From 247dbb04c0cbd98e6091f389419d6452bf2ab7d3 Mon Sep 17 00:00:00 2001
From: Alan Garny <agarny@hellix.com>
Date: Wed, 22 Oct 2025 14:25:40 +1300
Subject: [PATCH 1/6] New version.

---
 VERSION.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/VERSION.txt b/VERSION.txt
index 05de19166..9f0adfc11 100644
--- a/VERSION.txt
+++ b/VERSION.txt
@@ -1 +1 @@
-0.20251017.0
+0.20251022.0

From 10f9086e40a9acd762de9523becbabb1a5324c07 Mon Sep 17 00:00:00 2001
From: Alan Garny <agarny@hellix.com>
Date: Tue, 21 Oct 2025 17:00:09 +1300
Subject: [PATCH 2/6] Tests: reorganised our miscellaneous tests.

---
 tests/CMakeLists.txt                                 | 6 ++++--
 tests/misc/{compiler/tests.cpp => compilertests.cpp} | 0
 tests/misc/{compiler => }/tests.cmake                | 6 +++---
 3 files changed, 7 insertions(+), 5 deletions(-)
 rename tests/misc/{compiler/tests.cpp => compilertests.cpp} (100%)
 rename tests/misc/{compiler => }/tests.cmake (88%)

diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index 104d9383b..d304bd2b8 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -38,7 +38,7 @@ include(api/sed/tests.cmake)
 include(api/solver/tests.cmake)
 include(api/version/tests.cmake)
 
-include(misc/compiler/tests.cmake)
+include(misc/tests.cmake)
 
 include(support/cellml/tests.cmake)
 include(support/combine/tests.cmake)
@@ -170,7 +170,9 @@ include_directories(${CMAKE_SOURCE_DIR}/src/misc
 
 foreach(TEST ${TESTS})
     if(LIBOPENCOR_UNIT_TESTING)
-        if(NOT "${${TEST}_CATEGORY}" STREQUAL "")
+        if("${${TEST}_CATEGORY}" STREQUAL "")
+            set(TEST_CATEGORY)
+        else()
             set(TEST_CATEGORY "${${TEST}_CATEGORY}_")
         endif()
 
diff --git a/tests/misc/compiler/tests.cpp b/tests/misc/compilertests.cpp
similarity index 100%
rename from tests/misc/compiler/tests.cpp
rename to tests/misc/compilertests.cpp
diff --git a/tests/misc/compiler/tests.cmake b/tests/misc/tests.cmake
similarity index 88%
rename from tests/misc/compiler/tests.cmake
rename to tests/misc/tests.cmake
index 30f88984a..0537c7fdf 100644
--- a/tests/misc/compiler/tests.cmake
+++ b/tests/misc/tests.cmake
@@ -12,11 +12,11 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-set(TEST compiler)
+set(TEST misc)
 
 list(APPEND TESTS ${TEST})
 
-set(${TEST}_CATEGORY misc)
+set(${TEST}_CATEGORY)
 set(${TEST}_SOURCE_FILES
-    ${CMAKE_CURRENT_LIST_DIR}/tests.cpp
+    ${CMAKE_CURRENT_LIST_DIR}/compilertests.cpp
 )

From 13556a423a3fb0172decc0127e062ab95e4d5a2c Mon Sep 17 00:00:00 2001
From: Alan Garny <agarny@hellix.com>
Date: Tue, 21 Oct 2025 17:01:24 +1300
Subject: [PATCH 3/6] Tests: added a test for a failing simulation.

---
 tests/misc/failingsimulationtests.cpp |  50 ++++++++++++++++++++++++++
 tests/misc/res/tt04.omex              | Bin 0 -> 17242 bytes
 tests/misc/tests.cmake                |   1 +
 3 files changed, 51 insertions(+)
 create mode 100644 tests/misc/failingsimulationtests.cpp
 create mode 100644 tests/misc/res/tt04.omex

diff --git a/tests/misc/failingsimulationtests.cpp b/tests/misc/failingsimulationtests.cpp
new file mode 100644
index 000000000..0c2a8e6b0
--- /dev/null
+++ b/tests/misc/failingsimulationtests.cpp
@@ -0,0 +1,50 @@
+/*
+Copyright libOpenCOR contributors.
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+#include "tests/utils.h"
+
+#include <libopencor>
+
+TEST(FailingSimulationTest, basic)
+{
+    // Default simulation.
+
+    auto file = libOpenCOR::File::create(libOpenCOR::resourcePath("../misc/res/tt04.omex"));
+    auto document = libOpenCOR::SedDocument::create(file);
+    auto instance = document->instantiate();
+
+    instance->run();
+
+    EXPECT_FALSE(instance->hasIssues());
+
+    // Set the value of `membrane.test` to zero and rerun the simulation.
+
+    auto model = document->model(0);
+
+    model->addChange(libOpenCOR::SedChangeAttribute::create("membrane", "test", "0.0"));
+
+    instance->run();
+
+    EXPECT_TRUE(instance->hasIssues());
+
+    // Remove all changes and rerun the simulation.
+
+    model->removeAllChanges();
+
+    instance->run();
+
+    EXPECT_FALSE(instance->hasIssues());
+}
diff --git a/tests/misc/res/tt04.omex b/tests/misc/res/tt04.omex
new file mode 100644
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literal 0
HcmV?d00001

diff --git a/tests/misc/tests.cmake b/tests/misc/tests.cmake
index 0537c7fdf..5336fe44d 100644
--- a/tests/misc/tests.cmake
+++ b/tests/misc/tests.cmake
@@ -19,4 +19,5 @@ list(APPEND TESTS ${TEST})
 set(${TEST}_CATEGORY)
 set(${TEST}_SOURCE_FILES
     ${CMAKE_CURRENT_LIST_DIR}/compilertests.cpp
+    ${CMAKE_CURRENT_LIST_DIR}/failingsimulationtests.cpp
 )

From 456c0b76fb5217d340e9035089a3ca4d3a777128 Mon Sep 17 00:00:00 2001
From: Alan Garny <agarny@hellix.com>
Date: Tue, 21 Oct 2025 17:27:49 +1300
Subject: [PATCH 4/6] SedInstanceTask: some minor cleaning up.

---
 src/sed/sedinstancetask.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sed/sedinstancetask.cpp b/src/sed/sedinstancetask.cpp
index 387611acb..0d07ddbb2 100644
--- a/src/sed/sedinstancetask.cpp
+++ b/src/sed/sedinstancetask.cpp
@@ -219,7 +219,7 @@ double SedInstanceTask::Impl::run()
     auto startTime = std::chrono::high_resolution_clock::now();
 
     // (Re)initialise our model.
-    // Note: reinitialise our model in case we are running our model multiple times.
+    // Note: reinitialise our model because we initialised it when we created the instance task.
 
     initialise();
 

From bc8c99fff0d499c8362862e0561a6f3c2afb194b Mon Sep 17 00:00:00 2001
From: Alan Garny <agarny@hellix.com>
Date: Tue, 21 Oct 2025 17:39:17 +1300
Subject: [PATCH 5/6] SedInstanceTask: some minor improvement.

Makes maintenance easier and less error prone (with regards to our call to `applyChanges()`).
---
 src/sed/sedinstancetask.cpp | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/sed/sedinstancetask.cpp b/src/sed/sedinstancetask.cpp
index 0d07ddbb2..2c551f755 100644
--- a/src/sed/sedinstancetask.cpp
+++ b/src/sed/sedinstancetask.cpp
@@ -161,9 +161,17 @@ void SedInstanceTask::Impl::initialise()
 #else
         mRuntime->initialiseVariablesForDifferentialModel()(mStates, mRates, mConstants, mComputedConstants, mAlgebraic);
 #endif
+    } else {
+#ifdef __EMSCRIPTEN__
+        mRuntime->initialiseVariablesForAlgebraicModel(mConstants, mComputedConstants, mAlgebraic);
+#else
+        mRuntime->initialiseVariablesForAlgebraicModel()(mConstants, mComputedConstants, mAlgebraic);
+#endif
+    }
 
-        applyChanges();
+    applyChanges();
 
+    if (mSedUniformTimeCourse != nullptr) {
 #ifdef __EMSCRIPTEN__
         mRuntime->computeComputedConstantsForDifferentialModel(mStates, mRates, mConstants, mComputedConstants, mAlgebraic);
         mRuntime->computeRates(mVoi, mStates, mRates, mConstants, mComputedConstants, mAlgebraic);
@@ -174,14 +182,6 @@ void SedInstanceTask::Impl::initialise()
         mRuntime->computeVariablesForDifferentialModel()(mVoi, mStates, mRates, mConstants, mComputedConstants, mAlgebraic);
 #endif
     } else {
-#ifdef __EMSCRIPTEN__
-        mRuntime->initialiseVariablesForAlgebraicModel(mConstants, mComputedConstants, mAlgebraic);
-#else
-        mRuntime->initialiseVariablesForAlgebraicModel()(mConstants, mComputedConstants, mAlgebraic);
-#endif
-
-        applyChanges();
-
 #ifdef __EMSCRIPTEN__
         mRuntime->computeComputedConstantsForAlgebraicModel(mConstants, mComputedConstants, mAlgebraic);
         mRuntime->computeVariablesForAlgebraicModel(mConstants, mComputedConstants, mAlgebraic);

From 47c8ede00875d8b185aed07af765c030cbc194b4 Mon Sep 17 00:00:00 2001
From: Alan Garny <agarny@hellix.com>
Date: Wed, 22 Oct 2025 11:45:06 +1300
Subject: [PATCH 6/6] Tests: make sure that our failing simulation test passes.

---
 src/sed/sedinstance.cpp               | 14 ++++++++++++++
 src/sed/sedinstance_p.h               |  1 +
 tests/misc/failingsimulationtests.cpp |  9 +++------
 3 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/src/sed/sedinstance.cpp b/src/sed/sedinstance.cpp
index b402f3045..146297f36 100644
--- a/src/sed/sedinstance.cpp
+++ b/src/sed/sedinstance.cpp
@@ -67,6 +67,10 @@ SedInstance::Impl::Impl(const SedDocumentPtr &pDocument)
                 }
             }
         }
+
+        // Keep track of the issues of all the tasks.
+
+        mTasksIssues = mIssues;
     } else {
         addError("The simulation experiment description does not contain any tasks to run.");
     }
@@ -74,6 +78,12 @@ SedInstance::Impl::Impl(const SedDocumentPtr &pDocument)
 
 double SedInstance::Impl::run()
 {
+    // Reset iourselves.
+
+    removeAllIssues();
+
+    mIssues = mTasksIssues;
+
     // Run all the tasks associated with this instance unless they have some issues.
 
     auto res = 0.0;
@@ -84,6 +94,10 @@ double SedInstance::Impl::run()
 
             if (task->hasIssues()) {
                 addIssues(task);
+
+                // Reset the issues of the task so that they are not reported again should the instance be run again.
+
+                task->pimpl()->removeAllIssues();
             }
         }
     }
diff --git a/src/sed/sedinstance_p.h b/src/sed/sedinstance_p.h
index 4b5dbc183..7260ac1ea 100644
--- a/src/sed/sedinstance_p.h
+++ b/src/sed/sedinstance_p.h
@@ -26,6 +26,7 @@ class SedInstance::Impl: public Logger::Impl
 {
 public:
     SedInstanceTaskPtrs mTasks;
+    IssuePtrs mTasksIssues;
 
     static SedInstancePtr create(const SedDocumentPtr &pDocument);
 
diff --git a/tests/misc/failingsimulationtests.cpp b/tests/misc/failingsimulationtests.cpp
index 0c2a8e6b0..73edd599d 100644
--- a/tests/misc/failingsimulationtests.cpp
+++ b/tests/misc/failingsimulationtests.cpp
@@ -26,8 +26,7 @@ TEST(FailingSimulationTest, basic)
     auto document = libOpenCOR::SedDocument::create(file);
     auto instance = document->instantiate();
 
-    instance->run();
-
+    EXPECT_NE(instance->run(), 0.0);
     EXPECT_FALSE(instance->hasIssues());
 
     // Set the value of `membrane.test` to zero and rerun the simulation.
@@ -36,15 +35,13 @@ TEST(FailingSimulationTest, basic)
 
     model->addChange(libOpenCOR::SedChangeAttribute::create("membrane", "test", "0.0"));
 
-    instance->run();
-
+    EXPECT_EQ(instance->run(), 0.0);
     EXPECT_TRUE(instance->hasIssues());
 
     // Remove all changes and rerun the simulation.
 
     model->removeAllChanges();
 
-    instance->run();
-
+    EXPECT_NE(instance->run(), 0.0);
     EXPECT_FALSE(instance->hasIssues());
 }