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