separate out importer code

.github/workflows/test_petab_sciml.yml

@@ -2,14 +2,11 @@ name: PEtab
 on:
   push:
     branches:
-      - develop
       - main
       - 'release*'
   pull_request:
     branches:
       - main
-      - develop
-      - jax_sciml
   merge_group:
   workflow_dispatch:
 

.github/workflows/test_sbml_semantic_test_suite.yml

@@ -10,8 +10,8 @@ on:
       - python/sdist/amici/exporters/sundials/de_export.py
       - python/sdist/amici/de_model_components.py
       - python/sdist/amici/de_model.py
-      - python/sdist/amici/sbml_import.py
-      - python/sdist/amici/import_utils.py
+      - python/sdist/amici/importers/sbml/**
+      - python/sdist/amici/importers/utils.py
       - scripts/run-SBMLTestsuite.sh
       - tests/sbml/testSBMLSuite.py
       - tests/sbml/conftest.py

codecov.yml

@@ -41,6 +41,6 @@ flags:
     carryforward: false
   sbmlsuite:
     paths:
-      - "python/amici/sbml_import.py"
-      - "python/amici/de_export.py"
+      - python/amici/importers/sbml/**
+      - python/amici/exporters/sundials/de_export.py
     carryforward: true

doc/examples/example_large_models/example_performance_optimization.ipynb

@@ -72,15 +72,15 @@
     "\n",
     "#### Parameters as constants\n",
     "\n",
-    "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",
+    "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",
     "The PEtab import will automatically pass all parameters with `petab.ESTIMATE==False` as `constant_parameters` arguments.\n",
     "\n",
     "See also the following section for the case that no sensitivities are required at all.\n",
     "\n",
     "\n",
     "#### Not generating sensitivity code\n",
     "\n",
-    "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",
+    "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",
     "\n",
     "Example:\n",
     "```bash\n",
@@ -239,7 +239,7 @@
     "\n",
     "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",
     "\n",
-    "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",
+    "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",
     "\n",
     "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)."
    ]

doc/examples/example_splines/ExampleSplines.ipynb

@@ -223,10 +223,13 @@
    "outputs": [],
    "source": [
     "# Create a spline object\n",
-    "spline = amici.splines.CubicHermiteSpline(\n",
+    "from amici.importers.sbml.splines import CubicHermiteSpline, UniformGrid\n",
+    "from amici.importers.utils import amici_time_symbol\n",
+    "\n",
+    "spline = CubicHermiteSpline(\n",
     "    sbml_id=\"f\",\n",
-    "    evaluate_at=amici.sbml_utils.amici_time_symbol,  # the spline function is evaluated at the current time point\n",
-    "    nodes=amici.splines.UniformGrid(0, 1, number_of_nodes=3),\n",
+    "    evaluate_at=amici_time_symbol,  # the spline function is evaluated at the current time point\n",
+    "    nodes=UniformGrid(0, 1, number_of_nodes=3),\n",
     "    values_at_nodes=[1, -1, 2],\n",
     ")"
    ]
@@ -485,10 +488,10 @@
    },
    "outputs": [],
    "source": [
-    "spline = amici.splines.CubicHermiteSpline(\n",
+    "spline = CubicHermiteSpline(\n",
     "    sbml_id=\"f\",\n",
-    "    evaluate_at=amici.sbml_utils.amici_time_symbol,\n",
-    "    nodes=amici.splines.UniformGrid(0, 1, number_of_nodes=3),\n",
+    "    evaluate_at=amici_time_symbol,\n",
+    "    nodes=UniformGrid(0, 1, number_of_nodes=3),\n",
     "    values_at_nodes=sp.symbols(\"f0:3\"),\n",
     ")"
    ]
@@ -619,10 +622,10 @@
    "outputs": [],
    "source": [
     "# A simple spline for which finite differencing would give a different result\n",
-    "spline = amici.splines.CubicHermiteSpline(\n",
+    "spline = CubicHermiteSpline(\n",
     "    sbml_id=\"f\",\n",
-    "    evaluate_at=amici.sbml_utils.amici_time_symbol,\n",
-    "    nodes=amici.splines.UniformGrid(0, 1, number_of_nodes=3),\n",
+    "    evaluate_at=amici_time_symbol,\n",
+    "    nodes=UniformGrid(0, 1, number_of_nodes=3),\n",
     "    values_at_nodes=[1.0, -1.0, 1.0],\n",
     "    derivatives_at_nodes=[10.0, -10.0, -10.0],\n",
     ")"
@@ -717,10 +720,10 @@
    },
    "outputs": [],
    "source": [
-    "spline = amici.splines.CubicHermiteSpline(\n",
+    "spline = CubicHermiteSpline(\n",
     "    sbml_id=\"f\",\n",
-    "    evaluate_at=amici.sbml_utils.amici_time_symbol,\n",
-    "    nodes=amici.splines.UniformGrid(0, 1, number_of_nodes=3),\n",
+    "    evaluate_at=amici_time_symbol,\n",
+    "    nodes=UniformGrid(0, 1, number_of_nodes=3),\n",
     "    values_at_nodes=[-2, 1, -1],\n",
     "    extrapolate=(\n",
     "        None,\n",
@@ -812,10 +815,10 @@
    },
    "outputs": [],
    "source": [
-    "spline = amici.splines.CubicHermiteSpline(\n",
+    "spline = CubicHermiteSpline(\n",
     "    sbml_id=\"f\",\n",
-    "    evaluate_at=amici.sbml_utils.amici_time_symbol,\n",
-    "    nodes=amici.splines.UniformGrid(0, 1, number_of_nodes=3),\n",
+    "    evaluate_at=amici_time_symbol,\n",
+    "    nodes=UniformGrid(0, 1, number_of_nodes=3),\n",
     "    values_at_nodes=[-2, 1, -2],  # first and last node must coincide\n",
     "    extrapolate=\"periodic\",\n",
     ")"
@@ -904,10 +907,10 @@
    },
    "outputs": [],
    "source": [
-    "spline = amici.splines.CubicHermiteSpline(\n",
+    "spline = CubicHermiteSpline(\n",
     "    sbml_id=\"f\",\n",
-    "    evaluate_at=amici.sbml_utils.amici_time_symbol,\n",
-    "    nodes=amici.splines.UniformGrid(0, 1, number_of_nodes=4),\n",
+    "    evaluate_at=amici_time_symbol,\n",
+    "    nodes=UniformGrid(0, 1, number_of_nodes=4),\n",
     "    values_at_nodes=[-1, 2, 4, 2],\n",
     "    bc=\"zeroderivative\",\n",
     ")"
@@ -963,10 +966,10 @@
    },
    "outputs": [],
    "source": [
-    "spline = amici.splines.CubicHermiteSpline(\n",
+    "spline = CubicHermiteSpline(\n",
     "    sbml_id=\"f\",\n",
-    "    evaluate_at=amici.sbml_utils.amici_time_symbol,\n",
-    "    nodes=amici.splines.UniformGrid(0, 1, number_of_nodes=4),\n",
+    "    evaluate_at=amici_time_symbol,\n",
+    "    nodes=UniformGrid(0, 1, number_of_nodes=4),\n",
     "    values_at_nodes=[-1, 2, 4, 2],\n",
     "    bc=\"natural\",\n",
     ")"
@@ -1029,10 +1032,10 @@
    },
    "outputs": [],
    "source": [
-    "spline = amici.splines.CubicHermiteSpline(\n",
+    "spline = CubicHermiteSpline(\n",
     "    sbml_id=\"f\",\n",
-    "    evaluate_at=amici.sbml_utils.amici_time_symbol,\n",
-    "    nodes=amici.splines.UniformGrid(0, 1, number_of_nodes=5),\n",
+    "    evaluate_at=amici_time_symbol,\n",
+    "    nodes=UniformGrid(0, 1, number_of_nodes=5),\n",
     "    values_at_nodes=[2, 0.05, 0.1, 2, 1],\n",
     ")"
    ]
@@ -1068,10 +1071,10 @@
    },
    "outputs": [],
    "source": [
-    "spline = amici.splines.CubicHermiteSpline(\n",
+    "spline = CubicHermiteSpline(\n",
     "    sbml_id=\"f\",\n",
-    "    evaluate_at=amici.sbml_utils.amici_time_symbol,\n",
-    "    nodes=amici.splines.UniformGrid(0, 1, number_of_nodes=5),\n",
+    "    evaluate_at=amici_time_symbol,\n",
+    "    nodes=UniformGrid(0, 1, number_of_nodes=5),\n",
     "    values_at_nodes=[2, 0.05, 0.1, 2, 1],\n",
     "    logarithmic_parametrization=True,\n",
     ")"
@@ -1191,10 +1194,10 @@
     "df = None\n",
     "for n in num_nodes + amici_only_nodes:\n",
     "    # Create model\n",
-    "    spline = amici.splines.CubicHermiteSpline(\n",
+    "    spline = CubicHermiteSpline(\n",
     "        sbml_id=\"f\",\n",
-    "        evaluate_at=amici.sbml_utils.amici_time_symbol,\n",
-    "        nodes=amici.splines.UniformGrid(0, 1, number_of_nodes=n),\n",
+    "        evaluate_at=amici_time_symbol,\n",
+    "        nodes=UniformGrid(0, 1, number_of_nodes=n),\n",
     "        values_at_nodes=np.random.rand(n),\n",
     "    )\n",
     "    sbml_doc = libsbml.SBMLReader().readSBML(\"example_splines.xml\")\n",

doc/examples/example_splines_swameye/ExampleSplinesSwameye2003.ipynb

@@ -53,12 +53,14 @@
     "import os\n",
     "\n",
     "import amici\n",
+    "import amici.importers.sbml.splines as splines\n",
     "import libsbml\n",
     "import numpy as np\n",
     "import pandas as pd\n",
     "import petab\n",
     "import pypesto.petab\n",
     "import sympy as sp\n",
+    "from amici.importers.utils import amici_time_symbol\n",
     "from matplotlib import pyplot as plt"
    ]
   },
@@ -176,9 +178,9 @@
     "values_at_nodes = [\n",
     "    sp.Symbol(f\"pEpoR_t{str(t).replace('.', '_dot_')}\") for t in nodes\n",
     "]  # new parameter symbols for spline values\n",
-    "spline = amici.splines.CubicHermiteSpline(\n",
+    "spline = splines.CubicHermiteSpline(\n",
     "    sbml_id=\"pEpoR\",  # matches name of species in SBML model\n",
-    "    evaluate_at=amici.sbml_utils.amici_time_symbol,  # the spline is evaluated at the current time\n",
+    "    evaluate_at=amici_time_symbol,  # the spline is evaluated at the current time\n",
     "    nodes=nodes,\n",
     "    values_at_nodes=values_at_nodes,  # values at the nodes (in linear scale)\n",
     "    extrapolate=(None, \"constant\"),  # because steady state is reached\n",
@@ -782,9 +784,9 @@
     "values_at_nodes = [\n",
     "    sp.Symbol(f\"pEpoR_t{str(t).replace('.', '_dot_')}\") for t in nodes\n",
     "]\n",
-    "spline = amici.splines.CubicHermiteSpline(\n",
+    "spline = splines.CubicHermiteSpline(\n",
     "    sbml_id=\"pEpoR\",\n",
-    "    evaluate_at=amici.sbml_utils.amici_time_symbol,\n",
+    "    evaluate_at=amici_time_symbol,\n",
     "    nodes=nodes,\n",
     "    values_at_nodes=values_at_nodes,\n",
     "    extrapolate=(None, \"constant\"),\n",
@@ -1492,9 +1494,9 @@
     "    sp.Symbol(f\"derivative_pEpoR_t{str(t).replace('.', '_dot_')}\")\n",
     "    for t in nodes[:-1]\n",
     "]\n",
-    "spline = amici.splines.CubicHermiteSpline(\n",
+    "spline = splines.CubicHermiteSpline(\n",
     "    sbml_id=\"pEpoR\",\n",
-    "    evaluate_at=amici.sbml_utils.amici_time_symbol,\n",
+    "    evaluate_at=amici_time_symbol,\n",
     "    nodes=nodes,\n",
     "    values_at_nodes=values_at_nodes,\n",
     "    derivatives_at_nodes=derivatives_at_nodes\n",
@@ -1591,7 +1593,9 @@
    "source": [
     "# Derivative parameters must be added separately\n",
     "for p in derivatives_at_nodes:\n",
-    "    amici.sbml_utils.add_parameter(sbml_model, p, value=0.0, constant=True)"
+    "    amici.importers.sbml.utils.add_parameter(\n",
+    "        sbml_model, p, value=0.0, constant=True\n",
+    "    )"
    ]
   },
   {

doc/examples/example_steady_states/ExampleEquilibrationLogic.ipynb

@@ -109,7 +109,7 @@
     "from amici import (\n",
     "    MeasurementChannel as MC,\n",
     ")\n",
-    "from amici.antimony_import import antimony2sbml\n",
+    "from amici.importers.antimony import antimony2sbml\n",
     "from amici.plotting import (\n",
     "    plot_observable_trajectories,\n",
     "    plot_state_trajectories,\n",

doc/python_interface.rst

@@ -19,7 +19,7 @@ SBML import
 -----------
 
 AMICI can import :term:`SBML` models via the
-:py:func:`amici.sbml_import.SbmlImporter` class.
+:py:func:`amici.importers.sbml.SbmlImporter` class.
 
 .. _amici_python_sbml_support:
 
@@ -113,13 +113,13 @@ PySB import
 -----------
 
 AMICI can import :term:`PySB` models via
-:py:func:`amici.pysb_import.pysb2amici`.
+:py:func:`amici.importers.pysb.pysb2amici`.
 
 BNGL import
 -----------
 
 AMICI can import :term:`BNGL` models via
-:py:func:`amici.bngl_import.bngl2amici`.
+:py:func:`amici.importers.bngl.bngl2amici`.
 
 PEtab import
 ------------
@@ -162,7 +162,7 @@ An example using Antimony to specify the Lotka-Volterra equations is shown below
     end
     """
     module_name = "test_antimony_example_lv"
-    from amici.antimony_import import antimony2amici
+    from amici.importers.antimony import antimony2amici
     antimony2amici(
         ant_model,
         model_name=module_name,

doc/python_modules.rst

@@ -8,9 +8,15 @@ AMICI Python API
 
    amici
    amici.amici
-   amici.sbml_import
-   amici.pysb_import
-   amici.bngl_import
+   amici.importers.utils
+   amici.importers.sbml
+   amici.importers.sbml.conserved_quantities_demartino
+   amici.importers.sbml.conserved_quantities_rref
+   amici.importers.sbml.utils
+   amici.importers.sbml.splines
+   amici.importers.pysb
+   amici.importers.bngl
+   amici.importers.antimony
    amici.petab
    amici.petab.conditions
    amici.petab.import_helpers
@@ -21,7 +27,6 @@ AMICI Python API
    amici.petab.sbml_import
    amici.petab.simulations
    amici.petab.simulator
-   amici.import_utils
    amici.jax
    amici.exporters.sundials.de_export
    amici.de_model
@@ -30,9 +35,5 @@ AMICI Python API
    amici.pandas
    amici.logging
    amici.gradient_check
-   amici.conserved_quantities_demartino
-   amici.conserved_quantities_rref
    amici.numpy
-   amici.sbml_utils
-   amici.splines
    amici.adapters.fiddy

python/benchmark/benchmark_pysb.py

@@ -15,7 +15,7 @@
 import numpy as np
 import pandas as pd
 import pysb
-from amici.pysb_import import pysb2amici
+from amici.importers.pysb import pysb2amici
 from pysb.simulator import ScipyOdeSimulator
 
 sys.path.insert(0, os.path.join("..", "tests"))

python/sdist/amici/__init__.py

@@ -178,11 +178,11 @@ def get_model_dir(model_id: str | None = None, jax: bool = False) -> Path:
     # These modules don't require the swig interface
     from typing import Protocol, runtime_checkable
 
-    from .import_utils import MeasurementChannel  # noqa: F401
-    from .sbml_import import (  # noqa: F401
+    from .importers.sbml import (  # noqa: F401
         SbmlImporter,
         assignment_rules_to_observables,
     )
+    from .importers.utils import MeasurementChannel  # noqa: F401
 
     try:
         from .jax import JAXModel

python/sdist/amici/de_model.py

@@ -45,7 +45,7 @@
     var_in_function_signature,
 )
 from .exporters.sundials.cxxcodeprinter import csc_matrix
-from .import_utils import (
+from .importers.utils import (
     ObservableTransformation,
     SBMLException,
     _default_simplify,
@@ -63,7 +63,7 @@
 )
 
 if TYPE_CHECKING:
-    from .splines import AbstractSpline
+    from amici.importers.sbml.splines import AbstractSpline
 
 logger = get_logger(__name__, logging.ERROR)
 

python/sdist/amici/de_model_components.py

@@ -7,7 +7,7 @@
 import sympy as sp
 
 from .constants import SymbolId
-from .import_utils import (
+from .importers.utils import (
     RESERVED_SYMBOLS,
     ObservableTransformation,
     amici_time_symbol,