Stabilize new build in separate repository, and get CI/CD working#8
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Wires tests/unit/smoke_test.py into ctest as python_smoke_test via a PYTHON_TEST_INTERPRETER cache var. The entry is skipped at configure time when pyvcell_odesolver isn't importable, so CI's native ctest job stays green; cibuildwheel exercises the same file independently via pytest. Also rewrites CLAUDE.md, which still described the upstream multi-solver parent repo, and ignores wheelhouse/ + the pycache from the new test. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Stabilize the ODE solver against sanitizers, modernize the build, and ship a
Python distribution alongside the native CLI.
argparse,spdlog,libcurl); CMake minimum 3.13 → 3.16; consolidate platform detection onWIN32; new optionsOPTION_TARGET_PYTHON_BINDING,OPTION_TEST_WITH_LOCALHOST,OPTION_STATICALLY_LINK; warning cleanuppass and
sprintfremoval so the C++20 build compiles clean.VCellSolverInput+VCellSolverFactory; introduce abstractVCellSolverbase; replace the 273-line hand-rolled argv parser in
SundialsSolverStandalonewithargparse; expose a reusablesolve(input, output, tid)entry inSundialsSolverInterface(used byboth the CLI and the Python module).
SimulationMessagingintoMessageEventManager(worker thread + queue, with documented lockordering),
CurlProxyClasses(AbstractCurlProxy/NullCurlProxy/CurlProxy— replaces#ifdef USE_MESSAGINGforests with polymorphism),JobEventStatus(now aJobEvent::Statusnamespaced enum), andWorkerEvent. Fixes from TSAN/UBSAN/leak runs: data race,mutex-access-before-constructor-finished, undefined behavior, memory
leaks, int overflow in a test.
std::jthread→std::threadforcompiler portability. Net:
SimulationMessaging.cpp755 → 194 lines.pyvcell_odesolver): scikit-build-core + vendoredpybind11;src/main.cppexposesversion()andsolve(cvode_input_file_path, output_file_path, tid=-1).arm64, Python 3.10–3.13. Per-platform Conan profiles,
cibuildwheelPython wheels,
lipomacOS Universal build, GHCR manylinux images,moldlinker on Linux, sanitizer-enabled CMake.IDAWin/tests/smoke/smoke.pywith a top-leveltests/dir of GoogleTest C++ tests (smoke, hello, message-processing)plus a
test_basic.pythat exercises the wheel.Test plan
ctest -VVgreen locally (Linux, macOS); Windows via CISundialsSolverStandalone_x64runs the smoke.cvodeInputandmatches
*.ida.expected/*.cvode.expectedpip installof the built wheel exposespyvcell_odesolver.solve(...)and produces output matching the CLI-DOPTION_TARGET_MESSAGING=ONagainst a localhost broker(
-DOPTION_TEST_WITH_LOCALHOST=ON) — no TSAN/leak warningslipo -archs