Version 1.20260803.0

[agarny]

No description provided.

[Copilot]

Pull request overview

This PR bumps the library version, adds new benchmark harnesses/resources across C++/Python/JavaScript, and includes several runtime/solver improvements (notably around Emscripten/WASM function dispatch and KINSOL reuse), along with new regression/coverage tests.

Changes:

• Bump VERSION.txt and add benchmark resources (SED-ML) and runners for C++/Python/JavaScript.
• Extend solver and SED instance test coverage (KINSOL different system sizes; preserve issues after run()).
• Refactor runtime/solver internals (WASM function table usage, KINSOL object caching, logger issue counter fast-path, ORC JIT host CPU).

Reviewed changes

Copilot reviewed 33 out of 35 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
VERSION.txt	Version bump to 1.20260802.0.
tests/res/benchmark/tt04.sedml	Adds a benchmark SED-ML resource.
tests/res/benchmark/hypercapnea.sedml	Adds a benchmark SED-ML resource with parameter changes.
tests/res/api/solver/nla3.cellml	Adds a CellML model for larger NLA-system testing.
tests/CMakeLists.txt	Adds a native benchmark executable + benchmark target.
tests/bindings/python/test_solver_kinsol.py	Adds Python test for solving different NLA system sizes.
tests/bindings/python/test_sed_instance.py	Adds regression test: issues persist after run() on invalid instance.
tests/bindings/python/CMakeLists.txt	Generates Python benchmark script + adds python_benchmark target.
tests/bindings/python/benchmark.in.py	Implements Python benchmark driver.
tests/bindings/javascript/solver.kinsol.test.js	Adds JS test for solving different NLA system sizes.
tests/bindings/javascript/sed.instance.test.js	Adds regression test: issues persist after run() on invalid instance.
tests/bindings/javascript/res/res/libopencor.js	Adjusts JS resource loader to store libOpenCOR handle globally.
tests/bindings/javascript/CMakeLists.txt	Adds javascript_benchmark target.
tests/bindings/javascript/benchmark.js	Implements JavaScript benchmark driver.
tests/benchmark/benchmark.cpp	Implements C++ benchmark executable.
tests/api/solver/kinsoltests.cpp	Adds C++ unit test for different NLA system sizes.
tests/api/solver/coveragetests.cpp	Adds coverage test ensuring KINSOL objects are recreated/reused correctly across solves.
tests/api/sed/instancetests.cpp	Adds C++ regression test: issues persist after run() on invalid instance.
src/support/cellml/cellmlfileruntime.h	Adjusts runtime interface for WASM/table-based function dispatch.
src/support/cellml/cellmlfileruntime.cpp	Implements WASM table slot installation + per-thread base reuse.
src/support/cellml/cellmlfileruntime_p.h	Updates private runtime storage consistent with new dispatch approach.
src/solver/solverode.cpp	Caches compute-rates function pointer for faster calls.
src/solver/solverode_p.h	Stores cached compute-rates function pointer.
src/solver/solverkinsol.cpp	Adds KINSOL object caching + Emscripten objective-function slot resolution.
src/solver/solverkinsol_p.h	Adds cached KINSOL objects and associated state.
src/solver/solvercvode.cpp	Uses cached compute-rates function pointer via user-data.
src/solver/solvercvode_p.h	Stores cached compute-rates function pointer in CVODE user-data.
src/sed/sedinstancetask.cpp	Simplifies runtime calls via function-pointer getters.
src/sed/sedinstance.cpp	Restores initial task issues on run() and updates issue-count bookkeeping.
src/sed/sedinstance_p.h	Stores separate issue/error/warning snapshots for restoring on run.
src/misc/compiler.cpp	Tunes ORC JIT target machine builder to host CPU + aggressive opt.
src/logger/logger.cpp	Uses atomic counters for fast has*/*Count without locking.
src/logger/logger_p.h	Switches to std::mutex and adds atomic counters for issues/errors/warnings.

Suppressed comments (4)

src/logger/logger.cpp:58

• Same memory-ordering issue as for issue counts: hasErrors()/errorCount() are read without locking, so they should use memory_order_acquire to synchronize with memory_order_release updates in writer paths.

bool Logger::Impl::hasErrors() const
{
    return mErrorCount.load(std::memory_order_relaxed) != 0;
}

size_t Logger::Impl::errorCount() const
{
    return mErrorCount.load(std::memory_order_relaxed);
}

src/logger/logger.cpp:86

• Same memory-ordering issue as for issue counts: hasWarnings()/warningCount() are read without locking, so they should use memory_order_acquire to synchronize with memory_order_release updates in writer paths.

bool Logger::Impl::hasWarnings() const
{
    return mWarningCount.load(std::memory_order_relaxed) != 0;
}

size_t Logger::Impl::warningCount() const
{
    return mWarningCount.load(std::memory_order_relaxed);
}

src/logger/logger.cpp:136

• The issue vectors are mutated under the mutex, but the corresponding counters are updated with memory_order_relaxed, which permits reordering of the counter update ahead of the vector mutation as observed by lock-free readers. Use memory_order_release on these increments so hasIssues()/issueCount() (with acquire loads) won’t observe a non-zero count before the vectors are updated.

    auto issue {IssuePtr {new Issue {pType, pDescription, pContext}}};
    mIssues.push_back(issue);

    mIssueCount.fetch_add(1, std::memory_order_relaxed);

src/logger/logger.cpp:168

• removeAllIssues() updates the vectors and then resets the lock-free counters, but memory_order_relaxed allows the compiler to reorder the counter reset before the vector clears as observed by other threads. Use memory_order_release for these stores so lock-free readers doing acquire loads won’t see zero counts while old issues are still visible.

void Logger::Impl::removeAllIssues()
{
    const std::scoped_lock<std::mutex> lock(mMutex);

    mIssues.clear();
    mErrors.clear();
    mWarnings.clear();

    mIssueCount.store(0, std::memory_order_relaxed);
    mErrorCount.store(0, std::memory_order_relaxed);
    mWarningCount.store(0, std::memory_order_relaxed);

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