biosim-toolkit

Trusted utilities for process-bigraph simulations, collected in one package: the steps and functions that do not depend on any one simulator, reviewed and tested once.

Model adapters and format adapters join as their own subpackages.

Steps are registered by process-bigraph's discovery under their defining module: local:biosim_toolkit.sedml.Report.

SED-ML

process-bigraph-lang's sedml translate turns each task of a SED-ML file (a BioModels entry, a biosimulations.org project, an upload) into a composite: a generic time-course solver (pbsim-common's COPASI or Tellurium step, or any step with the same face), then DataGenerators (the solver's result as the SED-ML data generators, the points before the output start dropped), Report (a CSV per SED-ML report) and Plots (a Plotly figure per SED-ML plot). compose-api runs a task once per solver and compares the reports (compose-api docs/plan-sedml.md).

Development

uv sync                               # process-bigraph 1.0.5, bigraph-schema 1.0.14, pbsim-common, COPASI, Tellurium
uv pip install --reinstall --no-deps .  # discovery reads installed metadata, which an editable install hides
uv run --no-sync pytest

The end-to-end tests run instance archives made by process-bigraph-lang's sedml translate (tests/fixtures/<model>.<solver>.omex) the way compose-api's runner (pbest) does: a core with pbsim-common's types, Composite(...), run(...).

Releases: a GitHub release publishes the wheel to PyPI by trusted publishing (.github/workflows/release.yml).