skillflow-py 1.2.0

Config-agnostic LLM pipeline graph executor — turn skills into flows

Skillflow

Config-agnostic LLM pipeline graph executor with human-in-the-loop by design. Define multi-agent pipelines as YAML DAGs — skillflow handles deterministic traversal, tool execution, approval/reject checkpoints, loops, recovery, a full durable audit trace, and event streaming on SQLite. Provider-agnostic, custom tools, clean per-agent context.

Two ways agents plug in: embed skillflow in a host app so it drives real agents step-by-step (forced execution order — see Framework Mode), or have an external agent (e.g. Goose) drive pipelines over a stateless CLI (Runner Mode). An agent can even generate a pipeline from a natural-language description (skillflow-convert) and then execute it.

Why Skillflow

Most agent frameworks let the LLM improvise control flow, tool use, and file access — which is exactly why their runs can't be reproduced, audited, or trusted. Skillflow inverts that: the LLM is a constrained, contract-bound function; the engine is the runtime.

• Deterministic traversal — the pipeline is a YAML DAG walked by the engine. Loops, gates, retries, and recovery are the engine's job, not the model's. Same config, same path.
• Capability-gated I/O (least privilege) — a step sees only the context it declares, and for each declared output the engine generates a dedicated write tool (write_<slot> / create_<slot> / append_<slot>). An agent literally cannot read or write a file outside its contract — the tool to do so doesn't exist in its schema. Brain to brain, tools to tools. (It's also why cheap models suffice: small, focused, role-scoped context.)
• Human-in-the-loop by design — approve / reject-with-feedback checkpoints are first-class nodes, not bolted on.
• Immutable audit trace — every step, prompt, response, tool call, and verdict is appended to a trace that is never deleted, keyed by step_instance_id. "Why did this run do X?" is one query.
• Config- and provider-agnostic — a pipeline can be anything; nothing is hardcoded to a use case or a model.

Install

pip install skillflow-py      # PyPI
pip install -e ~/skillflow    # from repo (editable)

pip install (≥ 1.1.2) gives you both the library (from skillflow import SkillFlow) and the skillflow-* CLI commands as console entry points. The clone + install-script flow is an alternative that registers the same commands into ~/.local/bin/:

git clone https://github.com/linxuhao/SkillFlow.git
bash skillflow/scripts/install.sh

CLI commands registered in ~/.local/bin/:

Command	Description
skillflow-lint	Validate pipeline YAML files (one-shot)
skillflow-run	Stateless pipeline runner (agent calls via CLI)
skillflow-convert	Convert a skill description → pipeline YAML

skillflow-lint configs/*.yaml                       # one-shot validation
skillflow-run --graph pipeline.yaml --action start  # start a pipeline (returns JSON)
skillflow-run --action submit --run-id <id> --result '{"key": "val"}'
skillflow-convert --desc "Code review skill..." --action start  # start from inline text
skillflow-convert --desc-file my_skill.md --action start        # or from a file

PyPI publish

pip install build twine
python3 -m build
twine upload dist/*

Two modes

Skillflow has two distinct modes — one for embedding in code, one for LLM agents.

	Framework mode	Runner mode
Interface	Python library (from skillflow import SkillFlow)	CLI tools (skillflow-run, skillflow-convert)
State	In-process (or shared SQLite)	Stateless — each CLI call is a fresh process, state in SQLite
Tool execution	All tools auto-execute inline	Native tools auto-execute, everything else delegated to the agent
delegate_tools_to_agent	False (default)	True (hardcoded)
Use case	Embed skillflow in a host app	LLM agent drives pipelines via shell commands

Framework Mode

Skillflow is embedded in a host application. The host drives the loop — skillflow handles traversal, tool execution, and state. The host only executes agent steps via StepRunner.

from skillflow import SkillFlow, PipelineGraph, StepResult

graph = PipelineGraph.from_yaml("tests/fixtures/minimal_1step.yaml")

sf = SkillFlow(":memory:")
sf.register_graph(graph)
sf.register_agent_config("echo_agent", model="host")

run_id = sf.create_run("minimal_1step")
sf.start_run(run_id)

while True:
    sf.advance_run(run_id)
    claimed = sf.claim_next_step(run_id)
    if claimed is None:
        break  # completed or paused
    # Host StepRunner executes the agent step here
    sf.confirm_step(claimed.token, StepResult(outputs={}, flags={}))

Config reference: tests/fixtures/minimal_1step.yaml.

Runner Mode

Runner mode is the language-agnostic interface for LLM agents. Agents drive pipelines by calling CLI tools — skillflow-run and skillflow-convert. Each invocation is a fresh process that reads state from SQLite, does one thing, prints JSON, and exits. The agent loops: call → parse JSON → act → call again.

Pass --graph once with --action start. The graph path is stored in the DB. All subsequent calls use --run-id to reconnect — no --graph needed.

# 1. Start a pipeline — pass --graph once, get the first step back
$ skillflow-run --graph pipeline.yaml --action start
{"status": "in_progress", "run_id": "abc123", "step": "analyze", "instruction": "..."}

# 2. Submit work for the current step (no --graph needed)
$ skillflow-run --action submit --run-id abc123 \
    --result '{"issues": [{"file": "app.py", "severity": "high"}]}'
{"status": "in_progress", "run_id": "abc123", "step": "summarize", "instruction": "..."}

# 3. When a checkpoint step completes, the run pauses
{"status": "paused", "checkpoint_label": "Review Summary — approve to commit, reject to revise"}

# 3a. Human approves (no --graph needed)
$ skillflow-run --action approve --run-id abc123
{"status": "in_progress", "run_id": "abc123", "step": "apply_fixes", ...}

# 3b. Or human rejects with feedback
$ skillflow-run --action reject --run-id abc123 \
    --feedback "Severity of bare except should be high, not medium"

# 4. Loop continues until the pipeline completes
{"status": "completed", "steps_completed": 3, "outputs": {...}}

The agent drives this inline — there is no driver code. The agent itself calls skillflow-run as a command inside its own turn loop: call → read the JSON → do the work (stage the expected output files, or run a delegated tool) → call again, reacting to status each turn (in_progress → submit, paused → ask the human to approve/reject, completed/failed → done). The agent is the loop — it never writes a program to drive skillflow. The full, injectable manual is AGENT.md; load it via load_agent_guide() from skillflow.plugins.skill_runner and put it in the agent's system prompt.

Response fields beyond status:

Field	When present	Meaning
output_dir	Steps with output.fixed	.tmp staging dir — write expected files here; skillflow promotes them on submit
expected_files	Steps with output.fixed	File names to create (e.g. ["findings.json"])
validation_error	Submit rejected by validator	Why the previous submit failed — fix and re-submit
tool_name	Tool steps	Tool the agent must execute
tool_params	Tool steps	Parameters for the tool
tools	Agent steps	Write helpers (write_*, create_*, append_*) with format specs

Node Types

Type	Description
agent	LLM step — host app executes via StepRunner protocol
tool	Auto-executed by skillflow (native), or delegated to agent in runner mode (custom)
gate	Auto-resolved using match conditions against step output flags
loop	Iterates over a JSON list from a workspace file, instantiating sub-steps per item

Transition Matching

Five match strategies. See tests/fixtures/dpe_full.yaml for a complete pipeline using all of them:

match: { field: "passed", value: true }                          # step output flags
match: { from_file: "review_verdict.json", field: "passed", value: true }  # output file
match: { from: "checkpoint", value: "approved" }                 # checkpoint routing
match: { _error: true }                                          # error handler
# (no match key)                                                 # always match

Loopback (review & goal loops)

Any transition's to can point backward to an earlier step — that's how review and goal loops are built. max_loop caps how many times an edge may fire per run (tracked in skillflow_edge_counts); once the cap is hit the edge stops matching, so the run takes another branch instead of looping forever. Set feedback: true to inject the step's outputs as _feedback into the target on the way back, making the redo corrective.

# A Red-checker that sends work back to the maker until it passes (max 3×)
transitions:
  - to: "implement"          # backward edge → redo the step
    match: { passed: false }
    max_loop: 3
    feedback: true           # pass review notes back into 'implement'
  - to: "next_step"          # forward once the checker passes
    match: { passed: true }

This powers both inner review loops (e.g. review → implement, max_loop: 3) and goal loops (a final verifier routing back to planning until goals are met). See tests/fixtures/review_loop.yaml and tests/fixtures/dpe_full.yaml.

Context Injection

context:
  - source: { step: "1" }
  - source: { step: "2", mode: "interfaces" }
  - source: { config: "meta", output: "brief.md" }
  - source: { tool: "dir_tree" }

Checkpoints

Agent steps can pause for human approval (tests/fixtures/checkpoint_cycle.yaml). On reject, the feedback is injected (via the _feedback channel) so the re-run knows why it was rejected:

# Redo the rejected step itself
sf.reject_checkpoint(run_id, "draft", "Add more detail to the analysis")

# Or loop back to a DIFFERENT step — reopen the run earlier and carry the
# feedback to that target (e.g. reject the final review back to planning)
sf.reject_checkpoint(run_id, "final_review", "Goals not met", redirect_to="plan")

redirect_to makes rejection a human-driven loopback: it sets the run's current node to the target step and injects the feedback there. Over the CLI this is --redirect-to <step>. A checkpoint can also be rejected after a downstream failure (the only invariant is that the checkpoint step is completed), so you can reopen earlier work to recover.

Output Validation

Steps declare validation specs auto-executed by skillflow. See tests/fixtures/skill_review.yaml for inline JSON Schema validation, or tests/fixtures/lifecycle_hooks.yaml for syntax_lint + py_compile validators.

Available validators: json_schema, syntax_lint, py_compile, pytest, file_exists.

Lifecycle Hooks

Steps with output.mode: "write" can trigger deliver and post-deliver hooks. See tests/fixtures/lifecycle_hooks.yaml:

lifecycle:
  on_deliver:
    tool: "repo_apply"
    params:
      source_dir: "$STEP_DIR"
    on_failure: "retry"
    max_retries: 2
  after_deliver:
    - tool: "syntax_lint"
      files: ["*.py"]

Error Handling

Steps declare max_retries and an _error transition. See tests/fixtures/error_handler.yaml.

Feedback Loopback

Tool failures can inject output into the next step's inputs (feedback: true). See plugins/skill_converter/skill_converter.yaml — the validate_design step feeds lint errors into fix_issues.

End Conditions

Four termination strategies, combined with and/or. See tests/fixtures/end_conditions.yaml and tests/fixtures/dpe_full.yaml:

end_conditions:
  combinator: or
  conditions:
    - type: node_reached
      node: "5_review"
      result: "completed"
    - type: max_total_steps
      limit: 200
    - type: max_run_duration_seconds
      limit: 3600
    - type: flag_match
      flag: { fatal_error: true }

Stale Claim Recovery

Built into advance_run. A claim whose worker died before calling confirm, and that is older than stale_threshold_seconds (default 300), is auto-reset to pending and re-claimed:

sf = SkillFlow("pipeline.db", stale_threshold_seconds=300)

Crash-loop guard: if the same step instance is recovered 3 times, skillflow stops retrying and marks it failed ("worker crashed 3 times — likely a code bug or OOM"), emitting a non-retryable step_failed event — so a buggy or OOM-prone step can't loop forever.

Event Streaming

All state transitions are written to skillflow_outbox. Poll for real-time notifications:

events = sf.drain_outbox(batch_size=50)
for event in events:
    print(event.event_type, event.payload)
sf.ack_outbox([e.id for e in events])

In-process subscribers via NotificationBus:

from skillflow import NotificationBus

bus = NotificationBus()
bus.subscribe("step_completed", lambda n: print(n.payload))
sf = SkillFlow(":memory:", notification_bus=bus)

Durable Run Trace

Unlike the outbox (drained + ack'd for delivery), the trace is an append-only audit log that is never deleted. It records every step claim/completion, prompt, model response, tool call + result, and lifecycle-hook outcome — keyed by step_instance_id, so loop iterations never overwrite one another and a finished run can be reconstructed offline. Tool calls are traced across all invocation paths (agent-invoked incl. custom tools, tool-step nodes, lifecycle hooks, validators), each tagged with a source.

sf.trace(run_id, "event", "note", {"x": 1})          # hosts can add their own records
records = sf.get_trace(run_id)                        # chronological, by seq
for r in records:
    print(r["seq"], r["category"], r["event"], r["payload"])

Within a host, the claimed step exposes step.trace(category, event, payload) so prompts/responses land in the same timeline. Long fields are clipped; writes are cheap (an in-process per-run seq counter avoids a SELECT per record). Retention is the host's call:

SkillFlow(db, trace_enabled=False)                   # opt out entirely (zero overhead)
sf.prune_trace(run_id="...")                          # drop one run's trace
sf.prune_trace(keep_last_runs=200)                    # cap to recent runs

delete_project removes a project's trace automatically. This is what turns "why did this run do X?" from forensic git-archaeology into one query.

Tools

Native (13 built-in)

Tool	Description
read_file	Read a file with line numbers
write	Write content to workspace
list_tree	List directory structure
dir_tree	Context tree for prompt injection
json_schema	Validate JSON against inline schema
syntax_lint	Syntax check via ruff
py_compile	Python bytecode compile
pytest	Run pytest on test files
repo_apply	Copy files to repo + git commit
repo_validate	Multi-tool repo validation
draft_commit	Move draft files to final dir + commit
file_exists	Check files matching glob patterns
notify	Send user-visible notifications

Custom tools

Host apps add tool directories. Each tool: {name}/tool.yaml + {name}/impl.py. Function name must match directory name.

from skillflow.tool_loader import ToolLoader

loader = ToolLoader()
loader.add_tools_dir("my_app/tools")
sf = SkillFlow(":memory:", tool_loader=loader)

Auto-injected: finish_step

Every agent step (both content mode and write mode) automatically gets a finish_step tool injected as the last tool in the schema. This gives the agent a deterministic way to signal "I'm done writing outputs" instead of relying on the host runner to guess when the agent has stopped calling tools.

Contract:

• Skillflow generates the tool schema (always last in the array — the model is shown it last so it calls it last).
• Skillflow's tool executor returns {"status": "completed"} — a no-op.
• The host runner detects finish_step in the tool-calling loop and breaks the turn loop, proceeding to output validation and step completion.
• The runner MUST process all tool calls in the current turn before checking for finish_step, so multi-tool responses (e.g. write_sota + finish_step) work correctly — never short-circuit mid-turn.

Use Cases

1. Framework mode — embed skillflow in your app

Use skillflow as a library. Read the Getting Started section above and the fixture examples in tests/fixtures/.

from skillflow import SkillFlow, PipelineGraph
graph = PipelineGraph.from_yaml("my_pipeline.yaml")
sf = SkillFlow(":memory:")
sf.register_graph(graph)
# ... drive the loop with claim_next_step / confirm_step

2. Agent mode — convert skills to pipelines

skillflow-convert is a thin wrapper that calls skillflow-run with the built-in converter pipeline. The agent drives it the same way:

# Start conversion with a skill description
$ skillflow-convert --desc "Code review skill..." --action start
{"status": "in_progress", "run_id": "abc123", "step": "analyze_skill", "instruction": "..."}

# Submit analysis, continue through design → explain → lint → done (no --desc needed)
$ skillflow-convert --action submit --run-id abc123 --result '{"analysis": {...}}'

On completion, the generated pipeline YAML is at ~/.skillflow/workspaces/skill-converter/.../skill_pipeline.yaml.

Agent manuals (the tool schema + rules) are shipped in the package:

Plugin	Manual	Load via
skill_runner	Actions, response format, rules	load_agent_guide() from skillflow.plugins.skill_runner
skill_converter	Step-by-step: analyze → design → lint → fix	load_agent_guide() from skillflow.plugins.skill_converter

Inject these into the agent's system prompt so it knows how to call the CLI tools.

skillflow-lint pipeline.yaml                             # one-shot config validation
skillflow-run --graph pipeline.yaml --action start        # start a pipeline (returns JSON, --graph only once)
skillflow-convert --desc "..." --action start             # start a conversion

Linter (skillflow.plugins.linter)

Framework utility. Validates pipeline YAML — used as a skillflow tool (skillflow_lint) inside the converter's feedback loop, or standalone:

skillflow-lint tests/fixtures/skill_review.yaml
skillflow-lint configs/*.yaml

Package

src/skillflow/
├── core.py              # SkillFlow orchestrator (create/claim/confirm/advance)
├── graph.py             # PipelineGraph, StepNode, Transition, GraphResolver
├── tool_loader.py       # Dynamic tool schema + implementation loading
├── context.py           # ContextResolver: cross-config, step, tool sources
├── step_validation.py   # StepValidator: multi-tool output validation
├── write_tools.py       # Constrained write tool generation from output.fixed
├── workspace.py         # Per-step atomic staging directories
├── validation.py        # Optional external-schema output validation
├── recovery.py          # Stale claim recovery
├── schema.py            # SQLite DDL + migrations
├── exceptions.py        # SkillFlowError hierarchy
├── outbox.py            # OutboxConsumer for event polling
├── notifications.py     # NotificationBus for in-process subscribers
├── agent_registry.py    # Agent config registry + schema resolution
├── plugins/             # Built-in plugins
│   ├── linter/          # Config validator + skillflow_lint tool
│   ├── skill_runner/    # SkillTool — interactive pipeline facade
│   └── skill_converter/ # Skill description → pipeline YAML
└── tools/               # Native tools (13)
    ├── read_file/       ├── write/          ├── list_tree/
    ├── dir_tree/        ├── json_schema/    ├── syntax_lint/
    ├── py_compile/      ├── pytest/         ├── repo_apply/
    ├── repo_validate/   ├── draft_commit/   ├── file_exists/
    └── notify/

Tests

pytest tests/ -v                    # 330+ tests
pytest src/skillflow/plugins -v     # 27 plugin tests