Merge branch 'develop' into rdata_status_int

AMICI-dev · Jan 16, 2023 · de87340 · de87340
2 parents 75db04f + 6e44a70
commit de87340
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Showing 5 changed files with 25 additions and 4 deletions.
diff --git a/python/sdist/amici/__init__.py b/python/sdist/amici/__init__.py
@@ -120,14 +120,19 @@ def _imported_from_setup() -> bool:
     from .sbml_import import SbmlImporter, assignmentRules2observables
     from .ode_export import ODEModel, ODEExporter
 
-    from typing import Protocol
+    from typing import Protocol, runtime_checkable
 
 
+    @runtime_checkable
     class ModelModule(Protocol):
         """Enable Python static type checking for AMICI-generated model
         modules"""
+
         def getModel(self) -> amici.Model:
-            pass
+            ...
+
+        def get_model(self) -> amici.Model:
+            ...
 
 
 class add_path:

diff --git a/python/sdist/amici/__init__.template.py b/python/sdist/amici/__init__.template.py
@@ -14,6 +14,7 @@
         'version currently installed.'
     )
 
-from TPL_MODELNAME._TPL_MODELNAME import *
+from .TPL_MODELNAME import *
+from .TPL_MODELNAME import getModel as get_model
 
 __version__ = 'TPL_PACKAGE_VERSION'
diff --git a/python/sdist/amici/petab_objective.py b/python/sdist/amici/petab_objective.py
@@ -37,6 +37,7 @@
 RES = 'res'
 SRES = 'sres'
 RDATAS = 'rdatas'
+EDATAS = 'edatas'
 
 
 @log_execution_time('Simulating PEtab model', logger)
@@ -92,6 +93,7 @@ def simulate_petab(
 
         * cost function value (``LLH``),
         * list of :class:`amici.amici.ReturnData` (``RDATAS``),
+        * list of :class:`amici.amici.ExpData` (``EDATAS``),
 
         corresponding to the different simulation conditions.
         For ordering of simulation conditions, see
@@ -163,7 +165,8 @@ def simulate_petab(
 
     return {
         LLH: llh,
-        RDATAS: rdatas
+        RDATAS: rdatas,
+        EDATAS: edatas,
     }
 
 

diff --git a/python/tests/test_sbml_import.py b/python/tests/test_sbml_import.py
@@ -180,6 +180,11 @@ def test_logging_works(observable_dependent_error_model, caplog):
     assert rdata.status != amici.AMICI_SUCCESS
     assert "mxstep steps taken" in caplog.text
 
+@skip_on_valgrind
+def test_model_module_is_set(observable_dependent_error_model):
+    model_module = observable_dependent_error_model
+    assert isinstance(model_module.getModel().module, amici.ModelModule)
+
 
 @pytest.fixture(scope='session')
 def model_steadystate_module():

diff --git a/swig/modelname.template.i b/swig/modelname.template.i
@@ -10,5 +10,12 @@ using namespace amici;
 %}
 
 
+// Make model module accessible from the model
+%feature("pythonappend") amici::generic_model::getModel %{
+    import sys
+    val.module = sys.modules['.'.join(__name__.split('.')[:-1])]
+%}
+
+
 // Process symbols in header
 %include "wrapfunctions.h"