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Version 0.20251204.0.
2 parents 0a29d8c + 623fbec commit a7b4459

36 files changed

+232
-217
lines changed

‎.github/workflows/ci.yml‎

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@@ -399,7 +399,7 @@ jobs:
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run: uv pip install --system pytest pytest-html
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- name: Install Sphinx and some Sphinx packages
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if: ${{ matrix.documentation == 'ON' }}
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run: uv pip install --system sphinx sphinx-copybutton sphinx-inline-tabs
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run: uv pip install --system sphinx~=8.0 sphinx-copybutton sphinx-inline-tabs
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- name: Install Doxygen
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if: ${{ matrix.documentation == 'ON' }}
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run: |

‎VERSION.txt‎

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@@ -1 +1 @@
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0.20251030.0
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0.20251204.0

‎cmake/environmentchecks.cmake‎

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@@ -281,9 +281,19 @@ endif()
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if(DOXYGEN_EXE AND PATCH_EXE AND PYTHON_EXE AND SPHINX_EXE)
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set(EXPECTED_DOXYGEN_VERSION 1.9.3)
284+
set(UNSUPPORTED_SPHINX_VERSION 9.0.0)
285+
286+
execute_process(COMMAND ${SPHINX_EXE} --version
287+
OUTPUT_VARIABLE SPHINX_VERSION_OUTPUT
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OUTPUT_STRIP_TRAILING_WHITESPACE
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ERROR_QUIET)
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291+
string(REGEX REPLACE "^sphinx-build ([0-9]+\\.[0-9]+\\.[0-9]+).*$" "\\1" SPHINX_VERSION "${SPHINX_VERSION_OUTPUT}")
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if(NOT DOXYGEN_VERSION VERSION_EQUAL EXPECTED_DOXYGEN_VERSION)
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set(DOCUMENTATION_AVAILABLE_ERROR_MESSAGE "Documentation is requested and Doxygen ${DOXYGEN_VERSION} was found, but version ${EXPECTED_DOXYGEN_VERSION} is needed.")
295+
elseif(SPHINX_VERSION VERSION_GREATER_EQUAL UNSUPPORTED_SPHINX_VERSION)
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set(DOCUMENTATION_AVAILABLE_ERROR_MESSAGE "Documentation is requested and Sphinx ${SPHINX_VERSION} was found, but version ${UNSUPPORTED_SPHINX_VERSION}+ is not supported." )
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else()
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check_python_package(sphinx-copybutton PYTHON_SPHINX_COPY_BUTTON_AVAILABLE)
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check_python_package(sphinx-inline-tabs PYTHON_SPHINX_INLINE_TABS_AVAILABLE)

‎cmake/packages.cmake‎

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@@ -195,7 +195,7 @@ function(retrieve_package PACKAGE_NAME PACKAGE_VERSION PACKAGE_REPOSITORY RELEAS
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if("${PACKAGE_NAME}" STREQUAL "libCellML")
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#---GRY--- USE THIS VERSION OF libCellML WHICH CORRESPONDS TO PR #1256 UNTIL IT GETS MERGED IN.
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set(PACKAGE_URL "https://github.com/agarny/${PACKAGE_REPOSITORY}/releases/download/6d27883/${PACKAGE_FILE}")
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set(PACKAGE_URL "https://github.com/agarny/${PACKAGE_REPOSITORY}/releases/download/7cc5bea/${PACKAGE_FILE}")
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endif()
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set(ATTEMPT 1)

‎extern/README.md‎

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@@ -1,5 +1,5 @@
11
[libOpenCOR](https://opencor.ws/libopencor/index.html) relies on the following external projects:
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33
- [GoogleTest](https://github.com/google/googletest) [1.17.0](https://github.com/google/googletest/releases/tag/v1.17.0)
4-
- [modp_b64](https://chromium.googlesource.com/chromium/src/third_party/modp_b64/) at commit [bcb074f](https://chromium.googlesource.com/chromium/src/third_party/modp_b64/+/bcb074f6614b4cbda45c9f87f968f6743266a52a)
4+
- [modp_b64](https://chromium.googlesource.com/chromium/src/third_party/modp_b64/) at commit [5068510](https://chromium.googlesource.com/chromium/src/third_party/modp_b64/+/50685101d51ef9aabbd60c94f52d9e026d39c509)
55
- [nanobind](https://github.com/wjakob/nanobind) [2.9.2](https://github.com/wjakob/nanobind/releases/tag/v2.9.2)

‎extern/modp_b64/README.chromium‎

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@@ -3,6 +3,7 @@ Short Name: stringencoders
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URL: https://github.com/client9/stringencoders
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Version: 2.0.0
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Revision: 26701a1c1fcb98ae43eefcaee23abc58459a6e59
6+
Update Mechanism: Static.HardFork (https://crbug.com/422922180)
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License: BSD-3-Clause
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License File: LICENSE
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Security Critical: yes

‎src/3rdparty/libCellML/CMakeLists.txt‎

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@@ -34,49 +34,49 @@ if(LIBOPENCOR_PREBUILT_LIBCELLML)
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if(EMSCRIPTEN)
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retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
3636
${PACKAGE_REPOSITORY} ${RELEASE_TAG}
37-
f3087749522fb85a72d440180b9b4c3b5bf77eb4)
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5bee3b3c508fb274e084468243b43d9f83647beb)
3838
else()
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if(WIN32)
4040
if(RELEASE_MODE)
4141
if(INTEL_MODE)
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retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
4343
${PACKAGE_REPOSITORY} ${RELEASE_TAG}
44-
b1bfb0c9d197e7b858f5f27f305bda5ae40a9ad7)
44+
d277ce028be3806aa2514ba27ec4bed352faf069)
4545
else()
4646
retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
4747
${PACKAGE_REPOSITORY} ${RELEASE_TAG}
48-
4d06110bb96f71cff8f1fb0e0e463f94920f8fa9)
48+
388a936417a5681fbcf835bdda20e8ed0fbf3382)
4949
endif()
5050
else()
5151
if(INTEL_MODE)
5252
retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
5353
${PACKAGE_REPOSITORY} ${RELEASE_TAG}
54-
214b685fbaf9c616739ad8786800b75d59a47f8b)
54+
c768d8c59db5ee4a07baa0fc61d7a8ccac4ea6db)
5555
else()
5656
retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
5757
${PACKAGE_REPOSITORY} ${RELEASE_TAG}
58-
0d6d70f9fdf7443d82016216a78be7d2acea2e7e)
58+
2fd521abaf83b480e5b07c746ae310be529faa7e)
5959
endif()
6060
endif()
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elseif(APPLE)
6262
if(INTEL_MODE)
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retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
6464
${PACKAGE_REPOSITORY} ${RELEASE_TAG}
65-
8ccd4a8a95a3b4b243d900746340f167d9f31075)
65+
055181384ac2e4e942603c6b1f3d0c20f439b523)
6666
else()
6767
retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
6868
${PACKAGE_REPOSITORY} ${RELEASE_TAG}
69-
72b1e4f2e4a2b76a0d45efced9ef96cbba263d66)
69+
847c024d893e3a1f73172e8f6d2e55136e46dd86)
7070
endif()
7171
else()
7272
if(INTEL_MODE)
7373
retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
7474
${PACKAGE_REPOSITORY} ${RELEASE_TAG}
75-
623866e3cf071f652fe778a22868b5c6917db6f9)
75+
f8d847dffd74264a3074e742149dca0ab4c57653)
7676
else()
7777
retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
7878
${PACKAGE_REPOSITORY} ${RELEASE_TAG}
79-
9742ef210ca1cc88549b802c6f0fc5d1c0670f25)
79+
674bb536a67cc7e7d4afef553c843ac38d44d43f)
8080
endif()
8181
endif()
8282
endif()
@@ -86,7 +86,7 @@ elseif(NOT ONLY_BUILD_JAVASCRIPT_THIRD_PARTY_LIBRARIES)
8686
build_package(${PACKAGE_NAME}
8787
URL
8888
# https://github.com/opencor/${PACKAGE_REPOSITORY}/archive/refs/tags/${RELEASE_TAG}.tar.gz
89-
https://github.com/agarny/${PACKAGE_REPOSITORY}/archive/refs/tags/6d27883.tar.gz
89+
https://github.com/agarny/${PACKAGE_REPOSITORY}/archive/refs/tags/7cc5bea.tar.gz
9090
DOWNLOAD_NO_PROGRESS ON
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CMAKE_ARGS
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-DBINDINGS_PYTHON=OFF

‎src/api/libopencor/sedinstancetask.h‎

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Original file line numberDiff line numberDiff line change
@@ -288,7 +288,7 @@ class LIBOPENCOR_EXPORT SedInstanceTask: public Logger
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* @return The number of algebraic variables.
289289
*/
290290

291-
size_t algebraicCount() const;
291+
size_t algebraicVariableCount() const;
292292

293293
/**
294294
* @brief Get the values of the algebraic variable at the given index.
@@ -300,10 +300,10 @@ class LIBOPENCOR_EXPORT SedInstanceTask: public Logger
300300
* @return The values of the algebraic variable, as a @c Doubles, if the index is valid, an empty vector otherwise.
301301
*/
302302

303-
Doubles algebraic(size_t pIndex) const;
303+
Doubles algebraicVariable(size_t pIndex) const;
304304

305305
#ifdef __EMSCRIPTEN__
306-
emscripten::val algebraicAsArray(size_t pIndex) const;
306+
emscripten::val algebraicVariableAsArray(size_t pIndex) const;
307307
#endif
308308

309309
/**
@@ -317,7 +317,7 @@ class LIBOPENCOR_EXPORT SedInstanceTask: public Logger
317317
* otherwise.
318318
*/
319319

320-
std::string algebraicName(size_t pIndex) const;
320+
std::string algebraicVariableName(size_t pIndex) const;
321321

322322
/**
323323
* @brief Get the unit of the algebraic variable.
@@ -330,7 +330,7 @@ class LIBOPENCOR_EXPORT SedInstanceTask: public Logger
330330
* otherwise.
331331
*/
332332

333-
std::string algebraicUnit(size_t pIndex) const;
333+
std::string algebraicVariableUnit(size_t pIndex) const;
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335335
private:
336336
class Impl; /**< Forward declaration of the implementation class, @private. */

‎src/bindings/javascript/sed.cpp‎

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Original file line numberDiff line numberDiff line change
@@ -120,11 +120,11 @@ void sedApi()
120120
.function("computedConstantAsArray", &libOpenCOR::SedInstanceTask::computedConstantAsArray)
121121
.function("computedConstantName", &libOpenCOR::SedInstanceTask::computedConstantName)
122122
.function("computedConstantUnit", &libOpenCOR::SedInstanceTask::computedConstantUnit)
123-
.property("algebraicCount", &libOpenCOR::SedInstanceTask::algebraicCount)
124-
.function("algebraic", &libOpenCOR::SedInstanceTask::algebraic)
125-
.function("algebraicAsArray", &libOpenCOR::SedInstanceTask::algebraicAsArray)
126-
.function("algebraicName", &libOpenCOR::SedInstanceTask::algebraicName)
127-
.function("algebraicUnit", &libOpenCOR::SedInstanceTask::algebraicUnit);
123+
.property("algebraicVariableCount", &libOpenCOR::SedInstanceTask::algebraicVariableCount)
124+
.function("algebraicVariable", &libOpenCOR::SedInstanceTask::algebraicVariable)
125+
.function("algebraicVariableAsArray", &libOpenCOR::SedInstanceTask::algebraicVariableAsArray)
126+
.function("algebraicVariableName", &libOpenCOR::SedInstanceTask::algebraicVariableName)
127+
.function("algebraicVariableUnit", &libOpenCOR::SedInstanceTask::algebraicVariableUnit);
128128

129129
// SedModel API.
130130

‎src/bindings/python/sed.cpp‎

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Original file line numberDiff line numberDiff line change
@@ -124,10 +124,10 @@ void sedApi(nb::module_ &m)
124124
.def("computed_constant", &libOpenCOR::SedInstanceTask::computedConstant, "Return the values of a computed constant.")
125125
.def("computed_constant_name", &libOpenCOR::SedInstanceTask::computedConstantName, "Return the name of a computed constant.")
126126
.def("computed_constant_unit", &libOpenCOR::SedInstanceTask::computedConstantUnit, "Return the unit of a computed constant.")
127-
.def_prop_ro("algebraic_count", &libOpenCOR::SedInstanceTask::algebraicCount, "Return the number of algebraic variables.")
128-
.def("algebraic", &libOpenCOR::SedInstanceTask::algebraic, "Return the values of an algebraic variable.")
129-
.def("algebraic_name", &libOpenCOR::SedInstanceTask::algebraicName, "Return the name of an algebraic variable.")
130-
.def("algebraic_unit", &libOpenCOR::SedInstanceTask::algebraicUnit, "Return the unit of an algebraic variable.");
127+
.def_prop_ro("algebraic_variable_count", &libOpenCOR::SedInstanceTask::algebraicVariableCount, "Return the number of algebraic variables.")
128+
.def("algebraic_variable", &libOpenCOR::SedInstanceTask::algebraicVariable, "Return the values of an algebraic variable.")
129+
.def("algebraic_variable_name", &libOpenCOR::SedInstanceTask::algebraicVariableName, "Return the name of an algebraic variable.")
130+
.def("algebraic_variable_unit", &libOpenCOR::SedInstanceTask::algebraicVariableUnit, "Return the unit of an algebraic variable.");
131131

132132
// SedModel API.
133133

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