..

include/amici/serialization.h

@@ -150,6 +150,7 @@ void serialize(Archive& ar, amici::Model& m, unsigned int const /*version*/) {
     ar & m.steadystate_computation_mode_;
     ar & m.steadystate_sensitivity_mode_;
     ar & m.state_independent_events_;
+    ar & m.steadystate_mask_;
 }
 
 /**

include/amici/vector.h

@@ -430,8 +430,8 @@ inline span<realtype> make_span(N_Vector nv) {
 }
 
 /**
- * @brief Create span from N_Vector
- * @param nv
+ * @brief Create span from AmiVector
+ * @param av
  *
  */
 inline span<realtype const> make_span(amici::AmiVector const& av) {

python/sdist/amici/swig_wrappers.py

@@ -255,6 +255,7 @@ def writeSolverSettingsToHDF5(
     "SteadyStateSensitivityMode",
     ("t0", "setT0"),
     "Timepoints",
+    "_steadystate_mask",
 ]
 
 

python/tests/test_preequilibration.py

@@ -8,7 +8,10 @@
 from amici.debugging import get_model_for_preeq
 from numpy.testing import assert_allclose, assert_equal
 from test_pysb import get_data
-from amici.testing import TemporaryDirectoryWinSafe as TemporaryDirectory
+from amici.testing import (
+    TemporaryDirectoryWinSafe as TemporaryDirectory,
+    skip_on_valgrind,
+)
 
 
 @pytest.fixture
@@ -661,6 +664,7 @@ def test_get_model_for_preeq(preeq_fixture):
     )
 
 
+@skip_on_valgrind
 def test_partial_eq():
     """Check that partial equilibration is possible."""
     from amici.antimony_import import antimony2amici

python/tests/test_swig_interface.py

@@ -39,7 +39,7 @@ def test_copy_constructors(pysb_example_presimulation_module):
             val = get_val(obj, attr)
 
             try:
-                modval = get_mod_val(val, attr)
+                modval = get_mod_val(val, attr, obj)
             except ValueError:
                 # happens for everything that is not bool or scalar
                 continue
@@ -79,6 +79,10 @@ def test_copy_constructors(pysb_example_presimulation_module):
         tuple([1.0] + [0.0] * 35),
         tuple([0.1] * 36),
     ],
+    "_steadystate_mask": [
+        (),
+        tuple([0] * 3),
+    ],
     "MinimumSigmaResiduals": [
         50.0,
         60.0,
@@ -361,19 +365,21 @@ def get_val(obj, attr):
         return getattr(obj, attr)
 
 
-def get_mod_val(val, attr):
+def get_mod_val(val, attr, obj):
     if attr == "getReturnDataReportingMode":
         return amici.RDataReporting.likelihood
     elif attr == "getParameterList":
-        return tuple(get_mod_val(val[0], "") for _ in val)
+        return tuple(get_mod_val(val[0], "", obj) for _ in val)
     elif attr == "getStateIsNonNegative":
         raise ValueError("Cannot modify value")
+    elif attr == "get_steadystate_mask":
+        return [0 for _ in range(obj.nx_solver)]
     elif isinstance(val, bool):
         return not val
     elif isinstance(val, numbers.Number):
         return val + 1
     elif isinstance(val, tuple):
-        return tuple(get_mod_val(v, attr) for v in val)
+        return tuple(get_mod_val(v, attr, obj) for v in val)
 
     raise ValueError("Cannot modify value")
 

src/hdf5.cpp

@@ -1244,6 +1244,12 @@ void readModelDataFromHDF5(
             model.setInitialStates(x0);
     }
 
+    if (locationExists(file, datasetPath + "/steadystate_mask")) {
+        auto mask = getDoubleDataset1D(file, datasetPath + "/steadystate_mask");
+        if (!mask.empty())
+            model.set_steadystate_mask(mask);
+    }
+
     if (locationExists(file, datasetPath + "/sx0")) {
         hsize_t length0 = 0;
         hsize_t length1 = 0;

src/model.cpp

@@ -287,7 +287,9 @@ bool operator==(Model const& a, Model const& b) {
            && (a.nmaxevent_ == b.nmaxevent_)
            && (a.state_is_non_negative_ == b.state_is_non_negative_)
            && (a.sigma_res_ == b.sigma_res_) && (a.min_sigma_ == b.min_sigma_)
-           && a.state_ == b.state_;
+           && (a.state_ == b.state_)
+           && (a.steadystate_mask_.getVector()
+               == b.steadystate_mask_.getVector());
 }
 
 bool operator==(ModelDimensions const& a, ModelDimensions const& b) {

swig/model.i

@@ -94,6 +94,7 @@ using namespace amici;
 %ignore fdx_rdatadtcl;
 %ignore fdx_rdatadx_solver;
 %ignore fdsigmaydy;
+%ignore get_steadystate_mask_av;
 
 %newobject amici::Model::clone;