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agarnyagarny
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libCellML: upgraded to commit 387274c.
1 parent f5ddf39 commit b7b0dce

21 files changed

+121
-121
lines changed

‎cmake/packages.cmake‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -195,7 +195,7 @@ function(retrieve_package PACKAGE_NAME PACKAGE_VERSION PACKAGE_REPOSITORY RELEAS
195195
if("${PACKAGE_NAME}" STREQUAL "libCellML")
196196
#---GRY--- USE THIS VERSION OF libCellML WHICH CORRESPONDS TO PR #1256 UNTIL IT GETS MERGED IN.
197197

198-
set(PACKAGE_URL "https://github.com/agarny/${PACKAGE_REPOSITORY}/releases/download/7cc5bea/${PACKAGE_FILE}")
198+
set(PACKAGE_URL "https://github.com/agarny/${PACKAGE_REPOSITORY}/releases/download/387274c/${PACKAGE_FILE}")
199199
endif()
200200

201201
set(ATTEMPT 1)

‎src/3rdparty/libCellML/CMakeLists.txt‎

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -34,49 +34,49 @@ if(LIBOPENCOR_PREBUILT_LIBCELLML)
3434
if(EMSCRIPTEN)
3535
retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
3636
${PACKAGE_REPOSITORY} ${RELEASE_TAG}
37-
5bee3b3c508fb274e084468243b43d9f83647beb)
37+
73b647384623b4a44227e12ce459021a64d1ab9c)
3838
else()
3939
if(WIN32)
4040
if(RELEASE_MODE)
4141
if(INTEL_MODE)
4242
retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
4343
${PACKAGE_REPOSITORY} ${RELEASE_TAG}
44-
d277ce028be3806aa2514ba27ec4bed352faf069)
44+
6bc0af42c6264380a943b41e0bbe91b78729f40a)
4545
else()
4646
retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
4747
${PACKAGE_REPOSITORY} ${RELEASE_TAG}
48-
388a936417a5681fbcf835bdda20e8ed0fbf3382)
48+
be0e45fb8485333ebbc3fd50371452c6ea2c88ca)
4949
endif()
5050
else()
5151
if(INTEL_MODE)
5252
retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
5353
${PACKAGE_REPOSITORY} ${RELEASE_TAG}
54-
c768d8c59db5ee4a07baa0fc61d7a8ccac4ea6db)
54+
44759f0a9e37ddd7d29cee5388f15a83f18707f9)
5555
else()
5656
retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
5757
${PACKAGE_REPOSITORY} ${RELEASE_TAG}
58-
2fd521abaf83b480e5b07c746ae310be529faa7e)
58+
952a97fbd31ec36a6a48433da14a01f6fc58fa4b)
5959
endif()
6060
endif()
6161
elseif(APPLE)
6262
if(INTEL_MODE)
6363
retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
6464
${PACKAGE_REPOSITORY} ${RELEASE_TAG}
65-
055181384ac2e4e942603c6b1f3d0c20f439b523)
65+
b3c42571ed8942076b2ab0f198125d16a55d89ed)
6666
else()
6767
retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
6868
${PACKAGE_REPOSITORY} ${RELEASE_TAG}
69-
847c024d893e3a1f73172e8f6d2e55136e46dd86)
69+
349be7eb4d9ec091e4218622464f10e58d118723)
7070
endif()
7171
else()
7272
if(INTEL_MODE)
7373
retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
7474
${PACKAGE_REPOSITORY} ${RELEASE_TAG}
75-
f8d847dffd74264a3074e742149dca0ab4c57653)
75+
ece808783b4e17744d7d05df30f69aac7aa41fff)
7676
else()
7777
retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
7878
${PACKAGE_REPOSITORY} ${RELEASE_TAG}
79-
674bb536a67cc7e7d4afef553c843ac38d44d43f)
79+
c6f29a584775d86e02f01d05b6fdcc4ea7b241be)
8080
endif()
8181
endif()
8282
endif()
@@ -86,7 +86,7 @@ elseif(NOT ONLY_BUILD_JAVASCRIPT_THIRD_PARTY_LIBRARIES)
8686
build_package(${PACKAGE_NAME}
8787
URL
8888
# https://github.com/opencor/${PACKAGE_REPOSITORY}/archive/refs/tags/${RELEASE_TAG}.tar.gz
89-
https://github.com/agarny/${PACKAGE_REPOSITORY}/archive/refs/tags/7cc5bea.tar.gz
89+
https://github.com/agarny/${PACKAGE_REPOSITORY}/archive/refs/tags/387274c.tar.gz
9090
DOWNLOAD_NO_PROGRESS ON
9191
CMAKE_ARGS
9292
-DBINDINGS_PYTHON=OFF

‎src/sed/sedinstancetask.cpp‎

Lines changed: 20 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -112,7 +112,7 @@ SedInstanceTask::Impl::Impl(const SedAbstractTaskPtr &pTask)
112112

113113
mConstants = mConstantDoubles.data();
114114
mComputedConstants = mComputedConstantDoubles.data();
115-
mAlgebraic = mAlgebraicDoubles.data();
115+
mAlgebraicVariables = mAlgebraicDoubles.data();
116116

117117
mResults.constants.resize(mAnalyserModel->constantCount(), {});
118118
mResults.computedConstants.resize(mAnalyserModel->computedConstantCount(), {});
@@ -137,7 +137,7 @@ void SedInstanceTask::Impl::trackResults(size_t pIndex)
137137
}
138138

139139
for (size_t i {0}; i < mAnalyserModel->algebraicVariableCount(); ++i) {
140-
mResults.algebraic[i][pIndex] = mAlgebraic[i]; // NOLINT
140+
mResults.algebraic[i][pIndex] = mAlgebraicVariables[i]; // NOLINT
141141
}
142142
}
143143

@@ -169,37 +169,37 @@ void SedInstanceTask::Impl::initialise()
169169
mVoi = mSedUniformTimeCourse->pimpl()->mOutputStartTime;
170170

171171
#ifdef __EMSCRIPTEN__
172-
mRuntime->initialiseArraysForDifferentialModel(mStates, mRates, mConstants, mComputedConstants, mAlgebraic);
172+
mRuntime->initialiseArraysForDifferentialModel(mStates, mRates, mConstants, mComputedConstants, mAlgebraicVariables);
173173
#else
174-
mRuntime->initialiseArraysForDifferentialModel()(mStates, mRates, mConstants, mComputedConstants, mAlgebraic);
174+
mRuntime->initialiseArraysForDifferentialModel()(mStates, mRates, mConstants, mComputedConstants, mAlgebraicVariables);
175175
#endif
176176
} else {
177177
#ifdef __EMSCRIPTEN__
178-
mRuntime->initialiseArraysForAlgebraicModel(mConstants, mComputedConstants, mAlgebraic);
178+
mRuntime->initialiseArraysForAlgebraicModel(mConstants, mComputedConstants, mAlgebraicVariables);
179179
#else
180-
mRuntime->initialiseArraysForAlgebraicModel()(mConstants, mComputedConstants, mAlgebraic);
180+
mRuntime->initialiseArraysForAlgebraicModel()(mConstants, mComputedConstants, mAlgebraicVariables);
181181
#endif
182182
}
183183

184184
applyChanges();
185185

186186
if (mSedUniformTimeCourse != nullptr) {
187187
#ifdef __EMSCRIPTEN__
188-
mRuntime->computeComputedConstantsForDifferentialModel(mStates, mRates, mConstants, mComputedConstants, mAlgebraic);
189-
mRuntime->computeRates(mVoi, mStates, mRates, mConstants, mComputedConstants, mAlgebraic);
190-
mRuntime->computeVariablesForDifferentialModel(mVoi, mStates, mRates, mConstants, mComputedConstants, mAlgebraic);
188+
mRuntime->computeComputedConstantsForDifferentialModel(mVoi, mStates, mRates, mConstants, mComputedConstants, mAlgebraicVariables);
189+
mRuntime->computeRates(mVoi, mStates, mRates, mConstants, mComputedConstants, mAlgebraicVariables);
190+
mRuntime->computeVariablesForDifferentialModel(mVoi, mStates, mRates, mConstants, mComputedConstants, mAlgebraicVariables);
191191
#else
192-
mRuntime->computeComputedConstantsForDifferentialModel()(mStates, mRates, mConstants, mComputedConstants, mAlgebraic);
193-
mRuntime->computeRates()(mVoi, mStates, mRates, mConstants, mComputedConstants, mAlgebraic);
194-
mRuntime->computeVariablesForDifferentialModel()(mVoi, mStates, mRates, mConstants, mComputedConstants, mAlgebraic);
192+
mRuntime->computeComputedConstantsForDifferentialModel()(mVoi, mStates, mRates, mConstants, mComputedConstants, mAlgebraicVariables);
193+
mRuntime->computeRates()(mVoi, mStates, mRates, mConstants, mComputedConstants, mAlgebraicVariables);
194+
mRuntime->computeVariablesForDifferentialModel()(mVoi, mStates, mRates, mConstants, mComputedConstants, mAlgebraicVariables);
195195
#endif
196196
} else {
197197
#ifdef __EMSCRIPTEN__
198-
mRuntime->computeComputedConstantsForAlgebraicModel(mConstants, mComputedConstants, mAlgebraic);
199-
mRuntime->computeVariablesForAlgebraicModel(mConstants, mComputedConstants, mAlgebraic);
198+
mRuntime->computeComputedConstantsForAlgebraicModel(mConstants, mComputedConstants, mAlgebraicVariables);
199+
mRuntime->computeVariablesForAlgebraicModel(mConstants, mComputedConstants, mAlgebraicVariables);
200200
#else
201-
mRuntime->computeComputedConstantsForAlgebraicModel()(mConstants, mComputedConstants, mAlgebraic);
202-
mRuntime->computeVariablesForAlgebraicModel()(mConstants, mComputedConstants, mAlgebraic);
201+
mRuntime->computeComputedConstantsForAlgebraicModel()(mConstants, mComputedConstants, mAlgebraicVariables);
202+
mRuntime->computeVariablesForAlgebraicModel()(mConstants, mComputedConstants, mAlgebraicVariables);
203203
#endif
204204
}
205205

@@ -215,7 +215,7 @@ void SedInstanceTask::Impl::initialise()
215215

216216
if (mDifferentialModel) {
217217
if (!mOdeSolver->pimpl()->initialise(mVoi, mAnalyserModel->stateCount(), mStates, mRates,
218-
mConstants, mComputedConstants, mAlgebraic,
218+
mConstants, mComputedConstants, mAlgebraicVariables,
219219
mRuntime)) {
220220
addIssues(mOdeSolver, mOdeSolver->name());
221221

@@ -283,10 +283,10 @@ double SedInstanceTask::Impl::run()
283283

284284
#ifdef __EMSCRIPTEN__
285285
mRuntime->computeVariablesForDifferentialModel(mVoi, mStates, mRates,
286-
mConstants, mComputedConstants, mAlgebraic);
286+
mConstants, mComputedConstants, mAlgebraicVariables);
287287
#else
288288
mRuntime->computeVariablesForDifferentialModel()(mVoi, mStates, mRates,
289-
mConstants, mComputedConstants, mAlgebraic);
289+
mConstants, mComputedConstants, mAlgebraicVariables);
290290
#endif
291291

292292
//---GRY--- WE NEED TO CHECK FOR POSSIBLE NLA ISSUES, BUT FOR CODE COVERAGE WE NEED A MODEL THAT WOULD
@@ -315,7 +315,7 @@ double SedInstanceTask::Impl::run()
315315
}
316316

317317
for (size_t i {0}; i < mAnalyserModel->algebraicVariableCount(); ++i) {
318-
mResults.algebraic[i].resize(1, mAlgebraic[i]); // NOLINT
318+
mResults.algebraic[i].resize(1, mAlgebraicVariables[i]); // NOLINT
319319
}
320320
}
321321

‎src/sed/sedinstancetask_p.h‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -55,7 +55,7 @@ class SedInstanceTask::Impl: public Logger::Impl
5555
double *mRates {nullptr};
5656
double *mConstants {nullptr};
5757
double *mComputedConstants {nullptr};
58-
double *mAlgebraic {nullptr};
58+
double *mAlgebraicVariables {nullptr};
5959

6060
Doubles mStateDoubles;
6161
Doubles mRateDoubles;

‎src/solver/solvercvode.cpp‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -304,7 +304,7 @@ StringStringMap SolverCvode::Impl::properties() const
304304
}
305305

306306
bool SolverCvode::Impl::initialise(double pVoi, size_t pSize, double *pStates, double *pRates,
307-
double *pConstants, double *pComputedConstants, double *pAlgebraic,
307+
double *pConstants, double *pComputedConstants, double *pAlgebraicVariables,
308308
const CellmlFileRuntimePtr &pRuntime)
309309
{
310310
resetInternals();
@@ -313,7 +313,7 @@ bool SolverCvode::Impl::initialise(double pVoi, size_t pSize, double *pStates, d
313313
// Initialise the ODE solver itself.
314314

315315
SolverOde::Impl::initialise(pVoi, pSize, pStates, pRates,
316-
pConstants, pComputedConstants, pAlgebraic,
316+
pConstants, pComputedConstants, pAlgebraicVariables,
317317
pRuntime);
318318

319319
// Check the solver's properties.
@@ -398,7 +398,7 @@ bool SolverCvode::Impl::initialise(double pVoi, size_t pSize, double *pStates, d
398398

399399
mUserData.constants = pConstants;
400400
mUserData.computedConstants = pComputedConstants;
401-
mUserData.algebraic = pAlgebraic;
401+
mUserData.algebraic = pAlgebraicVariables;
402402
mUserData.runtime = pRuntime;
403403

404404
ASSERT_EQ(CVodeSetUserData(mSolver, &mUserData), CV_SUCCESS);

‎src/solver/solvercvode_p.h‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -89,7 +89,7 @@ class SolverCvode::Impl: public SolverOde::Impl
8989
StringStringMap properties() const override;
9090

9191
bool initialise(double pVoi, size_t pSize, double *pStates, double *pRates,
92-
double *pConstants, double *pComputedConstants, double *pAlgebraic,
92+
double *pConstants, double *pComputedConstants, double *pAlgebraicVariables,
9393
const CellmlFileRuntimePtr &pRuntime) override;
9494
/*---GRY--- TO BE UNCOMMENTED ONCE WE ACTUALLY NEED IT.
9595
bool reinitialise(double pVoi) override;

‎src/solver/solverforwardeuler.cpp‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -31,15 +31,15 @@ SolverPtr SolverForwardEuler::Impl::duplicate()
3131
}
3232

3333
bool SolverForwardEuler::Impl::initialise(double pVoi, size_t pSize, double *pStates, double *pRates,
34-
double *pConstants, double *pComputedConstants, double *pAlgebraic,
34+
double *pConstants, double *pComputedConstants, double *pAlgebraicVariables,
3535
const CellmlFileRuntimePtr &pRuntime)
3636
{
3737
removeAllIssues();
3838

3939
// Initialise the ODE solver itself.
4040

4141
return SolverOdeFixedStep::Impl::initialise(pVoi, pSize, pStates, pRates,
42-
pConstants, pComputedConstants, pAlgebraic,
42+
pConstants, pComputedConstants, pAlgebraicVariables,
4343
pRuntime);
4444
}
4545

‎src/solver/solverforwardeuler_p.h‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -30,7 +30,7 @@ class SolverForwardEuler::Impl: public SolverOdeFixedStep::Impl
3030
SolverPtr duplicate() override;
3131

3232
bool initialise(double pVoi, size_t pSize, double *pStates, double *pRates,
33-
double *pConstants, double *pComputedConstants, double *pAlgebraic,
33+
double *pConstants, double *pComputedConstants, double *pAlgebraicVariables,
3434
const CellmlFileRuntimePtr &pRuntime) override;
3535

3636
bool solve(double &pVoi, double pVoiEnd) override;

‎src/solver/solverfourthorderrungekutta.cpp‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -31,15 +31,15 @@ SolverPtr SolverFourthOrderRungeKutta::Impl::duplicate()
3131
}
3232

3333
bool SolverFourthOrderRungeKutta::Impl::initialise(double pVoi, size_t pSize, double *pStates, double *pRates,
34-
double *pConstants, double *pComputedConstants, double *pAlgebraic,
34+
double *pConstants, double *pComputedConstants, double *pAlgebraicVariables,
3535
const CellmlFileRuntimePtr &pRuntime)
3636
{
3737
removeAllIssues();
3838

3939
// Initialise the ODE solver itself.
4040

4141
if (!SolverOdeFixedStep::Impl::initialise(pVoi, pSize, pStates, pRates,
42-
pConstants, pComputedConstants, pAlgebraic,
42+
pConstants, pComputedConstants, pAlgebraicVariables,
4343
pRuntime)) {
4444
return false;
4545
}

‎src/solver/solverfourthorderrungekutta_p.h‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -40,7 +40,7 @@ class SolverFourthOrderRungeKutta::Impl: public SolverOdeFixedStep::Impl
4040
SolverPtr duplicate() override;
4141

4242
bool initialise(double pVoi, size_t pSize, double *pStates, double *pRates,
43-
double *pConstants, double *pComputedConstants, double *pAlgebraic,
43+
double *pConstants, double *pComputedConstants, double *pAlgebraicVariables,
4444
const CellmlFileRuntimePtr &pRuntime) override;
4545

4646
bool solve(double &pVoi, double pVoiEnd) override;

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