Add idle_output_timeout as Per-Step Recipe Override by Trecek · Pull Request #793 · TalonT-Org/AutoSkillit

Trecek · 2026-04-13T05:50:39Z

Summary

Thread idle_output_timeout through the same per-step override chain that stale_threshold
already uses. Add the field to RecipeStep, parse it from YAML, validate it (0 = disabled,
negative = error), whitelist it in rules_tools.py, add it to the HeadlessExecutor protocol,
thread it through tools_execution.py and both DefaultHeadlessExecutor.run() and
run_headless_core(), then set idle_output_timeout: 0 (disabled) on the five compute-heavy
steps in research.yaml.

The key semantic difference from stale_threshold: 0 is a valid recipe value meaning
"no idle timeout for this step" (maps to None in run_managed_async's API), whereas
stale_threshold rejects 0 as invalid. The 0→None conversion happens at the resolution
layer (both DefaultHeadlessExecutor.run() and run_headless_core()).

Architecture Impact

Process Flow Diagram

%%{init: {'flowchart': {'nodeSpacing': 45, 'rankSpacing': 55, 'curve': 'basis'}}}%%
flowchart TB
    %% CLASS DEFINITIONS %%
    classDef cli fill:#1a237e,stroke:#7986cb,stroke-width:2px,color:#fff;
    classDef stateNode fill:#004d40,stroke:#4db6ac,stroke-width:2px,color:#fff;
    classDef handler fill:#e65100,stroke:#ffb74d,stroke-width:2px,color:#fff;
    classDef phase fill:#6a1b9a,stroke:#ba68c8,stroke-width:2px,color:#fff;
    classDef newComponent fill:#2e7d32,stroke:#81c784,stroke-width:2px,color:#fff;
    classDef output fill:#00695c,stroke:#4db6ac,stroke-width:2px,color:#fff;
    classDef detector fill:#b71c1c,stroke:#ef5350,stroke-width:2px,color:#fff;
    classDef gap fill:#ff6f00,stroke:#ffa726,stroke-width:2px,color:#000;
    classDef terminal fill:#1a237e,stroke:#7986cb,stroke-width:2px,color:#fff;

    %% TERMINALS %%
    START([START: Recipe YAML loaded])
    COMPLETE_WATCH([COMPLETE: idle watchdog active])
    COMPLETE_NO_WATCH([COMPLETE: no idle watchdog])
    IDLE_STALL([IDLE_STALL: process killed])

    subgraph RecipeLayer ["Recipe Layer — ● schema.py · ● io.py · ● validator.py · ● rules_tools.py"]
        direction TB
        ParseStep["● _parse_step()<br/>━━━━━━━━━━<br/>recipe/io.py<br/>data.get('idle_output_timeout')"]
        StepSchema["● RecipeStep<br/>━━━━━━━━━━<br/>idle_output_timeout: int | None<br/>None = use global cfg<br/>0 = disabled for this step"]
        Validate["● validate_recipe()<br/>━━━━━━━━━━<br/>recipe/validator.py<br/>must be int ≥ 0, or None"]
        RulesTools["● _TOOL_PARAMS[run_skill]<br/>━━━━━━━━━━<br/>recipe/rules_tools.py<br/>idle_output_timeout registered<br/>as first-class MCP param"]
    end

    subgraph MCPLayer ["MCP Layer — ● tools_execution.py"]
        direction TB
        RunSkill["● run_skill MCP tool<br/>━━━━━━━━━━<br/>server/tools_execution.py<br/>idle_output_timeout: int | None<br/>→ float(v) if v is not None else None"]
    end

    subgraph ExecutorLayer ["Executor Layer — ● _type_protocols.py · ● headless.py"]
        direction TB
        Protocol["● HeadlessExecutor.run()<br/>━━━━━━━━━━<br/>core/_type_protocols.py<br/>idle_output_timeout: float | None"]
        DefaultExec["● DefaultHeadlessExecutor.run()<br/>━━━━━━━━━━<br/>execution/headless.py<br/>_raw = val ?? float(cfg.idle_output_timeout=600)"]
        ZeroGate{"_raw_idle > 0.0?<br/>━━━━━━━━━━<br/>0 → None gate"}
    end

    subgraph CoreExec ["Core Execution — ● headless.py · process.py"]
        direction TB
        HeadlessCore["● run_headless_core()<br/>━━━━━━━━━━<br/>execution/headless.py<br/>passes effective_idle to runner<br/>(0→None guard is no-op here)"]
        ManagedAsync["run_managed_async()<br/>━━━━━━━━━━<br/>execution/process.py<br/>idle_output_timeout: float | None"]
        WatchDecision{"idle_output_timeout<br/>is not None?<br/>━━━━━━━━━━<br/>start watchdog?"}
        WatchStdout["_watch_stdout_idle()<br/>━━━━━━━━━━<br/>anyio task group coroutine<br/>polls stdout for idle time"]
    end

    %% FLOW %%
    START --> ParseStep
    ParseStep --> StepSchema
    StepSchema --> Validate
    Validate -->|"valid: int ≥ 0 or None"| RulesTools
    Validate -->|"invalid: raises error"| IDLE_STALL
    RulesTools --> RunSkill

    RunSkill --> Protocol
    Protocol --> DefaultExec
    DefaultExec --> ZeroGate
    ZeroGate -->|"yes → effective_idle: float"| HeadlessCore
    ZeroGate -->|"no (0.0) → effective_idle: None"| HeadlessCore
    HeadlessCore --> ManagedAsync
    ManagedAsync --> WatchDecision
    WatchDecision -->|"not None"| WatchStdout
    WatchDecision -->|"None (disabled)"| COMPLETE_NO_WATCH
    WatchStdout -->|"idle < threshold"| COMPLETE_WATCH
    WatchStdout -->|"idle ≥ threshold"| IDLE_STALL

    %% CLASS ASSIGNMENTS %%
    class START terminal;
    class COMPLETE_WATCH,COMPLETE_NO_WATCH output;
    class IDLE_STALL detector;
    class StepSchema stateNode;
    class ParseStep,RulesTools phase;
    class Validate detector;
    class RunSkill handler;
    class Protocol phase;
    class DefaultExec,HeadlessCore,ManagedAsync handler;
    class ZeroGate,WatchDecision stateNode;
    class WatchStdout phase;

Data Lineage Diagram

%%{init: {'flowchart': {'nodeSpacing': 50, 'rankSpacing': 65, 'curve': 'basis'}}}%%
flowchart LR
    %% CLASS DEFINITIONS %%
    classDef cli fill:#1a237e,stroke:#7986cb,stroke-width:2px,color:#fff;
    classDef stateNode fill:#004d40,stroke:#4db6ac,stroke-width:2px,color:#fff;
    classDef handler fill:#e65100,stroke:#ffb74d,stroke-width:2px,color:#fff;
    classDef phase fill:#6a1b9a,stroke:#ba68c8,stroke-width:2px,color:#fff;
    classDef output fill:#00695c,stroke:#4db6ac,stroke-width:2px,color:#fff;
    classDef detector fill:#b71c1c,stroke:#ef5350,stroke-width:2px,color:#fff;
    classDef integration fill:#c62828,stroke:#ef9a9a,stroke-width:2px,color:#fff;

    subgraph Origins ["Data Origins"]
        direction TB
        DEFAULTS["defaults.yaml<br/>━━━━━━━━━━<br/>run_skill:<br/>  idle_output_timeout: 600"]
        RESEARCH["● research.yaml<br/>━━━━━━━━━━<br/>5 steps: idle_output_timeout: 0<br/>implement / troubleshoot / experiment"]
    end

    subgraph GlobalCfg ["Global Config (Fallback Source of Truth)"]
        SETTINGS["settings.py RunSkillConfig<br/>━━━━━━━━━━<br/>idle_output_timeout: int = 600<br/>loaded from defaults.yaml"]
    end

    subgraph SchemaValidation ["● Schema, Parse & Validation"]
        direction TB
        PARSE["● io.py _parse_step()<br/>━━━━━━━━━━<br/>data.get('idle_output_timeout')<br/>raw int | None from YAML"]
        RECIPE_STEP["● schema.py RecipeStep<br/>━━━━━━━━━━<br/>idle_output_timeout: int | None<br/>None = use global; 0 = disabled"]
        VALIDATOR["● validator.py<br/>━━━━━━━━━━<br/>non-negative int required when set<br/>0 allowed (explicit disable)"]
        RULES["● rules_tools.py<br/>━━━━━━━━━━<br/>idle_output_timeout whitelisted<br/>in per-step field set (lint-time)"]
    end

    subgraph ExecPipeline ["● Execution Pipeline"]
        direction TB
        PROTOCOL["● _type_protocols.py<br/>━━━━━━━━━━<br/>HeadlessExecutor.run() protocol<br/>idle_output_timeout: float | None"]
        RUN_SKILL["● tools_execution.run_skill()<br/>━━━━━━━━━━<br/>int | None param<br/>→ float | None cast before executor"]
        HEADLESS["● HeadlessExecutor.run()<br/>━━━━━━━━━━<br/>None → fallback to cfg.idle_output_timeout<br/>0.0 → None (disabled)"]
        CORE["● run_headless_core()<br/>━━━━━━━━━━<br/>effective_idle: float | None<br/>passes to subprocess runner"]
    end

    subgraph Watchdog ["Process Watchdog (Consumption)"]
        direction TB
        MANAGED["run_managed_async()<br/>━━━━━━━━━━<br/>spawns _watch_stdout_idle task<br/>only when value is positive float"]
        WATCH["_watch_stdout_idle()<br/>━━━━━━━━━━<br/>polls stdout file size every 5s<br/>fires if size stalls ≥ timeout"]
        KILL["async_kill_process_tree()<br/>━━━━━━━━━━<br/>IDLE_STALL → kill headless Claude<br/>acc.idle_stall = True"]
    end

    %% PRIMARY DATA FLOWS %%
    DEFAULTS -->|"dynaconf load"| SETTINGS
    RESEARCH -->|"YAML parse"| PARSE
    PARSE -->|"RecipeStep(idle_output_timeout=...)"| RECIPE_STEP
    RECIPE_STEP -->|"validate at load time"| VALIDATOR
    RECIPE_STEP -->|"step.idle_output_timeout"| RUN_SKILL
    SETTINGS -->|"fallback when None"| HEADLESS
    RUN_SKILL -->|"float | None"| HEADLESS
    HEADLESS -->|"effective_idle: float | None"| CORE
    CORE -->|"runner(..., idle_output_timeout=...)"| MANAGED
    MANAGED -->|"tg.start_soon()"| WATCH
    WATCH -->|"trigger.set() on expiry"| KILL

    %% SECONDARY / STRUCTURAL FLOWS %%
    RECIPE_STEP -.->|"lint-time field whitelist"| RULES
    PROTOCOL -.->|"declares interface"| HEADLESS

    %% CLASS ASSIGNMENTS %%
    class DEFAULTS,RESEARCH cli;
    class SETTINGS,RECIPE_STEP,PROTOCOL stateNode;
    class PARSE,RUN_SKILL,MANAGED handler;
    class HEADLESS,CORE phase;
    class VALIDATOR,RULES,WATCH detector;
    class KILL integration;

Operational Diagram

%%{init: {'flowchart': {'nodeSpacing': 50, 'rankSpacing': 60, 'curve': 'basis'}}}%%
flowchart TB
    %% CLASS DEFINITIONS %%
    classDef cli fill:#1a237e,stroke:#7986cb,stroke-width:2px,color:#fff;
    classDef stateNode fill:#004d40,stroke:#4db6ac,stroke-width:2px,color:#fff;
    classDef handler fill:#e65100,stroke:#ffb74d,stroke-width:2px,color:#fff;
    classDef phase fill:#6a1b9a,stroke:#ba68c8,stroke-width:2px,color:#fff;
    classDef output fill:#00695c,stroke:#4db6ac,stroke-width:2px,color:#fff;
    classDef detector fill:#b71c1c,stroke:#ef5350,stroke-width:2px,color:#fff;
    classDef terminal fill:#1a237e,stroke:#7986cb,stroke-width:2px,color:#fff;

    %% ── CONFIGURATION SOURCES ── %%
    subgraph Config ["CONFIGURATION (read-only inputs)"]
        direction TB

        GLOBAL_CFG["RunSkillConfig<br/>━━━━━━━━━━<br/>idle_output_timeout = 600<br/>(global default, seconds)<br/>config/settings.py"]

        RESEARCH_YAML["● research.yaml<br/>━━━━━━━━━━<br/>5 compute-heavy steps:<br/>implement_phase<br/>run_experiment<br/>re_run_experiment<br/>adjust_experiment<br/>troubleshoot_implement_failure<br/>→ idle_output_timeout: 0"]
    end

    %% ── RECIPE PIPELINE ── %%
    subgraph RecipePipeline ["● RECIPE PIPELINE (parse → validate → schema)"]
        direction TB

        PARSE["● recipe/io.py<br/>━━━━━━━━━━<br/>_parse_step()<br/>data.get('idle_output_timeout')<br/>→ int | None"]

        SCHEMA["● recipe/schema.py<br/>━━━━━━━━━━<br/>RecipeStep.idle_output_timeout<br/>type: int | None<br/>default: None<br/>None = use global cfg<br/>0 = disabled for this step"]

        VALIDATE["● recipe/validator.py<br/>━━━━━━━━━━<br/>must be non-negative int or None<br/>negative values rejected<br/>0 explicitly permitted"]

        RULES["● recipe/rules_tools.py<br/>━━━━━━━━━━<br/>registered as known run_skill param<br/>prevents dead-with-param false positive"]
    end

    %% ── MCP SERVER ── %%
    subgraph MCPServer ["● MCP SERVER — run_skill tool"]
        direction TB

        RUN_SKILL["● tools_execution.py<br/>━━━━━━━━━━<br/>run_skill(idle_output_timeout: int | None)<br/>None → pass None (executor falls back to global)<br/>int → float(value) passed to executor<br/>0 → float(0.0) → executor disables timeout"]
    end

    %% ── PROTOCOL BOUNDARY ── %%
    subgraph Protocol ["● PROTOCOL BOUNDARY"]
        direction TB

        PROTOCOL["● _type_protocols.py<br/>━━━━━━━━━━<br/>HeadlessExecutor.run(<br/>  idle_output_timeout: float | None<br/>)<br/>None = use global cfg"]
    end

    %% ── EXECUTION LAYER ── %%
    subgraph Execution ["● EXECUTION LAYER"]
        direction TB

        EXECUTOR["● execution/headless.py<br/>━━━━━━━━━━<br/>DefaultHeadlessExecutor.run()<br/>Resolution:<br/>  None → float(cfg.idle_output_timeout)<br/>  0.0 → effective_idle = None (disabled)<br/>  >0.0 → effective_idle = value"]

        CORE["● run_headless_core()<br/>━━━━━━━━━━<br/>Receives pre-resolved float | None<br/>Passes effective_idle to runner<br/>None = no idle kill signal"]
    end

    %% ── SUBPROCESS ── %%
    subgraph Subprocess ["SUBPROCESS RUNNER"]
        direction TB

        RUNNER["Process Runner<br/>━━━━━━━━━━<br/>idle_output_timeout=effective_idle<br/>None → timeout disabled<br/>600.0 → kill after 600s idle<br/>custom float → step override active"]
    end

    %% ── FLOWS ── %%
    RESEARCH_YAML -->|"idle_output_timeout: 0 (YAML field)"| PARSE
    PARSE --> SCHEMA
    SCHEMA --> VALIDATE
    SCHEMA --> RULES
    VALIDATE -->|"valid RecipeStep.idle_output_timeout"| RUN_SKILL

    GLOBAL_CFG -->|"fallback default (600s)"| EXECUTOR

    RUN_SKILL -->|"int|None → float|None"| PROTOCOL
    PROTOCOL --> EXECUTOR
    EXECUTOR -->|"resolved float|None"| CORE
    CORE --> RUNNER

    %% CLASS ASSIGNMENTS %%
    class GLOBAL_CFG phase;
    class RESEARCH_YAML cli;
    class PARSE,SCHEMA handler;
    class VALIDATE,RULES detector;
    class RUN_SKILL handler;
    class PROTOCOL phase;
    class EXECUTOR handler;
    class CORE handler;
    class RUNNER output;

Closes #785

Implementation Plan

Plan file: /home/talon/projects/autoskillit-runs/impl-785-20260412-214909-105758/.autoskillit/temp/make-plan/idle_output_timeout_per_step_plan_2026-04-12_215200.md

🤖 Generated with Claude Code via AutoSkillit

Token Usage Summary

Step	uncached	output	cache_read	cache_write	count	time
plan	183	20.7k	809.0k	51.9k	1	10m 58s
verify	216	15.6k	1.6M	70.9k	1	4m 23s
implement	688	33.9k	5.4M	85.4k	1	11m 9s
prepare_pr	70	6.0k	224.2k	25.6k	1	1m 44s
run_arch_lenses	182	22.0k	483.6k	133.0k	3	10m 24s
compose_pr	67	7.6k	232.0k	28.9k	1	2m 10s
Total	1.4k	105.8k	8.7M	395.8k		40m 52s

…parser Add idle_output_timeout: int | None = None to RecipeStep dataclass, register it in _PARSE_STEP_HANDLED_FIELDS, and thread it through _parse_step() via data.get(). 0 means disabled for this step; None means fall back to global config.

…ist entry Validate that idle_output_timeout is a non-negative integer when set (0 is valid and means disabled). Add idle_output_timeout to the run_skill tool parameter whitelist so the recipe orchestrator can pass it as a kwarg.

Extend HeadlessExecutor.run() protocol signature with optional idle_output_timeout: float | None = None parameter, matching the same pattern as stale_threshold.

Add idle_output_timeout: int | None = None parameter to run_skill(), convert to float and pass to executor.run(). The None passthrough is intentional; 0→None (disabled) conversion happens in the executor layer.

… layers Add idle_output_timeout: float | None = None to run_headless_core() and DefaultHeadlessExecutor.run(). Both layers apply the same 0→None resolution (raw=0 means disabled, maps to None for run_managed_async). When not provided, falls back to float(cfg.idle_output_timeout).

…h steps Add idle_output_timeout: 0 (disabled) to implement_phase, troubleshoot_implement_failure, run_experiment, adjust_experiment, and re_run_experiment. These steps use skills that may produce no stdout for long periods (LLM thinking, compilation, experiments).

T1: RecipeStep parses idle_output_timeout from YAML (120, None, 0) T2: Validator rejects negative values, accepts 0 and positive T3: HeadlessExecutor protocol includes idle_output_timeout param T4/T5: run_skill passes idle_output_timeout to executor (120→120.0, None→None) T6: run_headless_core applies 0→None conversion and cfg fallback Also update MockExecutor signatures in existing server tests.

Reformatted rules_tools.py, tools_execution.py, and test_context.py to comply with ruff line-length and style rules.

Trecek

AutoSkillit PR Review — Verdict: changes_requested

Found 14 actionable findings (10 critical, 4 warning). See inline comments.

src/autoskillit/execution/headless.py

src/autoskillit/recipes/research.yaml

Trecek · 2026-04-13T06:03:27Z

tests/execution/test_headless.py

+        tool_ctx.runner.push(self._success_payload(marker))
+        await run_headless_core(
+            "/investigate foo", cwd="/tmp", ctx=tool_ctx, idle_output_timeout=None
+        )


[critical] tests: Same fragile call_args_list 4-tuple unpacking issue as L3599.

Investigated — this is intentional. Same as L3599 — MockSubprocessRunner stores explicit 4-tuples, documented in conftest.py:49. Unpacking is correct.

Trecek · 2026-04-13T06:03:27Z

tests/execution/test_headless.py

+    ) -> None:
+        """idle_output_timeout=None falls back to float(cfg.idle_output_timeout)."""
+        from autoskillit.execution.headless import run_headless_core
+


[warning] tests: Tautological assertion: cfg_value is read from the live config then asserted equal to the result. If the implementation simply reads the same config field, this always passes regardless of correctness. Assert against a known constant (e.g. == 600.0) to make the test meaningful.

Agreed — fixed in e8e772a. Replaced cfg_value = float(tool_ctx.config.run_skill.idle_output_timeout) reference with a direct assertion against 600.0 (the known config default per defaults.yaml:47 and settings.py:96). Test now catches implementations that ignore the config entirely.

Trecek · 2026-04-13T06:03:27Z

src/autoskillit/execution/headless.py

+        _raw_idle = (
+            idle_output_timeout
+            if idle_output_timeout is not None
+            else float(cfg.idle_output_timeout)


[warning] defense: float(cfg.idle_output_timeout) is called unconditionally with no error context. If dynaconf surfaces this as a string via an env-var override, the resulting ValueError is uncontextualised. Validate the type in the config dataclass or wrap with a descriptive try/except.

Investigated — this is intentional. settings.py:402 performs idle_output_timeout=int(val(...)) at config load time, coercing env-var overrides before they reach headless.py. By the time float(cfg.idle_output_timeout) is called at headless.py:995, the value is a validated int. An env-var string like 'abc' would raise ValueError at config load (settings.py), not here.

Trecek · 2026-04-13T06:03:27Z

src/autoskillit/server/tools_execution.py

            expected_output_patterns=expected_output_patterns,
            write_behavior=write_spec,
            stale_threshold=float(stale_threshold) if stale_threshold is not None else None,
+            idle_output_timeout=float(idle_output_timeout)


[warning] defense: float(idle_output_timeout) is called without guarding against non-numeric input. FastMCP deserialises from JSON; an unexpected type raises a confusing TypeError instead of a clean validation error. Add an isinstance guard or try/except with a descriptive message.

Investigated — this is intentional. Parameter typed as int | None at tools_execution.py:154. FastMCP validates JSON schema types before invoking the function body; non-numeric inputs are rejected at the MCP transport layer with a schema error, never reaching the float() call.

tests/server/test_tools_execution.py

…ltHeadlessExecutor.run() DefaultHeadlessExecutor.run() was pre-resolving idle_output_timeout (0.0→None) before passing it to run_headless_core(). run_headless_core() then treated None as "not supplied" and fell back to float(cfg.idle_output_timeout), re-enabling the very timeout the step intended to disable. Fix: pass raw idle_output_timeout directly to run_headless_core(), which is the single authoritative resolution layer. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

…put_timeout fallback test The previous assertion read float(cfg.idle_output_timeout) from the same config the implementation reads, making the test tautological — it would pass even if the implementation used an arbitrary config field. Assert the known default 600.0 directly. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Trecek added 8 commits April 12, 2026 22:08

feat(core): add idle_output_timeout to HeadlessExecutor protocol

daf5bc9

Extend HeadlessExecutor.run() protocol signature with optional idle_output_timeout: float | None = None parameter, matching the same pattern as stale_threshold.

feat(server): thread idle_output_timeout through run_skill MCP tool

84168b8

Add idle_output_timeout: int | None = None parameter to run_skill(), convert to float and pass to executor.run(). The None passthrough is intentional; 0→None (disabled) conversion happens in the executor layer.

style: apply ruff format auto-fixes

c5da48b

Reformatted rules_tools.py, tools_execution.py, and test_context.py to comply with ruff line-length and style rules.

Trecek commented Apr 13, 2026

View reviewed changes

Trecek and others added 2 commits April 12, 2026 23:08

Trecek added this pull request to the merge queue Apr 13, 2026

Merged via the queue into integration with commit 974920e Apr 13, 2026
2 checks passed

Trecek deleted the add-idle-output-timeout-as-per-step-recipe-override/785 branch April 13, 2026 06:34

Trecek mentioned this pull request Apr 13, 2026

run_skill: channel_won branch unconditionally SIGKILLs Claude CLI, producing systematic exit_code=-9 + success=true ambiguity #804

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Add idle_output_timeout as Per-Step Recipe Override#793

Add idle_output_timeout as Per-Step Recipe Override#793
Trecek merged 10 commits intointegrationfrom
add-idle-output-timeout-as-per-step-recipe-override/785

Trecek commented Apr 13, 2026 •

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Summary

Architecture Impact

Process Flow Diagram

Data Lineage Diagram

Operational Diagram

Implementation Plan

Token Usage Summary

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Trecek commented Apr 13, 2026 •

edited

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