diff --git a/CHANGELOG.md b/CHANGELOG.md index 4d12d40d..8712d235 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,81 @@ # PEtab changelog +## 0.6 series + +### 0.6.0 + +**Fixes** + +* Implement proper truncation for prior distributions + (parameter bounds now truncate the prior distribution instead of putting + extra probability mass on the bounds) + (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/335) +* Fixed `get_required_parameters_for_parameter_table` + (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/340) +* Fixed `Prior.from_par_dict` for missing `priorParameters` columns + (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/341) +* Fixed petablint v2 warning + (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/342) +* Fixed linter failing on missing `noiseFormula` + (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/367) +* Fixed v2 import Deprecation warning + (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/346) +* petab.calculate: compare all common columns + (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/347) +* Fixed version checks + (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/350) +* Create output directories in `write_*_df` + (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/352) +* Handle `observableTransformation` in `petab.v1.simulate.sample_noise` + (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/383) +* Fixed residual calculation in `v1.calculate` + (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/395) +* Allow empty string "" in columns to be overridden with default values in priors + (by @PaulJonasJost in https://github.com/PEtab-dev/libpetab-python/pull/384) +* Fixed `goodness_of_fit` plot and add color parameter + (by @plakrisenko in https://github.com/PEtab-dev/libpetab-python/pull/402 + & https://github.com/PEtab-dev/libpetab-python/pull/437, + by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/440) +* Plot without vis spec without `ids_per_plot` + (by @PaulJonasJost in https://github.com/PEtab-dev/libpetab-python/pull/386) + +**Deprecations** + +* Using any PEtab-v2-related functionality currently in `petab.v1` is + deprecated and will be removed in a subsequent release. + Use `petab.v2` instead. + + This affects, for example, PEtab-v2-specific constants `petab.v1.C` + (use `petab.v2.C` instead), `petab.v1.mapping`, + or anything mapping-table-related in `petab.v1.Problem`. + +**Features** + +* Substantially extended and updated `petab.v2` for working with PEtab v2 problems. + + PEtab v2 is still in [draft](https://petab.readthedocs.io/en/latest/v2/documentation_data_format.html) stage -- feedback is welcome! + + * PEtab v2 support for `petablint` + * The library uses pydantic-based objects for most PEtab entities instead of + plain DataFrames + * Functionality for converting PEtab v1 problems to (the current state of) PEtab v2 + + At least until PEtab v2 is finalized, the `petab.v2` API may change rapidly, and should not be considered stable. + +* SbmlModel enhancements + (by @fbergmann in https://github.com/PEtab-dev/libpetab-python/pull/333) +* Added `SbmlModel.from_antimony` (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/331) +* Added `SbmlModel.{to_antimony,to_sbml_str}` (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/371) +* Enable passing the base path to `Problem.from_yaml` (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/327) +* Functions for adding conditions/observables/parameter to `Problem` (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/328) +* Added `evaluate: bool` argument to math parser (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/365) +* Added petab-compatible sympy string-printer (`PetabStrPrinter`/`petab_math_str`) (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/364) +* Prettified linter output (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/401) +* Store problem configuration in `Problem` (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/326) +* Store path info in *Table objects (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/416) + +**Full Changelog**: https://github.com/PEtab-dev/libpetab-python/compare/v0.5.0...v0.6.0 + ## 0.5 series ### 0.5.0 diff --git a/petab/version.py b/petab/version.py index ca57250b..1b607c15 100644 --- a/petab/version.py +++ b/petab/version.py @@ -1,3 +1,3 @@ """PEtab library version""" -__version__ = "0.5.0" +__version__ = "0.6.0"