Prepare release 0.6.0

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

petab/version.py

@@ -1,3 +1,3 @@
 """PEtab library version"""
 
-__version__ = "0.5.0"
+__version__ = "0.6.0"