Merge branch 'develop' into fix_cmake_dbg

.github/workflows/deploy_branch.yml

@@ -1,5 +1,5 @@
 name: Deploy Branch
-on: [push, merge_group, workflow_dispatch]
+on: [push, pull_request, merge_group, workflow_dispatch]
 
 jobs:
   sdist:

.github/workflows/test_install.yml

@@ -1,5 +1,5 @@
 name: Installation
-on: [push, merge_group, workflow_dispatch]
+on: [push, pull_request, merge_group, workflow_dispatch]
 
 jobs:
   archive:

.github/workflows/test_petab_test_suite.yml

@@ -85,6 +85,7 @@ jobs:
             tests/petab_test_suite/
 
       - name: Codecov
+        if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
         uses: codecov/[email protected]
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/test_python_cplusplus.yml

@@ -6,6 +6,7 @@ on:
   pull_request:
     branches:
       - master
+      - develop
 
 jobs:
   ubuntu-cpp-python-tests:
@@ -65,6 +66,7 @@ jobs:
           ${AMICI_DIR}/python/tests/test_splines.py
 
     - name: Codecov Python
+      if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
       uses: codecov/[email protected]
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
@@ -84,6 +86,7 @@ jobs:
         && lcov -a coverage_cpp.info -a coverage_py.info -o coverage.info
 
     - name: Codecov CPP
+      if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
       uses: codecov/[email protected]
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
@@ -92,6 +95,7 @@ jobs:
         fail_ci_if_error: true
 
     - name: Run sonar-scanner
+      if: ${{ env.SONAR_TOKEN != '' }}
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
@@ -137,6 +141,7 @@ jobs:
           ${AMICI_DIR}/python/tests/test_splines_short.py
 
     - name: Codecov Python
+      if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
       uses: codecov/[email protected]
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
@@ -156,6 +161,7 @@ jobs:
         && lcov -a coverage_cpp.info -a coverage_py.info -o coverage.info
 
     - name: Codecov CPP
+      if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
       uses: codecov/[email protected]
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
@@ -164,6 +170,7 @@ jobs:
         fail_ci_if_error: true
 
     - name: Run sonar-scanner
+      if: ${{ env.SONAR_TOKEN != '' }}
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}

.github/workflows/test_sbml_semantic_test_suite.yml

@@ -54,6 +54,7 @@ jobs:
         path: tests/amici-semantic-results
 
     - name: Codecov SBMLSuite
+      if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
       uses: codecov/[email protected]
       with:
         token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/test_windows.yml

@@ -7,6 +7,7 @@ on:
     - cron:  '48 4 * * *'
   pull_request:
     branches:
+      - develop
       - master
 
 jobs:

include/amici/forwardproblem.h

@@ -250,6 +250,21 @@ class ForwardProblem {
 
     void handleEvent(realtype* tlastroot, bool seflag, bool initial_event);
 
+    /**
+     * @brief Store pre-event model state
+     *
+     * @param seflag Secondary event flag
+     * @param initial_event initial event flag
+     */
+    void store_pre_event_state(bool seflag, bool initial_event);
+
+    /**
+     * @brief Check for, and if applicable, handle any secondary events
+     *
+     * @param tlastroot pointer to the timepoint of the last event
+     */
+    void handle_secondary_event(realtype* tlastroot);
+
     /**
      * @brief Extract output information for events
      */

src/forwardproblem.cpp

@@ -182,6 +182,77 @@ void ForwardProblem::handleEvent(
     if (model->nz > 0)
         storeEvent();
 
+    store_pre_event_state(seflag, initial_event);
+
+    if (!initial_event)
+        model->updateHeaviside(roots_found_);
+
+    applyEventBolus();
+
+    if (solver->computingFSA()) {
+        /* compute the new xdot  */
+        model->fxdot(t_, x_, dx_, xdot_);
+        applyEventSensiBolusFSA();
+    }
+
+    handle_secondary_event(tlastroot);
+
+    /* only reinitialise in the first event fired */
+    if (!seflag) {
+        solver->reInit(t_, x_, dx_);
+        if (solver->computingFSA()) {
+            solver->sensReInit(sx_, sdx_);
+        }
+    }
+}
+
+void ForwardProblem::storeEvent() {
+    if (t_ == model->getTimepoint(model->nt() - 1)) {
+        // call from fillEvent at last timepoint
+        model->froot(t_, x_, dx_, rootvals_);
+        for (int ie = 0; ie < model->ne; ie++) {
+            roots_found_.at(ie) = (nroots_.at(ie) < model->nMaxEvent()) ? 1 : 0;
+        }
+        root_idx_.push_back(roots_found_);
+    }
+
+    if (getRootCounter() < getEventCounter()) {
+        /* update stored state (sensi) */
+        event_states_.at(getRootCounter()) = getSimulationState();
+    } else {
+        /* add stored state (sensi) */
+        event_states_.push_back(getSimulationState());
+    }
+
+    /* EVENT OUTPUT */
+    for (int ie = 0; ie < model->ne; ie++) {
+        /* only look for roots of the rootfunction not discontinuities */
+        if (nroots_.at(ie) >= model->nMaxEvent())
+            continue;
+
+        /* only consider transitions false -> true or event filling */
+        if (roots_found_.at(ie) != 1
+            && t_ != model->getTimepoint(model->nt() - 1)) {
+            continue;
+        }
+
+        if (edata && solver->computingASA())
+            model->getAdjointStateEventUpdate(
+                slice(dJzdx_, nroots_.at(ie), model->nx_solver * model->nJ), ie,
+                nroots_.at(ie), t_, x_, *edata
+            );
+
+        nroots_.at(ie)++;
+    }
+
+    if (t_ == model->getTimepoint(model->nt() - 1)) {
+        // call from fillEvent at last timepoint
+        // loop until all events are filled
+        fillEvents(model->nMaxEvent());
+    }
+}
+
+void ForwardProblem::store_pre_event_state(bool seflag, bool initial_event) {
     /* if we need to do forward sensitivities later on we need to store the old
      * x and the old xdot */
     if (solver->getSensitivityOrder() >= SensitivityOrder::first) {
@@ -212,18 +283,9 @@ void ForwardProblem::handleEvent(
         xdot_disc_.push_back(xdot_);
         xdot_old_disc_.push_back(xdot_old_);
     }
+}
 
-    if (!initial_event)
-        model->updateHeaviside(roots_found_);
-
-    applyEventBolus();
-
-    if (solver->computingFSA()) {
-        /* compute the new xdot  */
-        model->fxdot(t_, x_, dx_, xdot_);
-        applyEventSensiBolusFSA();
-    }
-
+void ForwardProblem::handle_secondary_event(realtype* tlastroot) {
     int secondevent = 0;
 
     /* check whether we need to fire a secondary event */
@@ -260,60 +322,6 @@ void ForwardProblem::handleEvent(
             );
         handleEvent(tlastroot, true, false);
     }
-
-    /* only reinitialise in the first event fired */
-    if (!seflag) {
-        solver->reInit(t_, x_, dx_);
-        if (solver->computingFSA()) {
-            solver->sensReInit(sx_, sdx_);
-        }
-    }
-}
-
-void ForwardProblem::storeEvent() {
-    if (t_ == model->getTimepoint(model->nt() - 1)) {
-        // call from fillEvent at last timepoint
-        model->froot(t_, x_, dx_, rootvals_);
-        for (int ie = 0; ie < model->ne; ie++) {
-            roots_found_.at(ie) = (nroots_.at(ie) < model->nMaxEvent()) ? 1 : 0;
-        }
-        root_idx_.push_back(roots_found_);
-    }
-
-    if (getRootCounter() < getEventCounter()) {
-        /* update stored state (sensi) */
-        event_states_.at(getRootCounter()) = getSimulationState();
-    } else {
-        /* add stored state (sensi) */
-        event_states_.push_back(getSimulationState());
-    }
-
-    /* EVENT OUTPUT */
-    for (int ie = 0; ie < model->ne; ie++) {
-        /* only look for roots of the rootfunction not discontinuities */
-        if (nroots_.at(ie) >= model->nMaxEvent())
-            continue;
-
-        /* only consider transitions false -> true or event filling */
-        if (roots_found_.at(ie) != 1
-            && t_ != model->getTimepoint(model->nt() - 1)) {
-            continue;
-        }
-
-        if (edata && solver->computingASA())
-            model->getAdjointStateEventUpdate(
-                slice(dJzdx_, nroots_.at(ie), model->nx_solver * model->nJ), ie,
-                nroots_.at(ie), t_, x_, *edata
-            );
-
-        nroots_.at(ie)++;
-    }
-
-    if (t_ == model->getTimepoint(model->nt() - 1)) {
-        // call from fillEvent at last timepoint
-        // loop until all events are filled
-        fillEvents(model->nMaxEvent());
-    }
 }
 
 void ForwardProblem::handleDataPoint(int /*it*/) {