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/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:
 

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.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/sdist/amici/__init__.py

@@ -11,7 +11,6 @@
 import importlib.util
 import os
 import re
-import sys
 import warnings
 from collections.abc import Callable
 from pathlib import Path
@@ -178,11 +177,11 @@ 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,

python/sdist/amici/exporters/sundials/cxxcodeprinter.py

@@ -12,7 +12,7 @@
 from sympy.utilities.iterables import numbered_symbols
 from toposort import toposort
 
-from ...import_utils import symbol_with_assumptions
+from amici.importers.utils import symbol_with_assumptions
 
 
 class AmiciCxxCodePrinter(CXX11CodePrinter):

python/sdist/amici/exporters/sundials/de_export.py

@@ -28,10 +28,10 @@
     __commit__,
     __version__,
     get_model_dir,
-    splines,
 )
 from ...de_model import DEModel
 from ...de_model_components import *
+from ...importers.sbml import splines
 from ...logging import get_logger, log_execution_time, set_log_level
 from ...sympy_utils import (
     _custom_pow_eval_derivative,

python/sdist/amici/importers/__init__.py

@@ -0,0 +1,81 @@
+"""Unified model import interface for AMICI.
+
+This subpackage aggregates functionality for importing models from various
+formats into AMICI.
+
+Re-exported symbols (imported conditionally where dependencies are optional):
+- SBML:    `SbmlImporter` (requires `libsbml` and related deps)
+- PySB:    `pysb2amici`, `pysb2jax`, `ode_model_from_pysb_importer` (requires `pysb`)
+- Antimony:`antimony2sbml`, `antimony2amici` (requires `antimony` Python package)
+- Utils:   `MeasurementChannel`, noise helpers, `RESERVED_SYMBOLS`,
+           `ObservableTransformation`
+"""
+
+from __future__ import annotations
+
+# Utils are internal and safe to import unconditionally
+from .utils import (
+    RESERVED_SYMBOLS,
+    MeasurementChannel,
+    ObservableTransformation,
+    noise_distribution_to_cost_function,
+    noise_distribution_to_observable_transformation,
+)
+
+__all__: list[str] = [
+    # Utils
+    "MeasurementChannel",
+    "noise_distribution_to_cost_function",
+    "noise_distribution_to_observable_transformation",
+    "RESERVED_SYMBOLS",
+    "ObservableTransformation",
+]
+
+# SBML importer (optional)
+try:
+    from .sbml import (
+        SbmlImporter,  # noqa: E402,F401
+        sbml2jax,  # noqa: E402,F401
+        smbl2amici,  # noqa: E402,F401
+    )
+
+    __all__ += [
+        "sbml2amici",
+        "sbml2jax",
+        "SbmlImporter",
+    ]
+except Exception:
+    # Leave unavailable if optional dependency is missing
+    pass
+
+# PySB importer (optional)
+try:
+    from .pysb import (
+        ode_model_from_pysb_importer,  # noqa: E402,F401
+        pysb2amici,  # noqa: E402,F401
+        pysb2jax,  # noqa: E402,F401
+    )
+
+    __all__ += [
+        "pysb2amici",
+        "pysb2jax",
+        "ode_model_from_pysb_importer",
+    ]
+except Exception:
+    pass
+
+# Antimony importer (optional)
+try:
+    from .antimony import antimony2amici, antimony2sbml  # noqa: E402,F401
+
+    __all__ += ["antimony2sbml", "antimony2amici"]
+except Exception:
+    pass
+
+# BNGL importer (optional)
+try:
+    from .bngl import bngl2amici  # noqa: E402,F401
+
+    __all__.append("bngl2amici")
+except Exception:
+    pass

python/sdist/amici/antimony_import.py → python/sdist/amici/importers/antimony/__init__.py

@@ -53,7 +53,7 @@ def antimony2amici(ant_model: str | Path, *args, **kwargs):
 
     For documentation see :meth:`amici.sbml_import.SbmlImporter.sbml2amici`.
     """
-    from .sbml_import import SbmlImporter
+    from amici.importers.sbml import SbmlImporter
 
     sbml_str = antimony2sbml(ant_model)
     sbml_importer = SbmlImporter(sbml_str, from_file=False)

python/sdist/amici/bngl_import.py → python/sdist/amici/importers/bngl/__init__.py

@@ -7,7 +7,7 @@
 
 from pysb.importers.bngl import model_from_bngl
 
-from .pysb_import import pysb2amici
+from ..pysb import pysb2amici
 
 
 def bngl2amici(bngl_model: str, *args, **kwargs) -> None:

python/sdist/amici/pysb_import.py → python/sdist/amici/importers/pysb/__init__.py

@@ -23,9 +23,8 @@
 import sympy as sp
 
 import amici
-
-from .de_model import DEModel
-from .de_model_components import (
+from amici.de_model import DEModel
+from amici.de_model_components import (
     Constant,
     DifferentialState,
     Event,
@@ -37,7 +36,7 @@
     Parameter,
     SigmaY,
 )
-from .import_utils import (
+from amici.importers.utils import (
     MeasurementChannel,
     _default_simplify,
     _get_str_symbol_identifiers,
@@ -46,7 +45,7 @@
     noise_distribution_to_cost_function,
     noise_distribution_to_observable_transformation,
 )
-from .logging import get_logger, log_execution_time, set_log_level
+from amici.logging import get_logger, log_execution_time, set_log_level
 
 CL_Prototype = dict[str, dict[str, Any]]
 ConservationLaw = dict[str, dict | str | sp.Basic]
@@ -267,7 +266,7 @@ def pysb2amici(
         events=_events,
     )
 
-    from .exporters.sundials.de_export import (
+    from amici.exporters.sundials.de_export import (
         DEExporter,
     )
 

python/sdist/amici/sbml_import.py → python/sdist/amici/importers/sbml/__init__.py

@@ -27,12 +27,13 @@
 from sympy.matrices.dense import MutableDenseMatrix
 
 import amici
-
-from . import get_model_dir, has_clibs
-from .constants import SymbolId
-from .de_model import DEModel
-from .de_model_components import Expression, symbol_to_type
-from .import_utils import (
+from amici import get_model_dir, has_clibs
+from amici.constants import SymbolId
+from amici.de_model import DEModel
+from amici.de_model_components import Expression, symbol_to_type
+from amici.importers.sbml.splines import AbstractSpline
+from amici.importers.sbml.utils import SBMLException
+from amici.importers.utils import (
     RESERVED_SYMBOLS,
     MeasurementChannel,
     _check_unsupported_functions,
@@ -55,10 +56,8 @@
     symbol_with_assumptions,
     toposort_symbols,
 )
-from .logging import get_logger, log_execution_time, set_log_level
-from .sbml_utils import SBMLException
-from .splines import AbstractSpline
-from .sympy_utils import smart_is_zero_matrix, smart_multiply
+from amici.logging import get_logger, log_execution_time, set_log_level
+from amici.sympy_utils import smart_is_zero_matrix, smart_multiply
 
 SymbolicFormula = dict[sp.Symbol, sp.Expr]
 
@@ -398,7 +397,7 @@ def sbml2amici(
 
         output_dir = output_dir or get_model_dir(model_name)
 
-        from .exporters.sundials.de_export import (
+        from amici.exporters.sundials.de_export import (
             DEExporter,
         )
 
@@ -2947,7 +2946,7 @@ def _transform_dxdt_to_concentration(
         an assignment or rate rule.
 
         :param species_id:
-            The identifier of the species (generated in "sbml_import.py").
+            The identifier of the species (generated in "__init__.py").
 
         :param dxdt:
             The element-wise product of the row in the stoichiometric

python/sdist/amici/conserved_quantities_demartino.py → python/sdist/amici/importers/sbml/conserved_quantities_demartino.py

@@ -4,7 +4,7 @@
 import sys
 from collections.abc import MutableSequence, Sequence
 
-from .logging import get_logger
+from amici.logging import get_logger
 
 logger = get_logger(__name__, logging.ERROR)