+
+Armistead, Joy, Sebastian Höpfl, Pierre Goldhausen, Andrea
+Müller-Hartmann, Evelin Fahle, Julia Hatzold, Rainer Franzen, Susanne
+Brodesser, Nicole E. Radde, and Matthias Hammerschmidt. 2024.
“A
+Sphingolipid Rheostat Controls Apoptosis Versus Apical Cell Extrusion as
+Alternative Tumour-Suppressive Mechanisms.” Cell Death &
+Disease 15 (10).
https://doi.org/10.1038/s41419-024-07134-2.
+
Baltussen, Mathieu G., Thijs J. de Jong, Quentin Duez, William E.
Robinson, and Wilhelm T. S. Huck. 2024.
“Chemical Reservoir
@@ -22,6 +31,16 @@ Computation in a Self-Organizing Reaction Network.”
Nature, June.
https://doi.org/10.1038/s41586-024-07567-x.
+
+Barthel, Lars, Philipp Kunz, Rudibert King, and Vera Meyer. 2024.
+
“Harnessing Genetic and Microfluidic Approaches to Model Shear
+Stress Response in Cell Wall Mutants of the Filamentous Cell Factory
+Aspergillus Niger.” In
Dispersity, Structure and Phase
+Changes of Proteins and Bio Agglomerates in Biotechnological
+Processes, edited by Arno Kwade and Ingo Kampen, 467–90. Cham:
+Springer Nature Switzerland.
https://doi.org/10.1007/978-3-031-63164-1_15.
+
Dorešić, Domagoj, Stephan Grein, and Jan Hasenauer. 2024.
“Efficient Parameter Estimation for ODE Models of Cellular
diff --git a/include/amici/forwardproblem.h b/include/amici/forwardproblem.h
index ffcca63666..40a4147f4e 100644
--- a/include/amici/forwardproblem.h
+++ b/include/amici/forwardproblem.h
@@ -2,6 +2,7 @@
#define AMICI_FORWARDPROBLEM_H
#include "amici/defines.h"
+#include "amici/edata.h"
#include "amici/misc.h"
#include "amici/model.h"
#include "amici/vector.h"
@@ -195,7 +196,7 @@ class ForwardProblem {
if (model->getTimepoint(it) == initial_state_.t)
return getInitialSimulationState();
auto map_iter = timepoint_states_.find(model->getTimepoint(it));
- assert(map_iter != timepoint_states_.end());
+ Ensures(map_iter != timepoint_states_.end());
return map_iter->second;
};
@@ -441,8 +442,20 @@ class FinalStateStorer : public ContextManager {
* @brief destructor, stores simulation state
*/
~FinalStateStorer() {
- if (fwd_)
+ if (fwd_) {
fwd_->final_state_ = fwd_->getSimulationState();
+ // if there is an associated output timepoint, also store it in
+ // timepoint_states if it's not present there.
+ // this may happen if there is an error just at
+ // (or indistinguishably before) an output timepoint
+ auto final_time = fwd_->getFinalTime();
+ auto const timepoints = fwd_->model->getTimepoints();
+ if (!fwd_->timepoint_states_.count(final_time)
+ && std::find(timepoints.cbegin(), timepoints.cend(), final_time)
+ != timepoints.cend()) {
+ fwd_->timepoint_states_[final_time] = fwd_->final_state_;
+ }
+ }
}
private:
diff --git a/include/amici/logging.h b/include/amici/logging.h
index 6af039d4c4..9441c21042 100644
--- a/include/amici/logging.h
+++ b/include/amici/logging.h
@@ -80,7 +80,7 @@ struct LogItem {
)
: severity(severity)
, identifier(identifier)
- , message(message){};
+ , message(message) {};
/** Severity level */
LogSeverity severity = LogSeverity::error;
diff --git a/scripts/run-valgrind-cpp.sh b/scripts/run-valgrind-cpp.sh
index fd08cbda54..a96b1d90e6 100755
--- a/scripts/run-valgrind-cpp.sh
+++ b/scripts/run-valgrind-cpp.sh
@@ -10,4 +10,4 @@ set -eou pipefail
# run tests
cd "${AMICI_PATH}/build/"
VALGRIND_OPTS="--leak-check=full --error-exitcode=1 --trace-children=yes --show-leak-kinds=definite"
-valgrind ${VALGRIND_OPTS} ctest
+CTEST_OUTPUT_ON_FAILURE=1 valgrind ${VALGRIND_OPTS} ctest
diff --git a/src/rdata.cpp b/src/rdata.cpp
index a2fa02dd62..4ec983af2b 100644
--- a/src/rdata.cpp
+++ b/src/rdata.cpp
@@ -241,7 +241,7 @@ void ReturnData::processForwardProblem(
if (edata)
initializeObjectiveFunction(model.hasQuadraticLLH());
- auto initialState = fwd.getInitialSimulationState();
+ auto const& initialState = fwd.getInitialSimulationState();
if (initialState.x.getLength() == 0 && model.nx_solver > 0)
return; // if x wasn't set forward problem failed during initialization
@@ -259,7 +259,7 @@ void ReturnData::processForwardProblem(
realtype tf = fwd.getFinalTime();
for (int it = 0; it < model.nt(); it++) {
if (model.getTimepoint(it) <= tf) {
- auto simulation_state = fwd.getSimulationStateTimepoint(it);
+ auto const simulation_state = fwd.getSimulationStateTimepoint(it);
model.setModelState(simulation_state.state);
getDataOutput(it, model, simulation_state, edata);
} else {
@@ -273,7 +273,7 @@ void ReturnData::processForwardProblem(
if (nz > 0) {
auto rootidx = fwd.getRootIndexes();
for (int iroot = 0; iroot <= fwd.getEventCounter(); iroot++) {
- auto simulation_state = fwd.getSimulationStateEvent(iroot);
+ auto const simulation_state = fwd.getSimulationStateEvent(iroot);
model.setModelState(simulation_state.state);
getEventOutput(
simulation_state.t, rootidx.at(iroot), model, simulation_state,
diff --git a/src/solver_cvodes.cpp b/src/solver_cvodes.cpp
index 72fcfa78ed..f777011329 100644
--- a/src/solver_cvodes.cpp
+++ b/src/solver_cvodes.cpp
@@ -91,8 +91,7 @@ static_assert(
"AMICI_FIRST_QRHSFUNC_ERR != CV_FIRST_QRHSFUNC_ERR"
);
static_assert(
- amici::AMICI_WARNING == CV_WARNING,
- "AMICI_WARNING != CV_WARNING"
+ amici::AMICI_WARNING == CV_WARNING, "AMICI_WARNING != CV_WARNING"
);
/*
diff --git a/src/solver_idas.cpp b/src/solver_idas.cpp
index 8e64edb92e..12ac2d2084 100644
--- a/src/solver_idas.cpp
+++ b/src/solver_idas.cpp
@@ -71,8 +71,7 @@ static_assert(
"AMICI_IDAS_CONSTR_FAIL != IDA_CONSTR_FAIL"
);
static_assert(
- amici::AMICI_WARNING == IDA_WARNING,
- "AMICI_WARNING != IDA_WARNING"
+ amici::AMICI_WARNING == IDA_WARNING, "AMICI_WARNING != IDA_WARNING"
);
/*
diff --git a/tests/cpp/unittests/testMisc.cpp b/tests/cpp/unittests/testMisc.cpp
index b06880072f..0cc7a017dc 100644
--- a/tests/cpp/unittests/testMisc.cpp
+++ b/tests/cpp/unittests/testMisc.cpp
@@ -360,10 +360,9 @@ TEST_F(SolverTest, SettersGettersWithSetup)
ASSERT_EQ(static_cast(solver.getSensitivityMethod()),
static_cast(sensi_meth));
- sundials::Context sunctx;
auto rdata = std::make_unique(solver, testModel);
- AmiVector x(nx, sunctx), dx(nx, sunctx);
- AmiVectorArray sx(nx, 1, sunctx), sdx(nx, 1, sunctx);
+ AmiVector x(nx, solver.getSunContext()), dx(nx, solver.getSunContext());
+ AmiVectorArray sx(nx, 1, solver.getSunContext()), sdx(nx, 1, solver.getSunContext());
testModel.setInitialStates(std::vector{ 0 });
diff --git a/version.txt b/version.txt
index 3f45a6442e..1b58cc1018 100644
--- a/version.txt
+++ b/version.txt
@@ -1 +1 @@
-0.26.3
+0.27.0