fix: emergency dump one full-hierarchy step, not per-level

[igirault]

Fix by claude for #1275. Here his explanation:

Summary

• Emergency dumps (handle_dictionary_exception) looped dump_level(ilvl) per AMR level. Each dump_level call bumps VTKHDF's /Steps/NSteps and appends a Values entry once while writing only that level's data — VTKHDF OverlappingAMR requires one step to hold all levels, so a multi-level emergency dump produced split, partial steps that ParaView renders as blank. Single-level/no-AMR runs happened to survive since dump_level(0) is effectively a full snapshot in that case.
• dump_level also skipped compute(), leaving derived quantities ( P, V) stale in the emergency snapshot.
• Adds IDiagnosticsManager::dump_all(timeStamp): runs compute() on every diagnostic, then a single full-hierarchy dump() — one consistent VTKHDF step with all levels. The emergency handler now calls dump_all instead of the per-level loop.

Test plan

• Existing emergency-dump exercising tests still build/pass (verified on the branch this fix was developed on)
• CI

🤖 Generated with Claude Code

[coderabbitai]

📝 Walkthrough

Walkthrough

The diagnostics API adds an unconditional full-hierarchy dump operation. The concrete manager gathers all diagnostics into one writer call, and simulator emergency handling uses it instead of dumping each AMR level separately.

Changes

Emergency dump flow

Layer / File(s)	Summary
Full-hierarchy dump contract and implementation src/diagnostic/diagnostic_manager.hpp, src/diagnostic/diagnostics.hpp	Adds dump_all, recomputes derived diagnostics, writes the full active set in one operation, and updates the null implementation.
Emergency handler integration src/simulator/simulator.hpp	Replaces per-level emergency dumps with a single full-hierarchy dump at the current simulation time.

Estimated code review effort: 2 (Simple) | ~10 minutes

Sequence Diagram(s)

sequenceDiagram
  participant Simulator
  participant DiagnosticsManager
  participant DiagnosticWriter
  Simulator->>DiagnosticsManager: dump_all(currentTime_)
  DiagnosticsManager->>DiagnosticsManager: recompute derived quantities
  DiagnosticsManager->>DiagnosticWriter: dump all active diagnostics

Loading

Possibly related PRs

• PHAREHUB/PHARE#1123: Modifies the emergency dictionary-exception path to trigger an all-level diagnostics dump.

Suggested reviewers: philipdeegan

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Linked Issues check	✅ Passed	The PR directly addresses issue #1275 by fixing VTKHDF emergency dumps with multiple AMR levels to be visualizable in ParaView.
Out of Scope Changes check	✅ Passed	All changes are scoped to the emergency dump fix: new dump_all method, NullOpDiagnosticsManager override, and emergency handler update.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Title check	✅ Passed	The title clearly summarizes the main change: switching emergency dumps from per-level output to a single full-hierarchy step.
Description check	✅ Passed	The description matches the implemented fix and explains the emergency dump behavior change, compute step, and test plan.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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[coderabbitai]

🧹 Nitpick comments (1)

src/simulator/simulator.hpp (1)

591-595: 🗄️ Data Integrity & Integration | 🔵 Trivial | 🏗️ Heavy lift

Add a regression test for the emergency-dump contract.

Exercise a hierarchy with at least three AMR levels and assert that the emergency path performs exactly one full-hierarchy dump(...) after recomputing all diagnostics. This directly protects issue #1275 from regressing.

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@src/simulator/simulator.hpp` around lines 591 - 595, Add a regression test
for the emergency-dump path around the simulator code invoking
dMan->dump_all(currentTime_). Build a hierarchy with at least three AMR levels,
trigger the emergency snapshot, and assert diagnostics are recomputed before
exactly one full-hierarchy dump occurs, rather than one dump per level. Use the
existing dump and diagnostics test hooks or mocks to verify the call count and
ordering.

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Nitpick comments:
In `@src/simulator/simulator.hpp`:
- Around line 591-595: Add a regression test for the emergency-dump path around
the simulator code invoking dMan->dump_all(currentTime_). Build a hierarchy with
at least three AMR levels, trigger the emergency snapshot, and assert
diagnostics are recomputed before exactly one full-hierarchy dump occurs, rather
than one dump per level. Use the existing dump and diagnostics test hooks or
mocks to verify the call count and ordering.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: CHILL

Plan: Pro Plus

Run ID: 8526c185-97fc-4f39-9345-737570da0ccd

📥 Commits

Reviewing files that changed from the base of the PR and between 6ead776 and 99895c4.

📒 Files selected for processing (3)

• src/diagnostic/diagnostic_manager.hpp
• src/diagnostic/diagnostics.hpp
• src/simulator/simulator.hpp