diff --git a/CHANGELOG.rst b/CHANGELOG.rst index c56d4b29e..a46a808e0 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -6,6 +6,56 @@ Release notes .......... +0.5.5 (2025-01-10) +------------------- + +- **Breaking Changes** + - **PETab select**: There are some deprecated features that will show up as warnings. In addition: + + - The plotting methods ignore some arguments. You will need to reimplement these with the newer approach, which uses + plotting methods from the PEtab Select library instead. See the model selection notebook for examples. + + - All objects containing multiple models (e.g., dictionaries or lists) are now replaced by `petab_select.Models`, + which supports dictionary and list methods. + + To convert your old list of models: + + ```python + petab_select.Models(list_of_Model) + ``` +- General + - Exclude nlopt==2.9.0 from setup (#1519) + - Improve CI (#1521, #1523, #1532, #1536, #1508, #1544, #1531) + - Update references/documentation (#1506, #1491, #1516, #1543) + - **Docker Image** (#1083, #1538) +- Hierarchical + - Fix no error if inner observable parameter in noise formula & viceversa (#1504) + - Remove inner datas from relative calculator (#1505) + - Fix not scaling inner pars when applying to rdatas (#1534) +- Optimization + - ESSOptimizer: Fix priority for local search startpoints (#1503) + - Fix NLoptOptimizer.__repr__ (#1518) + - Improve exception-handling in SacessOptimizer (#1517) + - Fix ESSOptimizer min of empty sequence (#1510) + - Don't modify sys.path for amici model imports (#1522) + - Set OptimizerResult.optimizer in Optimizer.minimize (#1525) + - SacessOptimizer: More efficient saving of intermediate results (#1529) +- Objective + - AmiciObjective/PEtab import: Fix plist (#1493) + - PEtab: Fix warning from fill_in_parameters with fixed parameters (#1509) + - Amici: Fix handling of PEtab fixed parameters (#1514) + - Fix get_parameter_prior_dict docstring (#1537) +- Select + - Support user-provided calibration results (#1338) + - Problem-specific minimize method for SaCeSS (#1339) + - Update for the latest PEtab Select version; see example notebook or the PEtab Select repo (#1530) +- Storage + - Enable writing Optimize(r)Result directly in Writer (#1528) + - Update parameter scale storage (#1542 +- Visualize + - Fix flatten of observable mapping with one observable (#1515) + + 0.5.4 (2024-10-19) ------------------- diff --git a/pypesto/version.py b/pypesto/version.py index 6b27eeebf..86716a713 100644 --- a/pypesto/version.py +++ b/pypesto/version.py @@ -1 +1 @@ -__version__ = "0.5.4" +__version__ = "0.5.5"