Petab

Latest version: v0.5.0

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0.5

0.5.0

**Fixes**
* Circumvent `SettingWithCopyWarning`

by m-philipps in https://github.com/PEtab-dev/libpetab-python/pull/306

* If `flatten_timepoint_specific_output_overrides` makes the visualization
table invalid, remove it from `Problem`

by m-philipps in https://github.com/PEtab-dev/libpetab-python/pull/316

**Features**

* Added `petab.v2.models` by dweindl in https://github.com/PEtab-dev/libpetab-python/pull/302
* Added `petab.v1.priors.priors_to_measurements(...)` for replacing
`objectivePrior*` by observables/measurements

by dweindl in https://github.com/PEtab-dev/libpetab-python/pull/309, https://github.com/PEtab-dev/libpetab-python/pull/315, https://github.com/PEtab-dev/libpetab-python/pull/317

* Make model id optional for `PySBModel`

by dweindl in https://github.com/PEtab-dev/libpetab-python/pull/318

* Implemented `Model.__repr__`

by dweindl in https://github.com/PEtab-dev/libpetab-python/pull/319

**Full Changelog**: https://github.com/PEtab-dev/libpetab-python/compare/v0.4.1...v0.5.0

0.4.1

* Fix: keep previously-optional dependencies optional by dweindl in https://github.com/PEtab-dev/libpetab-python/pull/298
* Add petab.v2.C by dweindl in https://github.com/PEtab-dev/libpetab-python/pull/299

**Full Changelog**: https://github.com/PEtab-dev/libpetab-python/compare/v0.4.0...v0.4.1

0.4

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.

0.4.0

**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 https://github.com/PEtab-dev/libpetab-python/pull/260
* Deprecate petablint with individual tables by dweindl in https://github.com/PEtab-dev/libpetab-python/pull/274
* Introduce petab.v1 package by dweindl in https://github.com/PEtab-dev/libpetab-python/pull/282
* Separate v1 and v2 tests by dweindl in https://github.com/PEtab-dev/libpetab-python/pull/284
* Add petab.v2.Problem by dweindl in https://github.com/PEtab-dev/libpetab-python/pull/285
* PEtab v1 to v2 converter by dweindl in https://github.com/PEtab-dev/libpetab-python/pull/281
* Fix imports related to v1 subpackage by dweindl in https://github.com/PEtab-dev/libpetab-python/pull/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 https://github.com/PEtab-dev/libpetab-python/pull/278
* Validator: check prior parameters by dweindl in https://github.com/PEtab-dev/libpetab-python/pull/279
* Fix validation for remote files by dweindl in https://github.com/PEtab-dev/libpetab-python/pull/287
* New validation API by dweindl in https://github.com/PEtab-dev/libpetab-python/pull/288

**Documentation**

* Fixed formatting / missing type annotations by dweindl in https://github.com/PEtab-dev/libpetab-python/pull/292
* Added versioning and deprecation policy by dweindl in https://github.com/PEtab-dev/libpetab-python/pull/277

**Other changes**

* Simplify yaml schema by dweindl in https://github.com/PEtab-dev/libpetab-python/pull/264
* Handle numpy types in sympify_petab by dweindl in https://github.com/PEtab-dev/libpetab-python/pull/294
* New `get_path_prefix` method to get the base path for relative paths in PEtab problem YAML by dweindl in https://github.com/PEtab-dev/libpetab-python/pull/280

**New Contributors**

* dependabot made their first contribution in https://github.com/PEtab-dev/libpetab-python/pull/267

**Full Changelog**: https://github.com/PEtab-dev/libpetab-python/compare/v0.3.0...v0.4.0

0.3

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