Fix DSL UQ ergonomics and harden quickstart CI apt install step

[Copilot]

Query-level .uq(...) was leaking into metrics that were explicitly configured as deterministic via compute(..., uncertainty=False). This broke expected per-metric override behavior in mixed deterministic/uncertainty queries.

• Per-metric UQ override semantics

  • Added explicit override tracking on compute items with a tri-state field:
    • None: not specified at metric level
    • True: explicitly enabled
    • False: explicitly disabled
  • This distinguishes default behavior from an intentional opt-out.

• UQ resolution precedence fix

  • Updated UQ resolution to treat uncertainty_explicit=False as an explicit metric-level opt-out from query-level .uq(...) when no metric-level UQ params are provided.
  • Preserved existing behavior where metric-level UQ params (e.g. method, n_samples) still take precedence.

• Code-level clarity

  • Documented tri-state semantics directly in AST and resolver comments to make precedence behavior explicit for future maintenance.

• CI hardening (from PR feedback)

  • Updated .github/workflows/tutorial-validation.yml to reduce apt mirror flakiness in Install system dependencies:
    • configured apt retries (Acquire::Retries "3")
    • configured apt HTTP/HTTPS timeouts (Acquire::http::Timeout "30", Acquire::https::Timeout "30")
    • forced noninteractive apt mode
    • used --no-install-recommends
    • increased step timeout from 5 to 10 minutes

result = (
    Q.nodes()
     .uq(method="perturbation", n_samples=10, seed=42)   # query-level default
     .compute("degree")                                   # uncertain
     .compute("clustering", uncertainty=False)            # explicit deterministic override
     .execute(net)
)

[SkBlaz]

@copilot The failure is in “Install system dependencies” and is caused by apt-get update hanging on Ubuntu mirrors until the step’s 5-minute timeout is hit:

• Workflow: .github/workflows/tutorial-validation.yml
• Failing lines: 50-52 (apt-get update + install)
• Error from logs: The action 'Install system dependencies' has timed out after 5 minutes.

Recommended fix

Make apt non-interactive, add retries/timeouts, and increase that step timeout slightly.

- name: Install system dependencies
  run: |
    sudo mkdir -p /etc/apt/apt.conf.d
    echo 'Acquire::Retries "3";' | sudo tee /etc/apt/apt.conf.d/80-retries
    echo 'Acquire::http::Timeout "30";' | sudo tee /etc/apt/apt.conf.d/80-timeout
    echo 'Acquire::https::Timeout "30";' | sudo tee -a /etc/apt/apt.conf.d/80-timeout

    sudo DEBIAN_FRONTEND=noninteractive apt-get update -y
    sudo DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
      gcc g++ build-essential
  timeout-minutes: 10

Optional optimization (best for this workflow)

You likely don’t need this step at all for quickstart validation (manylinux wheels usually cover numpy/scipy on 3.8/3.10/3.12). If your examples don’t compile native extensions, remove the whole “Install system dependencies” step to avoid flaky network dependency entirely.

So the two practical paths are:

1. Most robust/minimal CI flake risk: remove step 48–52.
2. If compilers are needed: keep step but apply the hardened apt config above + longer timeout.

[Copilot]

@copilot The failure is in “Install system dependencies” and is caused by apt-get update hanging on Ubuntu mirrors until the step’s 5-minute timeout is hit:

• Workflow: [`.github/workfl...

Applied the workflow hardening in .github/workflows/tutorial-validation.yml: added apt retries + HTTP/HTTPS timeouts, switched apt calls to noninteractive mode, used --no-install-recommends, and increased the step timeout to 10 minutes. Commit: 1ab4cc8.