Reorganize package: amici.exporters.sundials (#3021)

Move modules and templates related to generating C++ code for simulation with sundials solvers to `amici.exporters.sundials`.

Author: dweindl

.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