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Published July 1, 2024 | Version v0.4.0
Software Open

PEtab-dev/libpetab-python: libpetab-python v0.4.0

Authors/Creators

  • 1. @ICB-DCM
  • 2. Uni Bonn + Helmholtz Munich + TUM
  • 3. Helmholtz Center Munich, TUM
  • 4. The Francis Crick Insitute
  • 5. TNG, Technology Consulting GmbH
  • 6. IRU Biomathematics @ Uni Bonn
  • 7. @PumasAI
  • 8. Heidelberg University
  • 9. Biosim

Description

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

Files

PEtab-dev/libpetab-python-v0.4.0.zip

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Additional details

Related works

Is supplement to
Software: https://github.com/PEtab-dev/libpetab-python/tree/v0.4.0 (URL)