Improve the overall speed and memory use of libOpenCOR

[agarny]

Fixes #549.

[Copilot]

Pull request overview

This PR targets issue #549 by reducing avoidable allocations/copies across libOpenCOR (SED-ML/Sed runtime, logging, utilities), and by enabling stronger native build optimisations.

Changes:

• Reduce transient allocations/copies by reserving capacity, building strings without chained append(), and returning containers via new *Ref() accessors.
• Update bindings (Python/JavaScript) to use the new reference-returning accessors to avoid container copies.
• Improve native build performance via optional IPO/LTO, -O3 for non-MSVC release builds, and update CI/CD runner images and libCellML package pins.

Reviewed changes

Copilot reviewed 41 out of 41 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
src/support/sedml/sedmlfile.cpp	Avoid repeated string allocations and some container-copy patterns in SED-ML import/population.
src/support/combine/combinearchive.cpp	Reserve container sizes and reuse empty pointer singletons for out-of-range/null returns.
src/support/cellml/cellmlfileruntime.cpp	Reduce string concatenation overhead; improve NLA objective export handling; switch to unordered_set.
src/support/cellml/cellmlfile.cpp	Reuse an empty singleton pointer for early-return paths.
src/solver/solverodefixedstep.cpp	Reduce warning/error string construction overhead; factor unknown-parameter warning.
src/solver/solverkinsol.cpp	Reduce warning/error string construction overhead; factor unknown-parameter warning.
src/solver/solvercvode.cpp	Reduce warning/error string construction overhead; factor unknown-parameter warning.
src/sed/sedtask.cpp	Reduce repeated task error message construction.
src/sed/sedsimulation.cpp	Reduce repeated missing-solver error message construction.
src/sed/sedmodel_p.h	Change internal changes accessor to return by const reference.
src/sed/sedmodel.cpp	Return changes by const reference internally and add changesRef() public accessor.
src/sed/sedinstancetask.cpp	Use changesRef() and add several *Ref() accessors for result vectors; reuse empty singletons.
src/sed/sedinstance_p.h	Change internal tasks accessor to return by const reference.
src/sed/sedinstance.cpp	Use tasksRef() and reserve task instance container; add tasksRef() public accessor.
src/sed/seddocument_p.h	Change internal models/simulations/tasks accessors to return by const reference.
src/sed/seddocument.cpp	Avoid stringstream usage; add *Ref() accessors and reuse empty singletons for invalid indices.
src/sed/sedchangeattribute.cpp	Reduce repeated warning string construction and factor shared warning format.
src/misc/utils.h	Convert some globals to constexpr to reduce runtime overhead.
src/misc/utils.cpp	Optimize URL encoding and pointer-to-hex formatting; switch toString(int/size_t) to std::format.
src/misc/compiler.cpp	Reduce string churn in error construction and code assembly; minor cleanups.
src/logger/logger.cpp	Add empty singleton for invalid indices; add *Ref() accessors; reduce shared_ptr refcount churn in addIssue.
src/logger/issue.cpp	Reduce allocations in formatted issue description.
src/file/filemanager.cpp	Reduce temporary allocations when iterating children; reserve in files(); reuse empty singleton pointer.
src/file/file.cpp	Reuse empty singleton containers/pointers for “no child files” cases.
src/bindings/python/sed.cpp	Switch bindings to *Ref() accessors to avoid vector copies.
src/bindings/python/logger.cpp	Switch bindings to *Ref() accessors to avoid vector copies.
src/bindings/javascript/sed.cpp	Switch bindings to *Ref() accessors to avoid vector copies.
src/bindings/javascript/logger.cpp	Switch bindings to *Ref() accessors to avoid vector copies.
src/api/libopencor/sedmodel.h	Document/add changesRef() accessor.
src/api/libopencor/sedinstancetask.h	Document/add voiRef()/stateRef()/rateRef()/constantRef()/computedConstantRef()/algebraicVariableRef().
src/api/libopencor/sedinstance.h	Document/add tasksRef() accessor.
src/api/libopencor/seddocument.h	Document/add modelsRef()/simulationsRef()/tasksRef(); extend friend access for SedInstance.
src/api/libopencor/logger.h	Document/add issuesRef()/errorsRef()/warningsRef() accessors.
src/CMakeLists.txt	Enable IPO/LTO for native release builds when supported.
src/3rdparty/libCellML/CMakeLists.txt	Update prebuilt/build-from-source libCellML pins/URLs.
cmake/packages.cmake	Update libCellML release download tag used for prebuilt retrieval.
VERSION.txt	Bump library version.
CMakeLists.txt	Update macOS deployment target and prefer -O3 for non-MSVC release builds.
.github/workflows/ci.yml	Move CI jobs from Ubuntu 22.04 to 24.04 (including ARM runners).
.github/workflows/cd.yml	Move CD jobs from Ubuntu 22.04 to 24.04 (including ARM runners).
.github/workflows/buildThirdPartyLibrary.yml	Move third-party build workflow from Ubuntu 22.04 to 24.04 (including ARM runners).

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

Pull request overview

Copilot reviewed 80 out of 80 changed files in this pull request and generated 4 comments.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.