Releases: PEtab-dev/libpetab-python
libpetab-python v0.5.0
Fixes
-
Circumvent
SettingWithCopyWarning
by @m-philipps in #306
-
If
flatten_timepoint_specific_output_overrides
makes the visualization table invalid, remove it fromProblem
by @m-philipps in #316
Features
-
Added
petab.v1.priors.priors_to_measurements(...)
for replacingobjectivePrior*
by observables/measurements -
Made model id optional for
PySBModel
-
Implemented
Model.__repr__
Full Changelog: v0.4.1...v0.5.0
libpetab-python v0.4.1
This series contains many changes related to the new petab.v2
subpackage. petab.v2
should not be considered stable; the petab.v2
API may change rapidly until we release libpetab-python v1.0.0.
- Fix: keep previously-optional dependencies optional by @dweindl in #298
- Add petab.v2.C by @dweindl in #299
Full Changelog: v0.4.0...v0.4.1
libpetab-python v0.4.0
Prepare for PEtab v2
To enable ongoing support for PEtab v1, while "forking" the v1 code for PEtab v2, the old code base is now available at petab.v1
, and the new code base will be at petab.v2
. For now, old import petab.*
statements still work, but are marked as deprecated, and import petab.v1.*
should be used instead. petablint
will be designed for use with only full PEtab problems in future too, rather than individual tables -- partial problems will be supported to validate individual tables.
- Add PEtab math parser and sympy converter by @dweindl in #260
- Deprecate petablint with individual tables by @dweindl in #274
- Introduce petab.v1 package by @dweindl in #282
- Separate v1 and v2 tests by @dweindl in #284
- Add petab.v2.Problem by @dweindl in #285
- PEtab v1 to v2 converter by @dweindl in #281
- Fix imports related to v1 subpackage by @dweindl in #293
Validation
Validation will become increasingly atomic and OOP, to support extension-specific validation in PEtab v2.
- Validator: check for positive bounds for log-scaled parameter by @dweindl in #278
- Validator: check prior parameters by @dweindl in #279
- Fix validation for remote files by @dweindl in #287
- New validation API by @dweindl in #288
Documentation
- Fixed formatting / missing type annotations by @dweindl in #292
- Added versioning and deprecation policy by @dweindl in #277
Other changes
- Simplify yaml schema by @dweindl in #264
- Handle numpy types in sympify_petab by @dweindl in #294
- New
get_path_prefix
method to get the base path for relative paths in PEtab problem YAML by @dweindl in #280
New Contributors
- @dependabot made their first contribution in #267
Full Changelog: v0.3.0...v0.4.0
libpetab-python v0.3.0
This release requires python>=3.10
Features
- Visualization: Make line plot lines configurable via
petab.visualize.plotter.measurement_line_kwargs and
petab.visualize.plotter.simulation_line_kwargs`
by @dweindl in #254 - Validator: check that
datasetId
s referenced in visualization tables exists
in measurement tables
by @dweindl in #255
Fixes
New Contributors
- @PaulJonasJost made their first contribution in #250
Full Changelog: v0.2.9...v0.3.0
libpetab-python v0.2.9
libpetab-python v0.2.8
libpetab-python v0.2.7
- Fixed a bug in
flatten_timepoint_specific_output_overrides
, which
did not handle numeric values correctly
Full Changelog: v0.2.6...v0.2.7
libpetab-python v0.2.6
- Fixed
flatten_timepoint_specific_output_overrides
not supporting
observableParameter overrides as placeholders in noise formulae
by @dweindl in #235 - Visualization: fixed replicate sorting
by @plakrisenko in #232 - Doc: Revised visualization examples
by @dweindl in #236
Full Changelog: v0.2.5...v0.2.6
libpetab-python v0.2.5
libpetab-python v0.2.4
- Made figure sizes for visualization functions customizable via
petab.visualize.plotting.DEFAULT_FIGSIZE
by @dweindl in #222 - Fixed Handling missing
nominalValue
inProblem.get_x_nominal
by @dweindl in #223 - Fixed pandas 2.1.0
FutureWarnings
by @dweindl in #226 - Added pre-commit-config, ran black, isort, ...
by @dweindl in #225
Full Changelog: v0.2.3...v0.2.4