in parallel.
* The [documentation](https://optimas.readthedocs.io) has been greatly expanded and now includes a user guide covering the basic usage of `optimas` as well as many detailed examples.

For all details, see the pull requests below.

What's Changed
* Implement generator with user-defined `AxClient` by AngelFP in https://github.com/optimas-org/optimas/pull/100
* Update generator after running exploration by AngelFP in https://github.com/optimas-org/optimas/pull/101
* Updating for new libE interface by shuds13 in https://github.com/optimas-org/optimas/pull/88
* Improve documentation and examples by AngelFP in https://github.com/optimas-org/optimas/pull/104
* Documentation: add submission script on Perlmutter by RemiLehe in https://github.com/optimas-org/optimas/pull/106
* Add installation instructions for JUWELS Booster by AngelFP in https://github.com/optimas-org/optimas/pull/102

New Contributors
* shuds13 made their first contribution in https://github.com/optimas-org/optimas/pull/88

**Full Changelog**: https://github.com/optimas-org/optimas/compare/v0.1.1...v0.2.0

This release changes the default behavior of `dedicated_resources` in the generators, which is now set to `False`. This prevents issues where a GPU would be reserved for the generator, even if the generator is not able to use it. It also updates the documentation to install `optimas` from PyPI.

What's Changed
* Change instructions to install from PyPI and add post-release badges by AngelFP in https://github.com/optimas-org/optimas/pull/99
* dedicated_resources for Generators: False by default by RemiLehe in https://github.com/optimas-org/optimas/pull/103
* Increase version number to `0.1.1` by AngelFP in https://github.com/optimas-org/optimas/pull/105


**Full Changelog**: https://github.com/optimas-org/optimas/compare/v0.1.0...v0.1.1

This is the first official release of optimas.

What's Changed
* Add support for discrete fidelities by AngelFP in https://github.com/optimas-org/optimas/pull/4
* Restructure scripts by RemiLehe in https://github.com/optimas-org/optimas/pull/6
* Make sure a directory is created for each simulation by AngelFP in https://github.com/optimas-org/optimas/pull/10
* Enable non-string discrete fidelities by AngelFP in https://github.com/optimas-org/optimas/pull/9
* Add dummy_mf_disc example by MaxThevenet in https://github.com/optimas-org/optimas/pull/7
* Redesign as library by AngelFP in https://github.com/optimas-org/optimas/pull/11
* Take plasma_scale into account by RemiLehe in https://github.com/optimas-org/optimas/pull/14
* setup.py: fix classifier warning by ax3l in https://github.com/optimas-org/optimas/pull/19
* Change name of the script in submission scripts by RemiLehe in https://github.com/optimas-org/optimas/pull/17
* Four small fixes by delaossa in https://github.com/optimas-org/optimas/pull/21
* Modify import statement for gen_funcs by RemiLehe in https://github.com/optimas-org/optimas/pull/18
* Fix a few bugs by RemiLehe in https://github.com/optimas-org/optimas/pull/23
* Make the analysis script more robust by RemiLehe in https://github.com/optimas-org/optimas/pull/22
* Add support for WarpX by RemiLehe in https://github.com/optimas-org/optimas/pull/28
* Add a class to conveniently post-process the optimization by RemiLehe in https://github.com/optimas-org/optimas/pull/16
* Add automated tests for multi-fidelity cases by RemiLehe in https://github.com/optimas-org/optimas/pull/27
* [WIP] Plot timeline of worker utilization by RemiLehe in https://github.com/optimas-org/optimas/pull/29
* Copy persistent GP gen_func into this repo by RemiLehe in https://github.com/optimas-org/optimas/pull/31
* Log the parameters of the Gaussian model during the optimization by RemiLehe in https://github.com/optimas-org/optimas/pull/32
* Add multi-task optimization with Ax by AngelFP in https://github.com/optimas-org/optimas/pull/33
* [WIP] Add BoTorch/Ax optimisers by soerenjalas in https://github.com/optimas-org/optimas/pull/24
* Update libE_opt to make it compatible with `development` version of `libensemble` by RemiLehe in https://github.com/optimas-org/optimas/pull/34
* Add simulation scripts for Perlmutter by RemiLehe in https://github.com/optimas-org/optimas/pull/36
* Use proper Python version in CI by RemiLehe in https://github.com/optimas-org/optimas/pull/41
* Updated version of Implement Ax/Botorch by RemiLehe in https://github.com/optimas-org/optimas/pull/42
* [WIP] Implement Ax/Botorch optimizers by AngelFP in https://github.com/optimas-org/optimas/pull/35
* Exchanged ionization injection paramters mult and plasma_scale by MKirchen in https://github.com/optimas-org/optimas/pull/45
* adds back 'sim_template' as argument of 'run_ensemble' by delaossa in https://github.com/optimas-org/optimas/pull/44
* Corrected Juwels submission file by MKirchen in https://github.com/optimas-org/optimas/pull/47
* Fix crash when using latest Ax version by AngelFP in https://github.com/optimas-org/optimas/pull/49
* Add restart capabilities from history file when backend `ax` is selected by delaossa in https://github.com/optimas-org/optimas/pull/46
* Set noise of multi-task observations to NaN by AngelFP in https://github.com/optimas-org/optimas/pull/48
* Corrected libE field naming by MKirchen in https://github.com/optimas-org/optimas/pull/51
* Add multi-model MT example with FBPIC and Wake-T by AngelFP in https://github.com/optimas-org/optimas/pull/52
* Updates for latest version of libensemble by RemiLehe in https://github.com/optimas-org/optimas/pull/54
* Enable Ax to run on GPU by AngelFP in https://github.com/optimas-org/optimas/pull/53
* Fix memory issues in multitask generator by AngelFP in https://github.com/optimas-org/optimas/pull/57
* Improve GPU selection by AngelFP in https://github.com/optimas-org/optimas/pull/58
* Enable Sobol scrambling in multitask generator by AngelFP in https://github.com/optimas-org/optimas/pull/59
* A couple of small fixes for newer libEnsemble versions by delaossa in https://github.com/optimas-org/optimas/pull/61
* Use stable version of libensemble in CI by RemiLehe in https://github.com/optimas-org/optimas/pull/63
* Random sampling by delaossa in https://github.com/optimas-org/optimas/pull/62
* Undo recent changes commenting out the simulation script by RemiLehe in https://github.com/optimas-org/optimas/pull/65
* Undefine template as app argument in case of python script by delaossa in https://github.com/optimas-org/optimas/pull/66
* Implement new object-oriented API by AngelFP in https://github.com/optimas-org/optimas/pull/67
* Rename to `optimas` by AngelFP in https://github.com/optimas-org/optimas/pull/69
* Update readme by AngelFP in https://github.com/optimas-org/optimas/pull/70
* Speedup tests with new dependencies by AngelFP in https://github.com/optimas-org/optimas/pull/72
* Allow sharing the GPU between generator and simulations by AngelFP in https://github.com/optimas-org/optimas/pull/71
* Add documentation by AngelFP in https://github.com/optimas-org/optimas/pull/73
* Fix issues with openMPI by AngelFP in https://github.com/optimas-org/optimas/pull/75
* Add install instructions for Perlmutter by RemiLehe in https://github.com/optimas-org/optimas/pull/76
* Generalizes the script name that is registered in the Executor by delaossa in https://github.com/optimas-org/optimas/pull/78
* Add the save history period as parameter. by delaossa in https://github.com/optimas-org/optimas/pull/79
* Suppress varying parameter type warning in AxSingleFidelityGenerator by delaossa in https://github.com/optimas-org/optimas/pull/77
* Remove optimization folder by RemiLehe in https://github.com/optimas-org/optimas/pull/82
* Add files required for release by RemiLehe in https://github.com/optimas-org/optimas/pull/83
* Add online documentation by AngelFP in https://github.com/optimas-org/optimas/pull/84
* Update setuptools configuration by AngelFP in https://github.com/optimas-org/optimas/pull/85
* Fix missing modules in `pyproject.toml` by AngelFP in https://github.com/optimas-org/optimas/pull/89
* Fix FBPIC examples by AngelFP in https://github.com/optimas-org/optimas/pull/93
* Add zenodo file by AngelFP in https://github.com/optimas-org/optimas/pull/95
* Fail docs on warning by AngelFP in https://github.com/optimas-org/optimas/pull/92
* Pin libensemble version by AngelFP in https://github.com/optimas-org/optimas/pull/96
* Add installation instructions for Maxwell (DESY) by AngelFP in https://github.com/optimas-org/optimas/pull/91
* Publish to PyPI on release by AngelFP in https://github.com/optimas-org/optimas/pull/90
* Fix bug with executable in `sim_files` by AngelFP in https://github.com/optimas-org/optimas/pull/98

New Contributors
* AngelFP made their first contribution in https://github.com/optimas-org/optimas/pull/4
* RemiLehe made their first contribution in https://github.com/optimas-org/optimas/pull/6
* MaxThevenet made their first contribution in https://github.com/optimas-org/optimas/pull/7
* ax3l made their first contribution in https://github.com/optimas-org/optimas/pull/19
* delaossa made their first contribution in https://github.com/optimas-org/optimas/pull/21
* soerenjalas made their first contribution in https://github.com/optimas-org/optimas/pull/24
* MKirchen made their first contribution in https://github.com/optimas-org/optimas/pull/45

**Full Changelog**: https://github.com/optimas-org/optimas/commits/v0.1.0