MILAB-6205: activate vcvars on Windows runners in node-matrix workflows

[xnacly]

Add a Setup MSVC Dev Cmd step (using the shared setup-msvc-dev-cmd action) to the prebuild job in both reusable matrix workflows so that any downstream consumer building a C / C++ extension from source on Windows finds cl.exe and the SDK headers automatically.

What's added

- name: Setup MSVC Dev Cmd
  if: runner.os == 'Windows'
  uses: milaboratory/github-ci/actions/setup-msvc-dev-cmd@v4
  with:
    arch: ${{ matrix.arch == 'arm64' && 'arm64' || 'amd64' }}

Inserted between "Install pipx" and "Configure ccache" in:

• .github/workflows/node-matrix.yaml
• .github/workflows/node-matrix-pnpm.yaml

No-op on Linux and macOS runners (the if: runner.os == 'Windows' guard). On Windows runners it activates VS 2022 Build Tools via vcvarsall (the underlying ilammy/msvc-dev-cmd action) and exports the resulting env (INCLUDE / LIB / LIBPATH / PATH plus DISTUTILS_USE_SDK=1) to subsequent steps.

Why

The windows-latest runner ships VS 2022 Build Tools but doesn't activate them by default. Any subsequent build step that compiles a C extension (e.g. pip wheel against a setuptools/distutils sdist) fails with:

error: Microsoft Visual C++ 14.0 or greater is required.
Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/

This was surfaced by the runenv-python-3 PR #88 (freesasa addition) where the freesasa sdist's plain setup.py path couldn't find cl.exe. The original attempt rolled MSVC activation inside the runenv builder; once this PR merges and the v4 tag advances, that code is removed and runenv-python-3 just lists freesasa in deps + buildWheel.

Pattern mirrors the existing usage in milaboratory/pframes-rs, which already activates MSVC via this same shared action.

Blast radius

• runner.os == 'Windows' guard means non-Windows matrix cells skip the step entirely.
• Adds ~3 seconds to Windows prebuild jobs (vswhere lookup + env capture).
• Activates VS env vars unconditionally on Windows. Steps that previously relied on default GitHub Actions Windows env (no MSVC activation) will now see MSVC env. For cmake-based builds that pin their own toolchain (e.g. kalign-python via clang-cl + Ninja in runenv-python-3 clustering), cmake's toolchain discovery overrides the env anyway, so no behavioural change.
• For setuptools-based builds that previously fell back to system tools / failed silently, the activation enables them to succeed.

Verification

Local YAML syntax checked; the matrix.arch expression matches what both reusable workflows pass through (amd64 / arm64). Real verification is downstream PRs picking up the updated @v4 ref.

Greptile Summary

Adds a Setup MSVC Dev Cmd step (wrapping ilammy/msvc-dev-cmd) to the prebuild job in both node-matrix.yaml and node-matrix-pnpm.yaml, guarded by if: runner.os == 'Windows', so that downstream Windows build steps that compile C/C++ extensions from source can find cl.exe and the SDK headers automatically.

• node-matrix.yaml and node-matrix-pnpm.yaml: The new step is inserted between the pipx install steps and the ccache configuration step, in the correct position to export MSVC env vars (INCLUDE, LIB, PATH, DISTUTILS_USE_SDK=1) before any compilation happens.
• The underlying setup-msvc-dev-cmd shared action pins ilammy/msvc-dev-cmd to a specific commit SHA, which is good practice for supply-chain safety.

Confidence Score: 5/5

Safe to merge — the change is additive, well-guarded, and follows an existing pattern in the monorepo.

Both files receive an identical, minimal addition: a single step behind runner.os == Windows that activates the VS 2022 developer environment. The underlying shared action pins ilammy/msvc-dev-cmd to a specific commit SHA. The arch expression correctly collapses to arm64 or amd64. Non-Windows matrix cells are completely unaffected, and the step's position (after pipx, before ccache) is the right order for MSVC env vars to be visible to subsequent compilation steps.

No files require special attention.

Important Files Changed

Filename	Overview
.github/workflows/node-matrix.yaml	Adds a Windows-only MSVC activation step in the prebuild job between pipx setup and ccache configuration; guard and arch expression are both correct.
.github/workflows/node-matrix-pnpm.yaml	Identical MSVC activation step added to the pnpm variant's prebuild job; same correct guard and arch expression as node-matrix.yaml.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[checkout] --> B[Install pipx\nLinux / macOS]
    B --> C{runner.os == Windows?}
    C -- Yes --> D[Setup MSVC Dev Cmd\nilammy/msvc-dev-cmd\narch: arm64 or amd64]
    C -- No --> E[Skip MSVC setup]
    D --> F{inputs.enable-ccache?}
    E --> F
    F -- Yes --> G[Configure ccache]
    F -- No --> H[Cache additional paths]
    G --> H
    H --> I[Load milab-shell-utils]
    I --> J[node/test or pnpm build]

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[notion-workspace]

[backend] Write 3D Structure Based Liabilities block

[DenKoren]

nit: better to first merge to v4-beta, then use merge-beta script.