Reconcile stabilize-new-build with master (release branch → master) - #9
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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>
plus: now officially using uv
+ version output improvement
Also: adding windows on arm (woa) support(?)
Both libraries are shared with vcell-stochastic, which already consumes them as submodules. Vendoring them here let the copies drift apart. vcell-messaging: the public API is byte-identical to the copy it replaces (the apparent diff was CRLF vs LF), so no call sites change. The submodule additionally carries a deadlock fix and a shutdown fix: the lock order is now queue-before-stop rather than the reverse, and shutdown joins the worker instead of waiting for the queue to drain -- an empty queue is not "all work finished", since the worker pops under the lock but sends after releasing it. vcell-expressionparser: the in-tree copy here was the *newer* of the two -- the std::format/nullptr/warning cleanup from f3c3107 and 096ba48 existed only in this repo. Rather than lose it, that work was pushed up to the submodule (virtualcell/vcell-expressionparser @ 2fd45ae) and is pinned here, so the two repos converge on the better copy instead of the older one. The target rename ExpressionParser -> vcellexpressionparser is reflected in IDAWin. ExpressionParserTest/ is left alone; it was already wired into nothing. Verified: clean configure, full build, and all 4 gtest cases pass. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
OdeResultSet.cpp and VCellSundialsSolver.cpp call memset/memcpy without including <cstring>. Older libstdc++ pulled it in transitively through other headers; GCC 13 no longer does, so both fail to compile with "'memset' was not declared in this scope". Pre-existing and unrelated to the submodule migration -- it reproduces on a pristine checkout of this branch. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Added support for recursive submodule checkout in CI workflow.
The windows-latest runner moved to the windows-2025-vs2026 image, which
ships only Visual Studio 18 (MSVC 14.51). The x86_64 Conan profile pinned
compiler.runtime_version=v143, and for compiler=clang Conan derives the
Visual Studio version from that setting rather than from
tools.microsoft.msbuild:vs_version (see _vcvars_versions() in
conan/tools/microsoft/visual.py, which maps v143/v144 -> VS 17 and
v145 -> VS 18). VCVars therefore looked for a VS 17 install that no longer
exists and the job failed while building fmt from source:
ConanException: VS non-existing installation: Visual Studio 17
Bump the x86_64 profile to v145. Windows-ARM64 stays on v144 because the
windows-11-arm64 image still carries VS 17; it will need the same bump when
that image rolls forward.
Also record the runtime_version -> Visual Studio mapping in CLAUDE.md and in
the profile, since the setting's name does not suggest it selects a Visual
Studio installation.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Five issues introduced by this branch and left behind when it replaced the pybind11/scikit-build scaffold with ctypes + uv_build: - version() was annotated `-> str` but returned the ReturnValue pydantic model from call_version() unchanged, so callers got `success=True message='...'` instead of the version string. Unwrap `.message`, matching how solve() already unwraps `.success`. The existing test only asserted `is not None`, so it caught nothing either way. - .gitignore listed __pycache__ per directory and missed pyvcell_odesolver/_internal/, which appeared as untracked .pyc files. Replace the three entries with a single __pycache__/ rule. - [tool.ruff] src pointed at "src", a directory that has never existed in this layout (the package sits at the repo root), leaving first-party import resolution misconfigured. - argparse was fetched via FetchContent with no GIT_TAG, so every clean configure cloned whatever was on the default branch. Pin v3.2 to match the ">=3.2 <4.0" range conanfile.py already declares; googletest alongside it was already pinned. - extern/pybind11 (3.4 MB) had no remaining references anywhere -- no add_subdirectory, no find_package -- once the bindings became ctypes. CLAUDE.md documented the first four as known defects; updated accordingly. Verified: cmake configure/build clean with argparse pinned at v3.2, ctest 4/4, pytest 2/2, and version() now returns a str. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Picks up virtualcell/vcell-expressionparser#1, which fixes two format-string regressions from the modernization sweep this branch already pins: - ASTFloatNode::infixString rendered every non-zero float as the literal ":.20g", so Expression::infix() produced unparseable output. Here that showed up only in log and exception text -- the discontinuity and event traces in VCellSundialsSolver / VCellCVodeSolver / VCellIDASolver. The one real round-trip, OdeResultSet::copyInto, has no callers. - The pow() divide-by-zero diagnostic reported the mantissa where it meant the exponent, so it always read "v=0<0". Two files, +5/-2; no API change. Builds clean and ctest passes 4/4 locally. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01VGsqtezsNq8CxfamuLUK17
master's only commit not on stabilize-new-build is e21a479 ("Enable recursive submodule checkout for vcell-ode"), which added `submodules: recursive` to the checkout step of the old cd.yml. stabilize-new-build rewrote cd.yml and already checks out submodules recursively in every job (740e9e9), so the conflict resolves to the branch's cd.yml; master's intent is preserved. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…nparser) Since 16ef980 the messaging and expression-parser sources are git submodules; without them the image build fails at add_subdirectory. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…S 17 Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
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Brings
stabilize-new-build— the branch 0.9.4 was cut from, plus the 11 commits since — ontomaster, so that releases can be cut from the default branch (VCell solver-repo plan, PR A2, release contract §1.1). Supersedes #8 (same commits, conflict resolved).What diverged
stabilize-new-build: 55 commits not on master (all of Stabilize new build in separate repository, and get CI/CD working #8, including the 0.9.4 tag).master: 1 commit not on the branch — e21a479 "Enable recursive submodule checkout for vcell-ode", which addedsubmodules: recursiveto the checkout step of the oldcd.yml.Resolution
Merge commit
70900cc8merges master into the branch; the only conflict (cd.yml) resolves to the branch's rewrittencd.yml, which already checks out submodules recursively in every job (740e9e9). master's intent is kept; nothing of master is lost. History is preserved (no squash/rebase).One extra fix
docker-deploy.ymlcheckout now usessubmodules: recursive— since 16ef980 the messaging and expression-parser code are submodules, and the image build would otherwise fail.Also:
windows-11-armhas moved to Visual Studio 18 likewindows-latest, so the Windows ARM64 Conan profile now targetscompiler.runtime_version=v145(it failed with "VS non-existing installation: Visual Studio 17").The release-contract work (archives, multi-arch image, SIF, entrypoint, smoke test) follows in a separate PR.
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