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Load SBML in VCell's units: unit_system= and convert_vcml_units - #63
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- pyvcell.vcml.convert_units(bio_model, unit_system="vcell"|"sbml"): the Biomodel in VCell's units (um, uM, s) or VCell's SBML units (dm, umol, l, s), every quantity converted by VCell (libvcell vcml_convert_units). VCell imports SBML in the SBML's own units, so convert_units(load_sbml_str(sbml)) gives the model in VCell's units. - Model.unit_system holds VCML's <ModelUnitSystem> attributes. The reader and writer used to drop it, so a model imported from SBML (in dm, umol, l) was written back with its numbers read in VCell's default units. Results are unchanged for that case (the numbers are self-consistent either way; checked bit for bit on the 1D fixture), but generated names now carry the model's units (s0_init_umol_l_1 rather than s0_init_uM). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…type-checks Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Keeping <ModelUnitSystem> on the pyvcell Model broke a common pattern: a model from Antimony/SBML without units gets a unit system with a dimensionless length, and users then add a um geometry to it (examples/notebooks/sysbio-1-antimony.ipynb). The Model, reader and writer are back to main. Instead: - load_sbml_str/load_sbml_file(..., unit_system=None): "vcell" converts the imported VCML (which still carries its units) to VCell's units before reading; the default is unchanged. - convert_vcml_units(vcml_str, unit_system): the text-level utility. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
jcschaff
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Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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VCell imports SBML in the SBML's own units; VCell itself writes SBML in dm, µmol, l and s. This PR adds a way to get such models in VCell's units: µm, µM and s, which VCell's spatial and stochastic math assumes. VCell does the conversion, geometry included, through libvcell's new
vcml_convert_units(virtualcell/libvcell#26).New API
load_sbml_str(sbml_str, unit_system=None)andload_sbml_file(...): withunit_system="vcell", the imported VCML, which still carries its<ModelUnitSystem>, is converted before pyvcell reads it. The default leaves the numbers as imported, which is today's behaviour.convert_vcml_units(vcml_str, unit_system): the text-level utility, for"vcell"or"sbml".Why not on the
Biomodel. A first version kept<ModelUnitSystem>on pyvcell'sModelthrough VCML read and write, and brokeexamples/notebooks/sysbio-1-antimony.ipynb.Model, reader and writer are unchanged here, and conversion happens on the VCML text instead.Tests:
test_load_sbml_in_vcell_unitsusesSmallSpatialProject_3D.xml(in dm) and checks:convert_vcml_unitsgoes back to dm;It skips with a libvcell that lacks
vcml_convert_units, and mypy passes against the released libvcell. Locally, with a libvcell built from #26,tests/vcml/test_utils.pyandtest_simulations.pypass, andsysbio-1-antimony.ipynbexecutes.Context: Phase 6 of viva-pde-particle, reading PDE/particle hybrids from SBML Spatial (virtualcell/vcell#2175). Suggested by @jcschaff: VCell converts units internally anyway, so pyvcell and libvcell should expose it.
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