v2.1.2

What's Changed

• Bump sklearn compat by @penelopeysm in #1006
• Update email by @radka-j in #1009
• Rm version number from pip install instructions by @radka-j in #1015
• Fix pueue instruction by @radka-j in #1017
• Update pueue instructions by @radka-j in #1018
• docs: add SyedHaider2084 as a contributor for doc by @allcontributors[bot] in #1020
• docs: add z7076 as a contributor for doc by @allcontributors[bot] in #1021
• docs: add RemDelaporteMathurin as a contributor for doc by @allcontributors[bot] in #1023
• Add FESTIM links to case studies by @radka-j in #1022
• rm benchmarks dir by @radka-j in #1024
• Remove dead code by @radka-j in #1025
• docs: add AGENTS.md with build, test, and contribution guide by @ykd007 in #1005
• docs: add ykd007 as a contributor for doc by @allcontributors[bot] in #1027

New Contributors

• @penelopeysm made their first contribution in #1006
• @ykd007 made their first contribution in #1005

Full Changelog: v2.1.1...v2.1.2

v2.1.1

What's Changed

• Fix failing test and new warnings by @sgreenbury in #1000
• Fix docstrings by @sgreenbury in #1001
• Fix notebook show progress by @sgreenbury in #1002
• Update benchmarks README by @sgreenbury in #1004
• Bump to v2.1.1 by @sgreenbury in #1003

Full Changelog: v2.1.0...v2.1.1

v2.1.0

What's Changed

• docs: add z7076 as a contributor for code by @allcontributors[bot] in #955
• Add section on use of AI tools to contributing guidelines by @radka-j in #960
• Add evidence computation tutorials by @z7076 in #950
• Add new logo by @radka-j in #971
• Update workflows to use uv sync by @sgreenbury in #972
• docs: add RemDelaporteMathurin as a contributor for bug by @allcontributors[bot] in #976
• fixed class name by @RemDelaporteMathurin in #975
• docs: add pmeier as a contributor for bug by @allcontributors[bot] in #982
• Remove logging in tutorial by @radka-j in #973
• Update benchmarking instructions by @radka-j in #981
• Add deterministic flag for wrapping classes by @sgreenbury in #987
• Prevent CUDA test failures from deterministic algorithm mode by @radka-j in #985
• Update device handling in TorchDeviceMixin by @sgreenbury in #986
• Add method to move TransformedEmulator to new device by @radka-j in #983
• Fix MLP docstring tests by @sgreenbury in #989
• Fix library logging compatibility by @sgreenbury in #994
• Fix warnings in tests and revise make_positive_definite by @sgreenbury in #990
• Fix slow calibration tests by @sgreenbury in #993
• docs: add penelopeysm as a contributor for ideas, review, and 2 more by @allcontributors[bot] in #995
• Fix deterministic argument order by @sgreenbury in #996
• Refactor logging by @radka-j in #988
• Remove warning suppression from docs by @sgreenbury in #997
• Update the IES formulation by @sgreenbury in #998
• Bump to v2.1.0 by @sgreenbury in #999

New Contributors

• @z7076 made their first contribution in #950
• @RemDelaporteMathurin made their first contribution in #975

Full Changelog: v2.0.0...v2.1.0

v2.0.0

What's Changed

• Add Plot loss by @TheCSGuy25 in #939
• docs: add SyedHaider2084 as a contributor for code by @allcontributors[bot] in #947
• docs: add cmsamaaa as a contributor for doc by @allcontributors[bot] in #948
• chore: add instructions for running pre-commit hooks locally by @cmsamaaa in #946
• Add SEIR epidemic simulator by @SyedHaider2084 in #941
• docs: add cmsamaaa as a contributor for code by @allcontributors[bot] in #951
• Add a device-aware TorchSimulator base class by @cmsamaaa in #949

New Contributors

• @TheCSGuy25 made their first contribution in #939
• @cmsamaaa made their first contribution in #946
• @SyedHaider2084 made their first contribution in #941

Full Changelog: v1.2.1...v2.0.0

v1.2.1

What's Changed

• Add calibration plot by @radka-j in #897
• Update tutorial text by @radka-j in #899
• Fix ensemble tuning params bug by @radka-j in #898
• Add Gaussian MLP by @sgreenbury in #593
• Add Zero-One Inflated Beta MLP by @sgreenbury in #870
• adding general torchmetrics support by @EdwinB12 in #883
• Add emulator registry by @sgreenbury in #900
• docs: add vchhabra-turing as a contributor for ideas by @allcontributors[bot] in #903
• 718 update dependencies by @EdwinB12 in #908
• Update plots by @radka-j in #907
• Add CRPS metric by @sgreenbury in #904
• Update API for getting metric config by @sgreenbury in #912
• Update workflows to use uv by @sgreenbury in #915
• Enable custom metrics in AutoEmulate compare loop by @sgreenbury in #913
• Fix metrics, samples, transformed params by @sgreenbury in #917
• Update ensemble init update kwargs by @sgreenbury in #918
• docs: add era-23 as a contributor for bug by @allcontributors[bot] in #934
• rm seed from correlated GP by @radka-j in #935
• Add MSLL metric by @radka-j in #924
• Added Project email to the readme file by @TarryCarrot7309 in #920
• Let user specify test set by @radka-j in #938
• Make loss_history instance variable (not class variable) by @radka-j in #940
• docs: add TheCSGuy25 as a contributor for code by @allcontributors[bot] in #943

New Contributors

• @TarryCarrot7309 made their first contribution in #920

Full Changelog: v1.2.0...v1.2.1

What's Changed

• Add calibration plot by @radka-j in #897
• Update tutorial text by @radka-j in #899
• Fix ensemble tuning params bug by @radka-j in #898
• Add Gaussian MLP by @sgreenbury in #593
• Add Zero-One Inflated Beta MLP by @sgreenbury in #870
• adding general torchmetrics support by @EdwinB12 in #883
• Add emulator registry by @sgreenbury in #900
• docs: add vchhabra-turing as a contributor for ideas by @allcontributors[bot] in #903
• 718 update dependencies by @EdwinB12 in #908
• Update plots by @radka-j in #907
• Add CRPS metric by @sgreenbury in #904
• Update API for getting metric config by @sgreenbury in #912
• Update workflows to use uv by @sgreenbury in #915
• Enable custom metrics in AutoEmulate compare loop by @sgreenbury in #913
• Fix metrics, samples, transformed params by @sgreenbury in #917
• Update ensemble init update kwargs by @sgreenbury in #918
• docs: add era-23 as a contributor for bug by @allcontributors[bot] in #934
• rm seed from correlated GP by @radka-j in #935
• Add MSLL metric by @radka-j in #924
• Added Project email to the readme file by @TarryCarrot7309 in #920
• Let user specify test set by @radka-j in #938
• Make loss_history instance variable (not class variable) by @radka-j in #940
• docs: add TheCSGuy25 as a contributor for code by @allcontributors[bot] in #943
• Update version by @radka-j in #944

New Contributors

• @TarryCarrot7309 made their first contribution in #920

Full Changelog: v1.2.0...v1.2.1

1.2.0

What's Changed

• rm repetition from case study nb by @radka-j in #866
• Add tutorial on adding emulators suggestions by @sgreenbury in #869
• Add tutorial on adding emulators by @radka-j in #861
• Update default models by @radka-j in #865
• Add surface plotting functionality for predicted mean and variance by @sgreenbury in #857
• Iss867/update gp factory pr by @sgreenbury in #873
• Update GP factory by @radka-j in #871
• Update workflows by @sgreenbury in #875
• Improve handling of Gaussians distributions by @cisprague in #471
• Add support for emulator UQ to be included in sensitivity analysis by @sgreenbury in #877
• Improve emulator re-initialisation by @radka-j in #872
• Overwrite defaults with user supplied param values by @radka-j in #895

Full Changelog: v1.1.1...1.2.0

v1.1.1

What's Changed

• Pin AE version in case study by @radka-j in #805
• Update calibration tutorial by @radka-j in #801
• Dont standardize y values in AL tutorial by @radka-j in #808
• double pendulum simulator by @marjanfamili in #778
• Fix logging in history matching by @radka-j in #809
• Github action to pull data and write out to the branch. Also link in … by @EdwinB12 in #810
• Add dataset for reaction diffusion example by @sgreenbury in #794
• Add autoregressive predict by @sgreenbury in #819
• add dtype to dataset_class by @marjanfamili in #825
• Add dataset for advection-diffusion example by @ContiPaolo in #820
• Add tests for gradients by @sgreenbury in #812
• Add delta method for transforming mean and variance only by @sgreenbury in #771
• Add calibration method to provide level/excursion set by @sgreenbury in #821
• Fix formatting and docs for IES by @sgreenbury in #839
• Store default params if not tuning models by @radka-j in #845
• Handle no succesful sim results in forward_batch by @radka-j in #851
• Update performance plot by @radka-j in #850
• Use self.device in MLP for consistency by @radka-j in #859
• Add AD emulator info to table by @radka-j in #860
• Update PolynomialFeatures, use in poly regression by @radka-j in #853

Full Changelog: v1.1.0...v1.1.1

v1.1.0

⚠️ Breaking changes ⚠️

• Changed behaviour of Simulator.forward_batch (returns both y and x)
• AutoEmulate no longer takes in model_tuning argument, model tuning is not done if model_params != None, to use default params without tuning use model_params = {}

What's Changed

• Clear nb outputs by @radka-j in #685
• Update HMW notebook by @radka-j in #687
• Undo changes after experimental merge by @radka-j in #689
• Update tutorial title by @radka-j in #699
• Fix math in docstring by @radka-j in #703
• Fix install link in README by @radka-j in #705
• add reaction-diffusion gif by @ContiPaolo in #706
• return dict of results from simulator by @marjanfamili in #710
• Speed up tests by @EdwinB12 in #686
• remove poetry support by @EdwinB12 in #700
• Update contributing docs by @radka-j in #715
• Add emulator info by @radka-j in #701
• Pre-commit hook to strip nb output by @radka-j in #713
• Fix nbstripout issue by @radka-j in #717
• 681 add testing support for different os by @EdwinB12 in #702
• Use compare method in dim reduction tutorial by @radka-j in #714
• Add load_model method and update quickstart by @sgreenbury in #729
• Move logo to package, update pyproject.toml by @sgreenbury in #731
• Add AutoEmulate class to init to allow import from top level of package. by @EdwinB12 in #724
• Add option to save plots to file by @radka-j in #734
• Fix package data and revert logo path by @sgreenbury in #739
• Fix order of sobol indexes when creating df by @radka-j in #738
• Update install instructions by @radka-j in #736
• Revise transforms by @sgreenbury in #726
• Add support for optional bootstrap by @sgreenbury in #742
• Add transformed emulator params by @sgreenbury in #744
• Restructure tests by @radka-j in #747
• Add option to subset models by @radka-j in #753
• Re-initialise emulator before refitting in HMW by @radka-j in #752
• Add cloud sampling to HM by @radka-j in #725
• Add API to support plotting subset of data by @sgreenbury in #755
• Move import outside of test function by @EdwinB12 in #762
• Add API to support fixing GP mean and kernel hyperparameters during training by @sgreenbury in #761
• Add QMC Sobol sampling by @radka-j in #754
• Fix assertion and class resolution by @sgreenbury in #767
• Add experimental dataset, model and notebooks for spatio-temporal problems by @sgreenbury in #770
• Update BayesianCalibationto optionally include model variance and discrepancy by @sgreenbury in #765
• Add GP subclasses and functionality to generate new subclasses easily by @sgreenbury in #764
• Set random seeds in Bayes tutorial for reproducibility by @radka-j in #768
• should report failed doc builds by @EdwinB12 in #766
• Fix simulator setter bug by @radka-j in #777
• Ruff ignore arguments by @marjanfamili in #776
• add random seed into bayesian tutorial by @EdwinB12 in #779
• Build docs with autoemulate installed from branch by @radka-j in #781
• Update Simulator.forward_batch to always return x,y by @radka-j in #772
• Update calibration tutorial PR suggestions by @sgreenbury in #791
• Update calibration tutorial by @radka-j in #782
• Don't tune if user passes model_params by @radka-j in #780
• Fix tutorial by @radka-j in #793
• Refactor Naghavi case study by @radka-j in #632
• added README to case_studies directory by @ritkaarsingh30 in #799
• Add spatiotemporal deps as optional extra by @sgreenbury in #792
• Set log level in HM tutorials by @radka-j in #802
• Update version by @radka-j in #798

New Contributors

• @ritkaarsingh30 made their first contribution in #799

Full Changelog: v1.0.0...v1.1.0

v1.0.0

What's Changed

• Add MLP by @sgreenbury in #559
• Handle random_seed setting at higher level in package by @edwardchalstrey1 in #512
• Docs restructure by @radka-j in #573
• Refactor: add transforms and transformed emulator by @sgreenbury in #474
• Add Polynomials to experimental by @edwardchalstrey1 in #568
• Add more emulator subclasses by @sgreenbury in #561
• Fix MLP initialization by @sgreenbury in #581
• 492 simulator code contribution tutorial by @EdwinB12 in #577
• Add Radial Basis functions to experimental & update Tuner run loop by @edwardchalstrey1 in #567
• Add EarlyStopping for GPs by @radka-j in #587
• docs: add Apple-silicon test note (Refs #410) by @nayara-focs in #590
• changed the numbering of tutorial 08 to 07 by @marjanfamili in #592
• Add ensembles by @cisprague in #560
• Add GP with correlated tasks by @sgreenbury in #585
• Hmc re refactor by @marjanfamili in #599
• Add support for transforms of MultivariateNormal by @sgreenbury in #586
• Fix training only first batch by @sgreenbury in #604
• Add transforms to compare loop by @sgreenbury in #551
• Add learning rate scheduler by @edwardchalstrey1 in #582
• Grad handling by @radka-j in #605
• Refactor HMC calibration by @radka-j in #575
• 428 improve logging by @EdwinB12 in #608
• Set RBF supports_grad=False by @radka-j in #616
• Evaluate on test data, update compare loop and add Results/plots by @edwardchalstrey1 in #603
• Start experimental docs by @radka-j in #598
• Add bootstrap, fix evaluation and revise results by @sgreenbury in #620
• Add logging to Active Learner by @edwardchalstrey1 in #624
• Update docstrings by @radka-j in #626
• Common scheduler setup function for all emulators by @edwardchalstrey1 in #623
• Fix missing model config to pass to cv by @sgreenbury in #627
• Add logger to BayesianCalibrator by @edwardchalstrey1 in #628
• Remove experimental (v1) code reliance on v0 codebase by @radka-j in #630
• Fix reaction-diffusion example and update GP predictive by @sgreenbury in #639
• Revise GP predict approach by @sgreenbury in #638
• History Matching tutorials by @radka-j in #625
• Bayesian calibration tutorial by @radka-j in #636
• Add str and dict serialization option for emulators and transforms in AutoEmulate class by @sgreenbury in #641
• Add saving and loading models to experimental by @edwardchalstrey1 in #629
• Add fixes from further testing and benchmarking by @sgreenbury in #647
• Experimental sensitivity analysis tutorial by @edwardchalstrey1 in #642
• Add handling for failed simulations by @radka-j in #643
• Add API to update simulator parameters and enable sampling when equal bounds by @sgreenbury in #660
• Add standardization for x and y to Emulator by @sgreenbury in #650
• Remove obsolete preprocessing by @sgreenbury in #666
• Add docs lint config and update docstrings by @sgreenbury in #663
• Add script for benchmarking simulators with different parameters by @sgreenbury in #621
• Revise config to params by @sgreenbury in #667
• Update module structure to add core module by @sgreenbury in #670
• Fix pre-commit by @sgreenbury in #669
• Update config for experimental and API docs by @sgreenbury in #664
• Move modules from experimental, move current to v0 by @sgreenbury in #672
• Omit v0/ from coverage by @sgreenbury in #673
• Fix docs notebooks by @sgreenbury in #674
• Add datasets to package and update path by @sgreenbury in #675
• Update default to enable tuning by @sgreenbury in #677
• Update version to 1.0.0 by @sgreenbury in #678

New Contributors

• @nayara-focs made their first contribution in #590

Full Changelog: v0.4.0...v1.0.0

v0.4.0

Major Changes

• rm CNPs by @radka-j in #554

Other Changes

• Update quickstart tutorial by @radka-j in #523
• Update Simulator base class by @radka-j in #520
• Post-workshop improved tutorial setup instructions by @edwardchalstrey1 in #535
• Add target-version to ruff to extend lints by @sgreenbury in #541
• Refactor sensitivity analysis by @radka-j in #539
• Bug fixes by @radka-j in #556
• Add test for device to history matching by @sgreenbury in #562
• HM refactor by @radka-j in #504
• Add Gradient boosting to experimental by @edwardchalstrey1 in #565
• Execute nb when building docs except workflow example by @radka-j in #569
• Bump version to 0.4 by @radka-j in #570

Full Changelog: v0.3.3...v0.4.0