A translator from SED2 to a python script, using libSED2.
pysed2translate 00001.sed2.json --backend roadrunner -o 00001.py
python 00001.py --input-dir . --output-dir results/
See docs/generated-script-contract.md for exit codes and what the generated script reads and writes, and build.md for the project plan. Setup: scripts/setup_env.sh (or .ps1), then pip install -e . --no-deps inside the environment. The libsed2 wheel is not on PyPI; put it in this directory.
Backends: roadrunner (tellurium), COPASI (basico) and OpenCOR (libopencor with sbml2cellml); flux balance analysis runs on COBRApy (cobra, cobra:glpk, cobra:scipy). The translator handles constants, reports, calculations and data manipulation, ModelImport, explicit, one-step and bounded ODE simulations, SteadyState, JacobianFull and JacobianReduced, FluxBalanceAnalysis, ModelChange (setValues, removeElements), ModelElementList, the repeats (Scatter, Loop, ParameterScan), CsvImport, and the data behind Plot2D and Plot3D (pictures with matplotlib). A task a backend cannot perform is refused with a reason and exit status 11 (the capability table is in src/pysed2translate/capabilities, see docs/capability-table.md). What is waiting for the SED2 specification, and the choices made where it is silent, are in docs/deferred.md; simulator problems are logged in sed2-test-suite/disagreements.json.
All 273 semantic cases of sed2-test-suite run through the suite runner:
python -m pysed2translate.suite_runner --crosscheck # every case on every backend, and the backends against each other
The tests are described in docs/testing.md.