v2.2.2

PyEnzyme 2.2.2

This release updates package metadata and optional dependency configuration.

What changed

• Switched optional dependency declaration from [dependency-groups] to [project.optional-dependencies] in pyproject.toml.
• Removed default-groups = ["excel"] from [tool.uv] in pyproject.toml.

Full Changelog: v0.2.1...v2.2.2

v2.2.1

What's Changed

• Fix an issue where parameter estimation fails sometimes by @fbergmann in #89
• Fix BaseThinLayer removing species occurring in equations by @JR-1991 in #90
• Fix PySCeS and Copasi thinlayer imports by @jmrohwer in #93
• Refactor ChEBI models to ignore extra fields by @JR-1991 in #95
• Fix numpy>2.0 dependency and update fetchers by @JR-1991 in #98

Full Changelog: v2.2.0...v0.2.1

v2.2.0

What's Changed

• Add fit flag for Parameter by @JR-1991 in #85
• Basico v2 support by @fbergmann in #87

Full Changelog: v2.1.1...v2.2.0

v2.1.1

What's Changed

• Update docstrings in io.py by @jmrohwer in #81
• Retain unmodeled species by @JR-1991 in #84

Full Changelog: v2.1.0...v2.1.1

v2.1.0

What's Changed

• Sort by measurement group feature by @haeussma in #80
• Refactored import structure to avoid circular imports caused by top-level references, improving compatibility with third-party usage by @haeussma in #80

Full Changelog: v2.0.0...v2.1.0

v2.0.0

PyEnzyme 2.0.0 — Release Notes

We are pleased to announce the stable release of PyEnzyme 2.0.0. This major update fully implements the EnzymeML v2 specification and introduces a range of enhancements to streamline enzymatic data analysis and modelling.

Key improvements

• Redesigned API:
  JSON-LD support and an improved API for precise, fine-grained data manipulation.
• Integrated database connectivity:
  Direct retrieval of information from databases like PubChem, UniProt, and Rhea.
• PeTab & SBML export:
  Seamless generation of PeTab for use with any SBML-compatible modeling framework.
• Extended visualization suite:
  Publication-quality static plots and fully interactive figures for exploratory analysis in Jupyter.
• Backward compatibility:
  Automatic version detection and conversion to EnzymeML V2.

What's Changed

• Add celsius as unit by @haeussma in #68
• Fix 313 enum variants by @JR-1991 in #73
• PyEnzyme v2.0.0 by @JR-1991 in #67
• Add missing .gitmodules by @JR-1991 in #78

New Contributors

• @haeussma made their first contribution in #68

Full Changelog: v1.1.5...v2.0.0

v1.1.5

What's Changed

• PySCeS ThinLayer: Fit multiple replicates, plot fit result by @jmrohwer in #46
• PyYAML causing pip error fix by @JR-1991 in #60
• fix reading to be compatible with newer versions of libsbml by @fbergmann in #61
• #62 : use write.close rather than writer.save by @fbergmann in #63

Full Changelog: v1.1.4...v1.1.5

PyEnzyme 1.1.4

This release fixes some minor issues and an endless loop caused by PyDantic.

PyEnzyme 1.1.3

In the course of the upcoming "EnzymeML at work" manuscript, the PyEnzyme library has been extended and revisited to enhance functionalities. In addition, the syntax has been improved towards a more pythonic way that aligns well to common standards.

Important changes

• Thin Layers have been generalized and are built from a Base Thin Layer
• Syntax has been changed to fit python standards
• Measurement and experimental data management has been improved
• Export relevant data to Pandas DataFrames
• Direct visualization either static or interactively
• JSON export and import
• Improved data validation and creation of validation YAML files
• Documentation has been added
• Comprehensive testing suite to check on functionality

PyEnzyme 1.1.0-Alpha

v1.1.0-alpha

ENZML-83 Fixed enzmldoc missing