Move sundials-related functionality to amici.sim.sundials.*

Related to #3041.

Author: dweindl

.github/workflows/test_conda_install.yml

@@ -47,7 +47,7 @@ jobs:
       - name: Test import
         shell: bash -l {0}
         run: |
-          python -c "from amici import _amici; print(_amici)"
+          python -c "from amici._installation import _amici; print(_amici)"
           python -m amici
       - name: Run SBML import test
         shell: bash -l {0}

.gitignore

@@ -155,13 +155,13 @@ python/tests/piecewise_test/*
 
 python/sdist/amici.egg-info/*
 python/sdist/amici/version.txt
-python/sdist/amici/amici.py
-python/sdist/amici/amici_wrap.cxx
-python/sdist/amici/amici_without_hdf5.py
-python/sdist/amici/amici_wrap_without_hdf5.cxx
-python/sdist/amici/include/
-python/sdist/amici/lib/
-python/sdist/amici/share/
+python/sdist/amici/_installation/amici.py
+python/sdist/amici/_installation/amici_wrap.cxx
+python/sdist/amici/_installation/amici_without_hdf5.py
+python/sdist/amici/_installation/amici_wrap_without_hdf5.cxx
+python/sdist/amici/_installation/include/
+python/sdist/amici/_installation/lib/
+python/sdist/amici/_installation/share/
 python/sdist/build/*
 python/sdist/amici/git_version.txt
 

doc/conf.py

@@ -93,7 +93,7 @@ def install_doxygen():
 # -- Mock out some problematic modules-------------------------------------
 
 # Note that for sub-modules, all parent modules must be listed explicitly.
-autodoc_mock_imports = ["_amici", "amici._amici"]
+autodoc_mock_imports = ["_amici", "amici._installation._amici"]
 for mod_name in autodoc_mock_imports:
     sys.modules[mod_name] = mock.MagicMock()
 
@@ -363,7 +363,7 @@ def install_doxygen():
     "BoolVector": ":class:`bool`",
     "DoubleVector": ":class:`float`",
     "StringVector": ":class:`str`",
-    "ExpDataPtrVector": ":class:`amici.amici.ExpData`",
+    "ExpDataPtrVector": ":class:`amici.sim.sundials.ExpData`",
 }
 
 # TODO: alias for forward type definition, remove after release of petab_sciml

doc/python_modules.rst

@@ -7,7 +7,6 @@ AMICI Python API
    :toctree: generated
 
    amici
-   amici.amici
    amici.importers.utils
    amici.importers.sbml
    amici.importers.sbml.conserved_quantities_demartino
@@ -29,9 +28,8 @@ AMICI Python API
    amici.importers.petab.v1.simulator
    amici.jax
    amici.exporters.sundials.de_export
-   amici.plotting
-   amici.pandas
+   amici.sim.sundials
+   amici.sim.sundials.plotting
+   amici.sim.sundials.gradient_check
    amici.logging
-   amici.gradient_check
-   amici.numpy
    amici.adapters.fiddy

python/CMakeLists.txt

@@ -1,3 +1,9 @@
+# Build and install the AMICI Python package
+#
+# This file is not part of the AMICI Python package itself, but is included
+# in the main CMakeLists.txt to provide targets for building and installing
+# the AMICI Python package.
+
 if(DEFINED ENV{PYTHON_EXECUTABLE})
   set(Python3_EXECUTABLE $ENV{PYTHON_EXECUTABLE})
 endif()

python/sdist/MANIFEST.in

@@ -1,20 +1,20 @@
-recursive-include amici/ThirdParty/SuiteSparse *
-recursive-include amici/ThirdParty/sundials *
-recursive-include amici/ThirdParty/gsl *.hpp
-recursive-include amici/cmake *
-recursive-include amici/include/amici *.h
-recursive-include amici/src *
-recursive-include amici/swig *
+recursive-include amici/_installation/ThirdParty/SuiteSparse *
+recursive-include amici/_installation/ThirdParty/sundials *
+recursive-include amici/_installation/ThirdParty/gsl *.hpp
+recursive-include amici/_installation/cmake *
+recursive-include amici/_installation/include/amici *.h
+recursive-include amici/_installation/src *
+recursive-include amici/_installation/swig *
 recursive-include amici/exporters/sundials/templates *
 include amici/*
 include version.txt
 include LICENSE.md
-exclude amici/*.so
-exclude amici/*.dll
+exclude amici/_installation/*.so
+exclude amici/_installation/*.dll
 prune **/build
 prune **/install
-prune amici/share
-prune amici/lib
-prune amici/ThirdParty/SuiteSparse/lib
-prune amici/ThirdParty/SuiteSparse/include
+prune amici/_installation/share
+prune amici/_installation/lib
+prune amici/_installation/ThirdParty/SuiteSparse/lib
+prune amici/_installation/ThirdParty/SuiteSparse/include
 prune __pycache__

python/sdist/amici/CMakeLists.txt

@@ -135,49 +135,15 @@ def get_model_dir(model_id: str | None = None, jax: bool = False) -> Path:
 amiciSrcPath = os.path.join(amici_path, "src")
 #: absolute root path of the amici module
 amiciModulePath = os.path.dirname(__file__)
-#: boolean indicating if this is the full package with swig interface or
-#  the raw package without extension
-has_clibs: bool = any(
-    os.path.isfile(os.path.join(amici_path, wrapper))
-    for wrapper in ["amici.py", "amici_without_hdf5.py"]
-)
-#: boolean indicating if amici was compiled with hdf5 support
-hdf5_enabled: bool = False
+
 
 # Get version number from file
-with open(os.path.join(amici_path, "version.txt")) as f:
+with open(os.path.join(amici_path, "_installation", "version.txt")) as f:
     __version__ = f.read().strip()
 
 __commit__ = _get_commit_hash()
 
-# Import SWIG module and swig-dependent submodules if required and available
 if not _imported_from_setup():
-    if has_clibs:
-        # prevent segfaults under pytest
-        #  see also:
-        #  https://github.com/swig/swig/issues/2881
-        #  https://github.com/AMICI-dev/AMICI/issues/2565
-        with warnings.catch_warnings():
-            warnings.filterwarnings(
-                "ignore",
-                category=DeprecationWarning,
-                message="builtin type .* has no __module__ attribute",
-            )
-            from . import amici
-
-        from .amici import *
-
-        # has to be done before importing readSolverSettingsFromHDF5
-        #  from .swig_wrappers
-        hdf5_enabled = "readSolverSettingsFromHDF5" in dir()
-        # These modules require the swig interface and other dependencies
-        from .numpy import ExpDataView, ReturnDataView  # noqa: F401
-        from .pandas import *
-        from .swig_wrappers import *
-
-    # These modules don't require the swig interface
-    from typing import Protocol, runtime_checkable
-
     from .importers.sbml import (  # noqa: F401
         SbmlImporter,
         assignment_rules_to_observables,
@@ -189,20 +155,6 @@ def get_model_dir(model_id: str | None = None, jax: bool = False) -> Path:
     except (ImportError, ModuleNotFoundError):
         JAXModel = object
 
-    @runtime_checkable
-    class ModelModule(Protocol):  # noqa: F811
-        """Type of AMICI-generated model modules.
-
-        To enable static type checking."""
-
-        def get_model(self) -> amici.Model:
-            """Create a model instance."""
-            ...
-
-    AmiciModel = amici.Model | amici.ModelPtr
-else:
-    ModelModule = ModuleType
-
 
 class add_path:
     """Context manager for temporarily changing PYTHONPATH.
@@ -262,6 +214,9 @@ def _module_from_path(module_name: str, module_path: Path | str) -> ModuleType:
     return module
 
 
+ModelModule = ModuleType
+
+
 def import_model_module(
     module_name: str, module_path: Path | str
 ) -> ModelModule:

python/sdist/amici/ThirdParty

@@ -2,13 +2,17 @@
 
 import sys
 
-from . import (
-    CpuTimer,
-    __version__,
-    compiled_with_openmp,
-    has_clibs,
-    hdf5_enabled,
-)
+from . import __version__
+
+try:
+    from .sim.sundials import (
+        CpuTimer,
+        compiled_with_openmp,
+        has_clibs,
+        hdf5_enabled,
+    )
+except ImportError:
+    has_clibs = False
 
 
 def print_info():
@@ -20,14 +24,14 @@ def print_info():
     if has_clibs:
         features.append("extensions")
 
-    if compiled_with_openmp():
-        features.append("OpenMP")
+        if compiled_with_openmp():
+            features.append("OpenMP")
 
-    if hdf5_enabled:
-        features.append("HDF5")
+        if hdf5_enabled:
+            features.append("HDF5")
 
-    if CpuTimer.uses_thread_clock:
-        features.append("thread_clock")
+        if CpuTimer.uses_thread_clock:
+            features.append("thread_clock")
 
     print(
         f"AMICI ({sys.platform}) version {__version__} ({','.join(features)})"