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separate out importer code (#3023)
* move files & refactor * fixups * conditional import guards * fixup actions * remove unified import interface * fixups * fixup * fixup * fixup * Update ExampleSplinesSwameye2003.ipynb * fix doc
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‎.github/workflows/test_petab_sciml.yml‎

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on:
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push:
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branches:
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- develop
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- main
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- 'release*'
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pull_request:
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branches:
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- main
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- develop
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- jax_sciml
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merge_group:
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workflow_dispatch:
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‎.github/workflows/test_sbml_semantic_test_suite.yml‎

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- python/sdist/amici/exporters/sundials/de_export.py
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- python/sdist/amici/de_model_components.py
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- python/sdist/amici/de_model.py
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- python/sdist/amici/sbml_import.py
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- python/sdist/amici/import_utils.py
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- python/sdist/amici/importers/sbml/**
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- python/sdist/amici/importers/utils.py
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- scripts/run-SBMLTestsuite.sh
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- tests/sbml/testSBMLSuite.py
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- tests/sbml/conftest.py

‎codecov.yml‎

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carryforward: false
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sbmlsuite:
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paths:
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- "python/amici/sbml_import.py"
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- "python/amici/de_export.py"
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- python/amici/importers/sbml/**
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- python/amici/exporters/sundials/de_export.py
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carryforward: true

‎doc/examples/example_large_models/example_performance_optimization.ipynb‎

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"\n",
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"#### Parameters as constants\n",
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"\n",
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"By default, AMICI will generate sensitivity equations with respect to all model parameters. If it is clear upfront, that sensitivities with respect to certain parameters will not be required, their IDs can be passed to [amici.sbml_import.SbmlImporter.sbml2amici](https://amici.readthedocs.io/en/latest/generated/amici.sbml_import.SbmlImporter.html#amici.sbml_import.SbmlImporter.sbml2amici) or [amici.pysb_import.pysb2amici](https://amici.readthedocs.io/en/latest/generated/amici.pysb_import.html?highlight=pysb2amici#amici.pysb_import.pysb2amici) via the `constant_parameters` argument to not generate the respective equations. This will reduce CPU time and RAM requirements during import and simulation.\n",
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"By default, AMICI will generate sensitivity equations with respect to all model parameters. If it is clear upfront, that sensitivities with respect to certain parameters will not be required, their IDs can be passed to [amici.importers.sbml.SbmlImporter.sbml2amici](https://amici.readthedocs.io/en/latest/generated/amici.importers.sbml.SbmlImporter.html#amici.importers.sbml.SbmlImporter.sbml2amici) or [amici.importers.pysb.pysb2amici](https://amici.readthedocs.io/en/latest/generated/amici.importers.pysb.html?highlight=pysb2amici#amici.importers.pysb.pysb2amici) via the `constant_parameters` argument to not generate the respective equations. This will reduce CPU time and RAM requirements during import and simulation.\n",
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"The PEtab import will automatically pass all parameters with `petab.ESTIMATE==False` as `constant_parameters` arguments.\n",
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"\n",
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"See also the following section for the case that no sensitivities are required at all.\n",
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"\n",
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"\n",
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"#### Not generating sensitivity code\n",
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"\n",
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"If only forward simulations of a model are required, a modest import speedup can be obtained from not generating sensitivity code. This can be enabled via the `generate_sensitivity_code` argument of [amici.sbml_import.SbmlImporter.sbml2amici](https://amici.readthedocs.io/en/latest/generated/amici.sbml_import.SbmlImporter.html#amici.sbml_import.SbmlImporter.sbml2amici) or [amici.pysb_import.pysb2amici](https://amici.readthedocs.io/en/latest/generated/amici.pysb_import.html?highlight=pysb2amici#amici.pysb_import.pysb2amici).\n",
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"If only forward simulations of a model are required, a modest import speedup can be obtained from not generating sensitivity code. This can be enabled via the `generate_sensitivity_code` argument of [amici.importers.sbml.SbmlImporter.sbml2amici](https://amici.readthedocs.io/en/latest/generated/amici.importers.sbml.SbmlImporter.html#amici.importers.sbml.SbmlImporter.sbml2amici) or [amici.importers.pysb.pysb2amici](https://amici.readthedocs.io/en/latest/generated/amici.importers.pysb.html?highlight=pysb2amici#amici.importers.pysb.pysb2amici).\n",
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"\n",
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"Example:\n",
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"```bash\n",
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"\n",
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"By default, AMICI will try to perform some basic simplification of model expressions. For complex model expressions, or for large models, this can become costly. It very much depends on the model expressions, whether the benefits outweigh the cost.\n",
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"Simplification of model expressions can be disabled by passing `simplify=None` to [amici.sbml_import.SbmlImporter.sbml2amici](https://amici.readthedocs.io/en/latest/generated/amici.sbml_import.SbmlImporter.html#amici.sbml_import.SbmlImporter.sbml2amici) or [amici.pysb_import.pysb2amici](https://amici.readthedocs.io/en/latest/generated/amici.pysb_import.html?highlight=pysb2amici#amici.pysb_import.pysb2amici).\n",
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"Simplification of model expressions can be disabled by passing `simplify=None` to [amici.importers.sbml.SbmlImporter.sbml2amici](https://amici.readthedocs.io/en/latest/generated/amici.importers.sbml.SbmlImporter.html#amici.importers.sbml.SbmlImporter.sbml2amici) or [amici.importers.pysb.pysb2amici](https://amici.readthedocs.io/en/latest/generated/amici.importers.pysb.html?highlight=pysb2amici#amici.importers.pysb.pysb2amici).\n",
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"Depending on the given model, different simplification schemes may be cheaper or more beneficial than the default. SymPy's simplification functions are [well documented](https://docs.sympy.org/latest/modules/simplify/simplify.html)."
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‎doc/examples/example_splines/ExampleSplines.ipynb‎

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"outputs": [],
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"# Create a spline object\n",
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"spline = amici.splines.CubicHermiteSpline(\n",
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"from amici.importers.sbml.splines import CubicHermiteSpline, UniformGrid\n",
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"from amici.importers.utils import amici_time_symbol\n",
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"\n",
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"spline = CubicHermiteSpline(\n",
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" sbml_id=\"f\",\n",
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" evaluate_at=amici.sbml_utils.amici_time_symbol, # the spline function is evaluated at the current time point\n",
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" nodes=amici.splines.UniformGrid(0, 1, number_of_nodes=3),\n",
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" evaluate_at=amici_time_symbol, # the spline function is evaluated at the current time point\n",
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" nodes=UniformGrid(0, 1, number_of_nodes=3),\n",
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},
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"spline = CubicHermiteSpline(\n",
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" sbml_id=\"f\",\n",
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" evaluate_at=amici.sbml_utils.amici_time_symbol,\n",
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" nodes=amici.splines.UniformGrid(0, 1, number_of_nodes=3),\n",
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" evaluate_at=amici_time_symbol,\n",
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" nodes=UniformGrid(0, 1, number_of_nodes=3),\n",
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"spline = CubicHermiteSpline(\n",
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" evaluate_at=amici.sbml_utils.amici_time_symbol,\n",
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" nodes=amici.splines.UniformGrid(0, 1, number_of_nodes=3),\n",
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" evaluate_at=amici_time_symbol,\n",
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" nodes=UniformGrid(0, 1, number_of_nodes=3),\n",
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" evaluate_at=amici.sbml_utils.amici_time_symbol,\n",
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" evaluate_at=amici_time_symbol,\n",
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" nodes=UniformGrid(0, 1, number_of_nodes=3),\n",
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" evaluate_at=amici.sbml_utils.amici_time_symbol,\n",
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" nodes=amici.splines.UniformGrid(0, 1, number_of_nodes=3),\n",
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" evaluate_at=amici_time_symbol,\n",
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" evaluate_at=amici.sbml_utils.amici_time_symbol,\n",
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" nodes=amici.splines.UniformGrid(0, 1, number_of_nodes=4),\n",
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" evaluate_at=amici_time_symbol,\n",
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" evaluate_at=amici.sbml_utils.amici_time_symbol,\n",
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" spline = CubicHermiteSpline(\n",
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‎doc/examples/example_splines_swameye/ExampleSplinesSwameye2003.ipynb‎

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"values_at_nodes = [\n",
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" evaluate_at=amici.sbml_utils.amici_time_symbol, # the spline is evaluated at the current time\n",
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" evaluate_at=amici_time_symbol, # the spline is evaluated at the current time\n",
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{

‎doc/examples/example_steady_states/ExampleEquilibrationLogic.ipynb‎

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‎doc/python_interface.rst‎

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125125
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162162
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165-
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‎doc/python_modules.rst‎

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amici
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amici.importers.sbml.conserved_quantities_demartino
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amici.importers.sbml.conserved_quantities_rref
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amici.importers.sbml.utils
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amici.importers.sbml.splines
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amici.importers.pysb
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amici.importers.bngl
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amici.importers.antimony
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amici.petab.conditions
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amici.jax
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amici.pandas
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amici.logging
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amici.gradient_check
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amici.conserved_quantities_demartino
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amici.conserved_quantities_rref
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‎python/benchmark/benchmark_pysb.py‎

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