Changelog

All notable changes to this project will be documented in this file.

[Template]

Added

  • Feature X

  • Feature Y

Changed

  • Refactored module A to improve performance

Fixed

  • Bug in module B that caused a crash

[Unreleased] - unreleased

Added

  • Introduced automatic updates for the github actions through dependabot

Changed

Fixed

[0.11.0] - 2025-07-20

Changed

  • Switched from poetry to uv as project management tool

  • Switched to python 3.13 as default

  • Updating minimal python version to 3.11 to fix issues with cpp dependencies

  • Increased upper policy version of cmake in cpp example

[0.10.0] - 2024-11-22

Added

  • Added the AffineTransformation class to perform affine transformations on the data using jax

  • Added the method function forward_vectorized to the (Base)Model class and a specialized jax version in the JaxModel class.

Changed

  • Refactored the module eulerpi.core.data_transformation into the subpackage eulerpi.core.data_transformations. The data transformation classes can be import from this subpackage directly

  • Renamed eulerpi.core.data_transformation.DataNormalizer into eulerpi.core.data_transformations.DataNormalization

  • Removed the class/factory functions from_data and from_transformation from the DataTransformation subclasses. Use the constructors instead.

  • The inference function no longer has the parameter custom_data_transformation. You can pass an instance of the provided DataTransformation subclasses or pass a custom subclass.

  • The inference function no longer has the parameter n_components_pca. Instantiate a PCATransformation with the data and the number of components to keep. Pass it as as argument for the parameter data_transformation in the inference function.

  • Renamed the abstract base Model class to BaseModel. The usage of Model is still supported, but deprecated, and possibly removed in a future release.

  • Splitted the file model.py into multiple modules, one for each class, located in the subpackage eulerpi.core.models. The imports change from eulerpi.core.model to eulerpi.core.models.

  • Removed the function is_artificial from the (Base)Model class. Use isinstance(custom_model, ArtificialModelInterface) or issubclass(CustomModel, ArtificialModelInterface) instead.

[0.9.1] - 2024-09-08

Changed

  • Raised required amici version to 0.26.1

  • Ignoring sampler warnings caused by parameters outside the parameter limits

  • Limited the parameter range and increased the solver accuracy of the Corona model to avoid warnings

Fixed

  • Seed numpy random number generator for reproducibility of pytest runs

[0.9.0] - 2024-05-31

Changed

  • Raised the required python version to 3.10

  • Removed upper limit on the version number of dependencies

  • Updated amici to newest version to fix compilation with Intel MKL

[0.8.1] - 2024-05-31

Added

  • Added PyQt6 as dev dependency to allow developers to view plots in the development environment

Changed

  • Removed the redundant function evaluate_sample from sampling.py

Fixed

  • Switched from importlib.resources.path to importlib.resources.files due to deprecation

  • Removed argument name in call to files(...) that is changing from package to anchor

  • Removed unused kwargs passed to the plotting function contour that generated a warning in test_heat_model()

  • Bug that changed the model attribute central_param during inference

[0.8.0] - 2024-03-21

Added

  • Basic plotting function for sample results

  • Users can now check the models they want to use with a basic functionality check and a quick inference check on artificial data.

  • Added code usage examples to documentation.

Fixed

  • Fixed deprecated jax.config import

[0.7.0] - 2023-11-03

Breaking changes: The stock model is removed from the available example models! You can copy the model code and the data files from a previous version and import it as custom model, if you need it.

Changed

  • Removed the stock model, because it does not fulfill the requirements for the EPI method

  • Minor dependency updates

[0.6.1] - 2023-11-02

Added

  • Added link to changelog on pypi

[0.6.0] - 2023-11-02

Breaking changes: SBML support is now only available when install eulerpi with the “sbml” extra!

Added

Changed

  • Updated the dependencies to the latest possible versions

  • Made the sbml model support optional using the extra sbml

Fixed

  • Fixed poetry.lock containing faulty version 1.6.8 of debugpy

  • Fixed github actions failing due to missing sudo apt update

[0.5.0] - 2023-07-20

Added

  • Added support for for sbml models to select parameters and species used in the inference

  • Added support for evaluating sbml models at multiple time points

Changed

  • Switched from using parameter names to using parameter ids in the sbml model

  • Change spatial discretization of heat model example to proper second order central differences

  • Change the initial walker position generation of the emcee sampler

[0.4.0] - 2023-06-24

Added

  • Added a new example model, a 2d heat conduction equation

  • Added a function to model to specify more complex parameter domains

Changed

  • Removed old functions from corona model

  • Temporarily removed stock and sbml models from test examples

Fixed

  • Updated tutorial to be consistent with current state of the project

  • Fixed bug in dense grid generation causing parameter limits to be applied inconsistently when using slices

[0.3.1] - 2023-05-02

Fixed

  • Bug in result manager causing burn-in and thinning to be performed on the wrong samples.

  • Bug in result manager that caused density evals to be saved as data samples for non-full slices.

[0.3.0] - 2023-04-27

Added

  • Added data normalization to improve numerics and performance in the inference method.

  • Added possiblity to use no PCA transformation or completely custom transformation for inference.

  • More tests to validate EPI

Fixed

  • Fixed grid results beeing unusable due to numerical issues

  • Fixed sbml models ignoring parameter_names argument

[0.2.1] - 2023-04-21

Fixed

  • Fix sparse grid returning meaningless data

  • Fix menten data shape

  • Fix SBMLModel data_dim: Return states count instead of observables count

Added

  • Validating the shapes of the inference results

[0.2.0] - 2023-04-20

Changed

  • Now using default emcee move policy during MCMC sampling to improve convergence speed

  • Changed argument calc_walker_acceptance_bool to get_walker_acceptance

  • Changed meaning of argument num_burn_in_samples to refer to the number of samples burned per chain, not in total

Fixed

  • Fixed SwigPyObject pickling

  • Fixed dead lock for larger data sets and models

Added

  • ResultManager is saving meta data for inference

  • ResultManager uses saved meta data to load inference results

[0.1.5] - 2023-04-06

Changed

  • Renamed epipy to eulerpi

[0.1.4] - 2023-04-06

Changed

  • Updated installation instructions

[0.1.3] - 2023-04-05

Changed

  • Updated dependencies

[0.1.2] - 2023-04-05

Fixed

  • removed __pycache__, build and .so from pypi

[0.1.1] - 2023-04-05

Fixed

  • fixed epi logo not showing on pypi

[0.1.0] - 2023-04-05

Added

  • Initial release