Reorganize package: amici.exporters.sundials

.github/workflows/test_sbml_semantic_test_suite.yml

@@ -7,7 +7,7 @@ on:
   pull_request:
     paths:
       - .github/workflows/test_sbml_semantic_test_suite.yml
-      - python/sdist/amici/de_export.py
+      - 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

CMakeLists.txt

@@ -143,7 +143,8 @@ else()
   set(VENDORED_SUNDIALS_INSTALL_DIR ${VENDORED_SUNDIALS_BUILD_DIR})
 endif()
 set(SUNDIALS_ROOT "${VENDORED_SUNDIALS_INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}")
-find_package(SUNDIALS 7.1.1 REQUIRED CONFIG PATHS "${SUNDIALS_ROOT}/cmake/sundials/" )
+find_package(SUNDIALS 7.1.1 REQUIRED CONFIG PATHS
+             "${SUNDIALS_ROOT}/cmake/sundials/")
 message(STATUS "Found SUNDIALS: ${SUNDIALS_DIR}")
 
 set(GSL_LITE_INCLUDE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/ThirdParty/gsl")
@@ -306,22 +307,25 @@ if(AMICI_PYTHON_BUILD_EXT_ONLY)
                           "gsl_CONFIG_NARROW_THROWS_ON_TRUNCATION=1")
 endif()
 
-# Create targets to make the sources show up in IDEs for convenience
-# For template files
-add_custom_target(
-  fileTemplates
-  SOURCES src/CMakeLists.template.cmake
-          src/main.template.cpp
-          src/model_header.template.h
-          src/model.template.cpp
-          src/wrapfunctions.template.h
-          src/wrapfunctions.template.cpp
-          swig/CMakeLists_model.cmake
-          swig/modelname.template.i
-  COMMENT "Dummy target for SWIG files")
-set_target_properties(
-  fileTemplates PROPERTIES INCLUDE_DIRECTORIES
-                           "${CMAKE_CURRENT_SOURCE_DIR}/include/")
+if(NOT AMICI_PYTHON_BUILD_EXT_ONLY)
+  # Create targets to make the sources show up in IDEs for convenience For
+  # template files
+  set(template_dir "python/sdist/amici/exporters/sundials/templates")
+  add_custom_target(
+    fileTemplates
+    SOURCES ${template_dir}/CMakeLists.template.cmake
+            ${template_dir}//main.template.cpp
+            ${template_dir}//model_header.template.h
+            ${template_dir}//model.template.cpp
+            ${template_dir}//wrapfunctions.template.h
+            ${template_dir}//wrapfunctions.template.cpp
+            ${template_dir}//CMakeLists_model.cmake
+            ${template_dir}//modelname.template.i
+    COMMENT "Dummy target for SWIG files")
+  set_target_properties(
+    fileTemplates PROPERTIES INCLUDE_DIRECTORIES
+                             "${CMAKE_CURRENT_SOURCE_DIR}/include/")
+endif()
 
 if(NOT AMICI_PYTHON_BUILD_EXT_ONLY)
   include(clang-tools)

doc/python_modules.rst

@@ -23,7 +23,7 @@ AMICI Python API
    amici.petab.simulator
    amici.import_utils
    amici.jax
-   amici.de_export
+   amici.exporters.sundials.de_export
    amici.de_model
    amici.de_model_components
    amici.plotting

python/sdist/MANIFEST.in

@@ -5,6 +5,7 @@ recursive-include amici/cmake *
 recursive-include amici/include/amici *.h
 recursive-include amici/src *
 recursive-include amici/swig *
+recursive-include amici/exporters/sundials/templates *
 include amici/*
 include version.txt
 include LICENSE.md

python/sdist/amici/__init__.py

@@ -178,7 +178,6 @@ 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 .de_export import DEExporter  # noqa: F401
     from .import_utils import MeasurementChannel  # noqa: F401
     from .sbml_import import (  # noqa: F401
         SbmlImporter,

python/sdist/amici/de_model.py

@@ -15,13 +15,6 @@
 import sympy as sp
 from sympy import ImmutableDenseMatrix, MutableDenseMatrix
 
-from ._codegen.cxx_functions import (
-    nobody_functions,
-    sensi_functions,
-    sparse_functions,
-    var_in_function_signature,
-)
-from .cxxcodeprinter import csc_matrix
 from .de_model_components import (
     AlgebraicEquation,
     AlgebraicState,
@@ -45,6 +38,13 @@
     SigmaZ,
     State,
 )
+from .exporters.sundials.cxx_functions import (
+    nobody_functions,
+    sensi_functions,
+    sparse_functions,
+    var_in_function_signature,
+)
+from .exporters.sundials.cxxcodeprinter import csc_matrix
 from .import_utils import (
     ObservableTransformation,
     SBMLException,
@@ -1135,18 +1135,14 @@ def _generate_symbol(self, name: str) -> None:
                 components = sorted(
                     components,
                     key=lambda x: int(
-                        x.get_id().replace(
-                            "observableParameter", ""
-                        )
+                        x.get_id().replace("observableParameter", "")
                     ),
                 )
             if name == "np":
                 components = sorted(
                     components,
                     key=lambda x: int(
-                        x.get_id().replace(
-                            "noiseParameter", ""
-                        )
+                        x.get_id().replace("noiseParameter", "")
                     ),
                 )
             self._syms[name] = sp.Matrix(
@@ -1213,8 +1209,7 @@ def _generate_symbol(self, name: str) -> None:
                 [
                     [
                         sp.Symbol(
-                            f"s{tcl.get_id()}__"
-                            f"{par.get_id()}",
+                            f"s{tcl.get_id()}__{par.get_id()}",
                             real=True,
                         )
                         for par in self._parameters

python/sdist/amici/cxxcodeprinter.py → 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 ...import_utils import symbol_with_assumptions
 
 
 class AmiciCxxCodePrinter(CXX11CodePrinter):

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

@@ -24,16 +24,23 @@
 
 import sympy as sp
 
-from . import (
+from ... import (
     __commit__,
     __version__,
-    amiciModulePath,
-    amiciSrcPath,
-    amiciSwigPath,
     get_model_dir,
     splines,
 )
-from ._codegen.cxx_functions import (
+from ...de_model import DEModel
+from ...de_model_components import *
+from ...logging import get_logger, log_execution_time, set_log_level
+from ...sympy_utils import (
+    _custom_pow_eval_derivative,
+    _monkeypatched,
+    smart_is_zero_matrix,
+)
+from ..template import apply_template
+from .compile import build_model_extension
+from .cxx_functions import (
     _FunctionInfo,
     event_functions,
     event_sensi_functions,
@@ -44,38 +51,25 @@
     sparse_functions,
     sparse_sensi_functions,
 )
-from ._codegen.model_class import (
-    get_function_extern_declaration,
-    get_model_override_implementation,
-    get_sunindex_extern_declaration,
-    get_sunindex_override_implementation,
-)
-from ._codegen.template import apply_template
-from .compile import build_model_extension
 from .cxxcodeprinter import (
     AmiciCxxCodePrinter,
     get_initializer_list,
     get_switch_statement,
 )
-from .de_model import DEModel
-from .de_model_components import *
-from .logging import get_logger, log_execution_time, set_log_level
-from .sympy_utils import (
-    _custom_pow_eval_derivative,
-    _monkeypatched,
-    smart_is_zero_matrix,
+from .model_class import (
+    get_function_extern_declaration,
+    get_model_override_implementation,
+    get_sunindex_extern_declaration,
+    get_sunindex_override_implementation,
 )
 
+TEMPLATE_DIR = Path(__file__).parent / "templates"
 # Template for model simulation main.cpp file
-CXX_MAIN_TEMPLATE_FILE = os.path.join(amiciSrcPath, "main.template.cpp")
+CXX_MAIN_TEMPLATE_FILE = TEMPLATE_DIR / "main.template.cpp"
 # Template for model/swig/CMakeLists.txt
-SWIG_CMAKE_TEMPLATE_FILE = os.path.join(
-    amiciSwigPath, "CMakeLists_model.cmake"
-)
+SWIG_CMAKE_TEMPLATE_FILE = TEMPLATE_DIR / "CMakeLists_model.cmake"
 # Template for model/CMakeLists.txt
-MODEL_CMAKE_TEMPLATE_FILE = os.path.join(
-    amiciSrcPath, "CMakeLists.template.cmake"
-)
+MODEL_CMAKE_TEMPLATE_FILE = TEMPLATE_DIR / "CMakeLists.template.cmake"
 
 IDENTIFIER_PATTERN = re.compile(r"^[a-zA-Z_]\w*$")
 
@@ -950,7 +944,7 @@ def _write_wrapfunctions_cpp(self) -> None:
         """
         template_data = {"MODELNAME": self.model_name}
         apply_template(
-            os.path.join(amiciSrcPath, "wrapfunctions.template.cpp"),
+            TEMPLATE_DIR / "wrapfunctions.template.cpp",
             os.path.join(self.model_path, "wrapfunctions.cpp"),
             template_data,
         )
@@ -961,7 +955,7 @@ def _write_wrapfunctions_header(self) -> None:
         """
         template_data = {"MODELNAME": str(self.model_name)}
         apply_template(
-            os.path.join(amiciSrcPath, "wrapfunctions.template.h"),
+            TEMPLATE_DIR / "wrapfunctions.template.h",
             os.path.join(self.model_path, "wrapfunctions.h"),
             template_data,
         )
@@ -1184,13 +1178,13 @@ def event_initializer_list() -> str:
         tpl_data = {k: str(v) for k, v in tpl_data.items()}
 
         apply_template(
-            os.path.join(amiciSrcPath, "model_header.template.h"),
+            TEMPLATE_DIR / "model_header.template.h",
             os.path.join(self.model_path, f"{self.model_name}.h"),
             tpl_data,
         )
 
         apply_template(
-            os.path.join(amiciSrcPath, "model.template.cpp"),
+            TEMPLATE_DIR / "model.template.cpp",
             os.path.join(self.model_path, f"{self.model_name}.cpp"),
             tpl_data,
         )
@@ -1256,7 +1250,7 @@ def _write_swig_files(self) -> None:
         Path(self.model_swig_path).mkdir(exist_ok=True)
         template_data = {"MODELNAME": self.model_name}
         apply_template(
-            Path(amiciSwigPath, "modelname.template.i"),
+            TEMPLATE_DIR / "modelname.template.i",
             Path(self.model_swig_path, self.model_name + ".i"),
             template_data,
         )
@@ -1276,20 +1270,20 @@ def _write_module_setup(self) -> None:
             "PACKAGE_VERSION": "0.1.0",
         }
         apply_template(
-            Path(amiciModulePath, "setup.template.py"),
+            TEMPLATE_DIR / "setup.template.py",
             Path(self.model_path, "setup.py"),
             template_data,
         )
         apply_template(
-            Path(amiciModulePath, "MANIFEST.template.in"),
+            TEMPLATE_DIR / "MANIFEST.template.in",
             Path(self.model_path, "MANIFEST.in"),
             {},
         )
         # write __init__.py for the model module
         Path(self.model_path, self.model_name).mkdir(exist_ok=True)
 
         apply_template(
-            Path(amiciModulePath, "__init__.template.py"),
+            TEMPLATE_DIR / "__init__.template.py",
             Path(self.model_path, self.model_name, "__init__.py"),
             template_data,
         )

python/sdist/amici/setup.template.py → python/sdist/amici/exporters/sundials/templates/setup.template.py

@@ -5,11 +5,10 @@
 import sys
 from pathlib import Path
 
-from cmake_build_extension import CMakeExtension
-from setuptools import find_namespace_packages, setup
-
 from amici import _get_amici_path
 from amici.custom_commands import AmiciBuildCMakeExtension
+from cmake_build_extension import CMakeExtension
+from setuptools import find_namespace_packages, setup
 
 
 def get_extension() -> CMakeExtension:

python/sdist/amici/jax/nn.py

@@ -4,7 +4,8 @@
 import jax.numpy as jnp
 
 from amici import amiciModulePath
-from amici._codegen.template import apply_template
+
+from ..exporters.template import apply_template
 
 
 class Flatten(eqx.Module):

python/sdist/amici/jax/ode_export.py

@@ -21,9 +21,9 @@
 from amici import (
     amiciModulePath,
 )
-from amici._codegen.template import apply_template
-from amici.de_export import is_valid_identifier
 from amici.de_model import DEModel
+from amici.exporters.sundials.de_export import is_valid_identifier
+from amici.exporters.template import apply_template
 from amici.jax.jaxcodeprinter import AmiciJaxCodePrinter, _jnp_array_str
 from amici.jax.model import JAXModel
 from amici.jax.nn import generate_equinox

python/sdist/amici/pysb_import.py

@@ -24,18 +24,19 @@
 
 import amici
 
-from .de_export import (
+from .de_model import DEModel
+from .de_model_components import (
     Constant,
-    DEExporter,
     DifferentialState,
+    Event,
     Expression,
     LogLikelihoodY,
+    NoiseParameter,
     Observable,
+    ObservableParameter,
     Parameter,
     SigmaY,
 )
-from .de_model import DEModel
-from .de_model_components import Event, NoiseParameter, ObservableParameter
 from .import_utils import (
     MeasurementChannel,
     _default_simplify,
@@ -265,6 +266,11 @@ def pysb2amici(
         pysb_model_has_obs_and_noise=pysb_model_has_obs_and_noise,
         events=_events,
     )
+
+    from .exporters.sundials.de_export import (
+        DEExporter,
+    )
+
     exporter = DEExporter(
         ode_model,
         outdir=output_dir,

python/sdist/amici/sbml_import.py

@@ -30,9 +30,6 @@
 
 from . import get_model_dir, has_clibs
 from .constants import SymbolId
-from .de_export import (
-    DEExporter,
-)
 from .de_model import DEModel
 from .de_model_components import Expression, symbol_to_type
 from .import_utils import (
@@ -401,6 +398,10 @@ def sbml2amici(
 
         output_dir = output_dir or get_model_dir(model_name)
 
+        from .exporters.sundials.de_export import (
+            DEExporter,
+        )
+
         exporter = DEExporter(
             ode_model,
             model_name=model_name,

python/tests/test_cxxcodeprinter.py

@@ -1,6 +1,6 @@
 import pytest
 import sympy as sp
-from amici.cxxcodeprinter import AmiciCxxCodePrinter
+from amici.exporters.sundials.cxxcodeprinter import AmiciCxxCodePrinter
 from amici.testing import skip_on_valgrind
 from sympy.codegen.rewriting import optims_c99