doc: private / public / fix references

* Exclude private members from the sphinx documentation
* Make some supposed-to-be-private members private
* Fix references

To be continued...

Author: dweindl

doc/conf.py

@@ -207,6 +207,7 @@ def install_doxygen():
     "inherited-members": True,
     "undoc-members": True,
     "ignore-module-all": False,
+    "imported-members": True,
 }
 
 # sphinx-autodoc-typehints

doc/examples/example_presimulation/ExampleExperimentalConditions.ipynb

@@ -211,7 +211,7 @@
    "source": [
     "# Retrieve model output names and formulae from AssignmentRules and remove the respective rules\n",
     "observables = amici.assignment_rules_to_observables(\n",
-    "    sbml_importer.sbml,  # the libsbml model object\n",
+    "    sbml_importer.sbml_model,  # the libsbml model object\n",
     "    filter_function=lambda variable: variable.getName() == \"pPROT\",\n",
     ")\n",
     "print(\"Observables:\")\n",

python/sdist/amici/__init__.py

@@ -1,6 +1,5 @@
 """
-The AMICI Python module provides functionality for importing SBML or PySB
-models and turning them into C++ Python extensions.
+Top-level module.
 """
 
 import contextlib
@@ -133,12 +132,16 @@ def get_model_dir(model_id: str | None = None, jax: bool = False) -> Path:
 
 # Initialize AMICI paths
 #: absolute root path of the amici repository or Python package
+#: :meta private:
 amici_path = _get_amici_path()
 #: absolute path of the amici swig directory
+#: :meta private:
 amiciSwigPath = os.path.join(amici_path, "swig")
 #: absolute path of the amici source directory
+#: :meta private:
 amiciSrcPath = os.path.join(amici_path, "src")
 #: absolute root path of the amici module
+#: :meta private:
 amiciModulePath = os.path.dirname(__file__)
 
 
@@ -165,6 +168,8 @@ class add_path:
     """Context manager for temporarily changing PYTHONPATH.
 
     Add a path to the PYTHONPATH for the duration of the context manager.
+
+    :meta private:
     """
 
     def __init__(self, path: str | Path):
@@ -183,6 +188,8 @@ class set_path:
     """Context manager for temporarily changing PYTHONPATH.
 
     Set the PYTHONPATH to a given path for the duration of the context manager.
+
+    :meta private:
     """
 
     def __init__(self, path: str | Path):
@@ -226,7 +233,7 @@ def import_model_module(
     module_name: str, module_path: Path | str
 ) -> ModelModule:
     """
-    Import Python module of an AMICI model
+    Import Python module of an AMICI model.
 
     :param module_name:
         Name of the python package of the model

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

@@ -218,7 +218,7 @@ def __init__(
         # include/amici/model.h for details)
         self.model: DEModel = de_model
         self._code_printer.known_functions.update(
-            splines.spline_user_functions(
+            splines._spline_user_functions(
                 self.model._splines, self._get_index("p")
             )
         )

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

@@ -51,9 +51,10 @@ def antimony2sbml(ant_model: str | Path) -> str:
 def antimony2amici(ant_model: str | Path, *args, **kwargs):
     """Convert Antimony model to AMICI model.
 
-    Converts the Antimony model provided as string of file to SBML and then imports it into AMICI.
+    Converts the Antimony model provided as string or file to SBML and then
+    imports it into AMICI.
 
-    For documentation see :meth:`amici.sbml_import.SbmlImporter.sbml2amici`.
+    For documentation see :meth:`amici.importers.sbml.SbmlImporter.sbml2amici`.
     """
     from amici.importers.sbml import SbmlImporter
 

python/sdist/amici/importers/petab/_petab_importer.py

@@ -1107,7 +1107,7 @@ def __init__(self, petab_problem: v2.Problem):
         if not isinstance(petab_problem.model, PySBModel):
             raise ValueError("Only SBML models are supported.")
         model = petab_problem.model.model
-        compartment_ids = {c.name for c in model.compartments}
+        compartment_ids = {c.name for c in model._compartments}
         if compartment_ids and any(
             change.target_id in compartment_ids
             for cond in petab_problem.conditions

python/sdist/amici/importers/petab/v1/sbml_import.py

@@ -332,7 +332,7 @@ def import_model_sbml(
         sbml_model,
         discard_annotations=discard_sbml_annotations,
     )
-    sbml_model = sbml_importer.sbml
+    sbml_model = sbml_importer.sbml_model
 
     allow_n_noise_pars = (
         not petab.lint.observable_table_has_nontrivial_noise_formula(

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

@@ -325,6 +325,8 @@ def ode_model_from_pysb_importer(
     Creates an :class:`amici.DEModel` instance from a :class:`pysb.Model`
     instance.
 
+    :meta private:
+
     :param model:
         see :func:`amici.importers.pysb.pysb2amici`
 
@@ -1468,6 +1470,8 @@ def has_fixed_parameter_ic(
     :meth:`de_export.DEModel.state_has_fixed_parameter_initial_condition`
     from a pysb specie/model arguments
 
+    :meta private:
+
     :param specie:
         pysb species
 
@@ -1506,6 +1510,8 @@ def extract_monomers(
     Constructs a list of monomer names contained in complex patterns.
     Multiplicity of names corresponds to the stoichiometry in the complex.
 
+    :meta private:
+
     :param complex_patterns:
         (list of) complex pattern(s)