allow use of is_integrated_over_time

[jpfon]

fix(ODESimulationProperties-and-DynamicFBASimulator): allow use of is_integrated_over_time

for David and Thomas

[Copilot]

Pull request overview

This PR adds support for the is_integrated_over_time flag in ODE simulation properties and the dynamic FBA simulator. The change allows users to specify whether a flux expression should be integrated over time, with a default value of True to maintain backward compatibility.

Changes:

• Added is_integrated_over_time field to ODESimulationProperties with a default value of True
• Updated DynamicFBASimulator to pass the is_integrated_over_time flag when adding RHS expressions, with fallback handling for backward compatibility
• Incremented package version from 0.1.0 to 0.1.1

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.

File	Description
src/simulib/entities/dynamic.py	Added is_integrated_over_time boolean field to ODESimulationProperties class with default value True
src/simulib/methods/dynamic/dfba/simulator.py	Wrapped add_rhs_expression call in try-except block to pass is_integrated_over_time flag with fallback for backward compatibility
pyproject.toml	Bumped version from 0.1.0 to 0.1.1

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[jpfon]

tests are failing because it uses original dfba package, without changes in model.py