mellea-fy-generate

name	mellea-fy-generate
description	# Melleafy Steps 3 + 5: Skeleton Emission and Body Generation
metadata	{"user-invocable":true,"disable-model-invocation":true}

Melleafy Steps 3 + 5: Skeleton Emission and Body Generation

Version: 4.3.0 (2026-04-28) | Prereq: dependency_plan.json (Step 2.5 complete) | Produces: Populated Python package

Output path rule (Rule OUT-3): All .py files (pipeline.py, config.py, schemas.py, main.py, etc.) are written inside <package_name>/. pyproject.toml is the only file written at the skill root (NOT inside <package_name>/). See mellea-fy.md §Output directory layout for the full tree.

Step 3 emits skeleton files (imports, signatures, docstring placeholders) from the element mapping and dependency plan. Step 5 invokes the LLM to fill in every code body. Read /mellea-fy-behaviours before generating any code — the Known Behaviours mitigations must be baked into every generated file.

---

Step 3: File set and skeleton emission

File set determined by mapping + dependency plan

File	When generated
pipeline.py	Always
schemas.py	Always (at minimum contains Final[str] placeholder if no schemas found)
config.py	Always (persona text, model ID, loop budgets from dependency_plan.json:bundle entries)
requirements.py	When any VALIDATE_OUTPUT elements exist
slots.py	When any EXTRACT or CLASSIFY elements map to @generative
tools.py	When any C6 element has disposition real_impl
constrained_slots.py	When any C6 element has disposition stub or delegate_to_runtime
mobjects.py	When any TRANSFORM or QUERY elements exist
loader.py	When any C3 element has disposition load_from_disk
main.py	Always (CLI entry point)
pyproject.toml	Always
SETUP.md	When any C4, C5, C9, non-bundled C6, C7, non-default C8, or host-needing modality
README.md	Always
melleafy.json	Always (skeleton in Step 3; finalised in Step 6)
dependencies.yaml	When any C6/C7/C8 entry is non-bundle

Modality-specific entry-point shape (R21)

The run_pipeline function signature and main.py shape vary by modality from classification.json:

Modality	Entry point shape
synchronous_oneshot	run_pipeline(*params) -> OutputSchema — simple function call
streaming	run_pipeline(*params) -> Iterator[str] — generator yielding tokens
conversational_session	run_pipeline(session_id: str, *params) -> OutputSchema — session-keyed
review_gated	run_pipeline(*params) -> ReviewRequest — returns for human approval
scheduled	run_pipeline() -> None — no user-provided params; data fetched internally
event_triggered	run_pipeline(event: dict) -> None — event payload as input
heartbeat	run_pipeline(state: dict) -> dict — stateful loop, returns updated state
realtime_media	run_pipeline(stream: Iterator) -> Iterator — streaming I/O

Rule 3-1 — run_pipeline parameter type annotations: Every parameter in the generated run_pipeline function signature MUST have an explicit Python type annotation. If the source spec declares a type for a parameter (e.g. from a typed function signature, a schema field, or an explicit type note in the spec text), use that type. If the source spec is untyped or ambiguous, default to str. Do not emit bare parameter names (e.g. company_domain) — emit company_domain: str instead. This applies to both required and optional (defaulted) parameters.

Step 3a-pre: Bundled assets are already mirrored (Rule OUT-6)

Companion directories from the skill root (scripts/, references/, assets/) are mirrored into <package_name>/ deterministically by the compile pipeline, before mellea-fy runs. The model does not perform the copy — it is plumbing handled by mellea_skills_compiler.compile.compiler._mirror_companion_dirs. By the time Step 3 begins, any companion directory that existed at the skill root is already present at <package_name>/<dir>/ and can be referenced directly.

The model's responsibility is path-resolution discipline: any code emitted in Step 5 that loads or invokes a bundled asset MUST resolve its path package-relatively via Path(__file__).parent / "<dir>/<file>", not via a user-supplied repo_root argument or the process working directory. This invariant is what makes the generated package self-contained — a pip install-ed package, or one invoked from any cwd, finds its bundled assets via Python's own module-location machinery.

Step 7's bundled-asset-path-resolution lint catches violations at validation time. The pyproject.toml template (below) declares these directories under [tool.setuptools.package-data] so the mirrored copies ship with the installed wheel.

Skeleton contents per file

config.py: C1 and C2 bundle entries become Final[str] constants under # === C1: Identity === and # === C2: Operating Rules === section headers. C8 bundle entries (model ID, backend) also here. Every constant gets a # PROVENANCE: <source_file>:<source_lines> comment.

In Step 5, the model emits ONLY JSON intermediate/config_emission.json conforming to schemas/config_emission.schema.json — not Python source. The writer config_writer.py reads this JSON and renders the final config.py file.

C8 backend rule (CRITICAL): BACKEND and MODEL_ID values MUST be read from intermediate/runtime_directive.json (fields .backend and .model_id respectively). Read the file, extract the two values, and include them in the config_emission.json output exactly as they appear in runtime_directive.json. Do not invent alternatives or use values from any other source. The Step 7 runtime-defaults-bound lint enforces this — divergence from the runtime_directive.json values is a hard failure.

JSON the model emits to intermediate/config_emission.json:

{
  "constants": [
    {
      "name": "PREFIX_TEXT",
      "value": "<persona text from SOUL.md>",
      "type": "str",
      "category": "C1",
      "provenance": { "source_file": "SOUL.md", "source_lines": "1-45" }
    },
    {
      "name": "BACKEND",
      "value": "ollama",
      "type": "str",
      "category": "C8"
    },
    {
      "name": "MODEL_ID",
      "value" 
       
       
    
    
       
       
       
    
  

schemas.py: One Pydantic BaseModel per SCHEMA element. Field descriptions pulled from the spec's output format description. For two-step pattern: include both the simplified raw schema and the full schema.

requirements.py: One Requirement object per VALIDATE_OUTPUT element. Group by spec section. Structural checks use simple_validate(); semantic checks use bare Requirement(description=...). Include check_only=True for negative constraints.

slots.py: One @generative function per EXTRACT/CLASSIFY element. Return types:

• Classifications: -> Literal[...] — Ollama supports constrained decoding, so always use the typed return.
• Simple list extractions: -> str with "Set result to a comma-separated string of..." docstring — never -> list[str]. Split in pipeline.py: [p.strip() for p in raw.split(",") if p.strip()] if raw.strip() else []
• Structured extractions: Pydantic BaseModel (model fields provide the JSON structure; no bare-output risk)

Docstrings on all @generative slots MUST reference result explicitly (e.g. "Set result to..."). Never use "Reply with exactly one word", "Output only", "Return only". Simple schemas (≤4 fields, no Literal constraints, no nested models) go here directly. Complex schemas: slot extracts simplified version, Step 5 generates the m.instruct enrichment step inline in pipeline.py.

@generative definition convention: The decorator forbids m as a parameter name — passing it in the definition raises ValueError at import time. Function body must be .... m is passed as the first positional argument only at call time in pipeline.py.

# CORRECT — no m in definition, body is ...
@generative
def extract_sentiment(text: str) -> str:
    """Set `result` to one of: positive, negative, neutral."""
    ...

# WRONG — raises ValueError: cannot create a generative slot with disallowed parameter names: ['m']
@generative
def extract_sentiment(m, text: str) -> str:
    ...

Calling convention in pipeline.py (unchanged — m passed as first positional arg):

with start_session(BACKEND, MODEL_ID) as m:
    sentiment = extract_sentiment(m, text=user_input)

tools.py (when any C6 has disposition real_impl):

• Domain/command allowlist — hard-coded ALLOWED_DOMAINS or ALLOWED_COMMANDS
• Error handling with timeouts and HTTP error codes
• Auth tokens read from environment variables
• build_api_params() or equivalent mapping spec-level names to API parameter names
• Bundled-script invocation (Rule OUT-6): when the implementation invokes a script mirrored from the skill root (e.g. scripts/bash/check-prerequisites.sh), resolve the script path package-relatively. Use Path(__file__).parent / "scripts/<...>" — never Path(repo_root) / "scripts/<...>" and never rely on the process working directory. Example: script_path = Path(__file__).parent / "scripts" / "bash" / "check-prerequisites.sh". The mirror is established by Step 3a-pre, so the path is guaranteed to resolve at runtime regardless of where the package is invoked from.
• Example structure:

ALLOWED_DOMAINS = ["api.example.com"]
HTTP_TIMEOUT = 10

def http_get(url: str) -> str:
    """Fetch content from a URL. Validates against domain allowlist."""
    from urllib.parse import urlparse
    parsed = urlparse(url)
    if parsed.hostname not in ALLOWED_DOMAINS:
        raise ValueError(f"Domain '{parsed.hostname}' not in allowlist")
    # ... execute with timeout and error handling

Multi-mode subprocess wrappers: if a shell script exposes multiple modes (e.g. --check-prompt, --check-url, --check-command), inspect how each mode receives its input before generating the wrapper:

• Modes that read from stdin (e.g. input=$(cat) in the script body) → call subprocess.run(..., input=target, capture_output=True, text=True). Do NOT append target to the command list.
• Modes that take a positional argument → append target to the command list as before.

Apply this per-mode distinction at the call site in pipeline.py too: every branch calling the wrapper must forward the input correctly for that mode. A branch that omits target= for a stdin-consuming mode is a silent false-negative bug.

constrained_slots.py (when any C6 has disposition stub or delegate_to_runtime):

• Implements ConstrainedGenerativeSlot, constrained decorator, filter_actions locally
• Implements ReactTool / ReactToolbox locally
• Provides stub tool functions raising NotImplementedError with implementation instructions
• Wraps dependent slots from slots.py with constrained() — does NOT duplicate them

pipeline.py (standard structure):

• One function per ORCHESTRATE workflow

• with start_session(BACKEND, MODEL_ID) as m: context manager

• Calls slots, requirements, and mobjects from other files

• DECIDE logic: Python if/elif/else wrapping Mellea calls

• MUST thread the user input / per-call value into m.instruct(description=...) via user_variables + a {{ key }} Jinja placeholder in the description text — e.g. m.instruct("Classify: {{ user_query }} ...", user_variables={"user_query": str(user_query)}, ...). Reserve grounding_context for document or reference material the description text explicitly cites — that is the channel the docs reserve for it (see https://docs.mellea.ai/how-to/working-with-data, which pairs user_variables={"query": ...} with grounding_context={"doc0": doc0, ...}). The per-backend prompt template (e.g. mellea/templates/prompts/granite/Instruction.jinja2) renders the grounding_context block under the header "Write the response by aligning with the facts and items in the following grounding context" — that framing fits supporting documents, not the value the model must directly extract from or classify; with format=PydanticModel constrained decoding, putting the primary input there produces silent extraction failures.

• MUST convert any non-string grounding_context value with str().

• MUST use format=PydanticModel for every m.instruct() that produces structured output

• MUST parse the thunk after every m.instruct(format=Model) before accessing any field or calling any Pydantic method. m.instruct() returns a ComputedModelOutputThunk — NOT a Pydantic model. Direct field access (thunk.field_name) or .model_dump() raises AttributeError. Always include _parse_instruct_result and _safe_parse_with_fallback helpers in pipeline.py and call them immediately after every m.instruct(format=Model) call:

Canonical Mellea import paths — use these exact paths; do not guess or infer alternatives:

from mellea import start_session, generative
from mellea.stdlib.sampling import RepairTemplateStrategy
from mellea.stdlib.requirements import req, check, simple_validate

Rule 5-2 — Import path grounding. Fallback only — primary enforcement is via invariant 3 above. Before writing any from mellea.X import Y statement, verify that the module path mellea.X exists in intermediate/mellea_api_ref.json:.modules. Any path not present there is invalid and must not be generated.

Common error pattern: generating shortened paths that do not exist (e.g. mellea.model_options) when the symbol lives deeper in the hierarchy (e.g. mellea.backends.model_options). The .modules key is the ground truth — consult it, not training knowledge, for import paths.

The KB entries in /mellea-fy-behaviours already show the canonical import for each KB-relevant symbol. For symbols not covered by a KB entry, derive the import path from mellea_api_ref.json:.modules.

Rule 5-4 — Stdlib function signature grounding. Fallback only — primary enforcement is via invariant 3 above. Before emitting any call to a mellea.stdlib.* function, verify the function's argument count and keyword parameter names against the known-signature list below. Do not infer signatures by analogy to similar functions in other libraries (e.g. do not assume (fn, error_message) forms that exist in pytest or pydantic but not in Mellea).

Known signatures (static fallback when mellea_api_ref.json is absent or grounding_unavailable: true):

Function	Module	Signature
simple_validate	mellea.stdlib.requirements	simple_validate(fn) — 1 positional argument only
req	mellea.stdlib.requirements	req(description, *, validation_fn=None) — 1 required positional, 1 optional keyword
check	mellea.stdlib.requirements	check(requirement, output) — 2 positional arguments

Common error pattern: simple_validate(_check_fn, "error message") — the two-argument form is invalid. simple_validate wraps the validator function; the error message, if needed, is handled inside the validator function itself. The correct call is simple_validate(_check_fn).

For any mellea.stdlib.* function not in the table above, derive its signature from intermediate/mellea_api_ref.json:.modules.<module>.<symbol>.signature before emitting the call.

Pipeline structure by tool involvement:

P0 — No tools: pure pipeline.py calling slots.py and requirements.py.

P4 — Tools provide input: main.py gathers pre-pipeline data, passes as parameters to run_pipeline().

P2 — Pipeline calls tools (deterministic):

1. LLM classifies intent: intent_thunk = m.instruct(format=IntentSchema, ...) — result is a ComputedModelOutputThunk, NOT a Pydantic object; MUST parse immediately: intent = _safe_parse_with_fallback(intent_thunk, IntentSchema, query_type="out_of_scope", ...)
2. Scope check: if intent.query_type == "out_of_scope": return (deterministic, no tool call — intent here is the parsed Pydantic object, not the thunk)
3. Deterministic construction + tool execution: TEMPLATES[intent.query_type].format(...) → tool_fn(url_or_params)
4. LLM formats response (optional): response_thunk = m.instruct(format=ResponseSchema, ...) → response = _safe_parse_with_fallback(response_thunk, ResponseSchema, ...) with raw tool output as grounding MUST use two separate start_session() calls for steps 1 and 4 (schema priming).

P3 — Pipeline calls tools (LLM-directed):

• Uses m.react() with a toolbox, or m.instruct() with ModelOption.TOOLS
• Mellea's TOOL_PRE/POST_INVOKE hooks fire automatically for governance

pyproject.toml (always):

[build-system]
requires = ["setuptools>=68.0"]
build-backend = "setuptools.build_meta"

[project]
name = "<package-name>"
version = "0.1.0"
requires-python = ">=3.11"
dependencies = [
    "mellea[hooks]>=0.4.2",
    "pydantic>=2.0",
]

[project.scripts]
<package-name> = "<package_module>.main:main"

# Rule OUT-6 — declare mirrored companion directories as package data so
# bundled scripts/references/assets ship with the installed wheel. Include
# only the directories that exist after Step 3a-pre's mirror.
[tool.setuptools.package-data]
"<package_module>" = ["scripts/**/*", "references/**/*", "assets/**/*"]

Note: the openai-agents package is NOT added to dependencies for Agents SDK source specs — the generated package uses Mellea, not the Agents SDK.

---

Step 5: Code body generation

Step 5 fills every skeleton placeholder with real code. For config.py, the model emits JSON and the writer config_writer.py renders Python source (invariant 1).

Parallelization strategy: Step 5 is structured in three phases to maximize throughput:

• Phase A (parallel): Emit all 7 independent files in a single turn using parallel tool calls: schemas.py, config.py, requirements.py, slots.py, tools.py/constrained_slots.py, mobjects.py, loader.py. These files have no inter-file dependencies at generation time.
• Phase B (sequential, after A completes): Generate pipeline.py (references all Phase A symbols).
• Phase C (sequential, after B completes): Generate main.py (references pipeline.py).

In repair mode, only re-generate the files listed in intermediate/step_7_report.json failure entries; unchanged files pass through without re-generation.

Step 5 invariants

Read once; apply throughout all file generation.

1. config.py output is JSON, not Python source. Emit a JSON object conforming to schemas/config_emission.schema.json. The deterministic writer config_writer.py renders the file — do not write Python source for config.py directly.

2. All other files output Python source. Generate one file per LLM invocation (Rule 5-3). Wait for each file's body before starting the next.

3. Before generating any file, consult intermediate/mellea_api_ref.json:

• .modules — valid mellea.* paths for imports
• .modules.<module>.<symbol>.signature — exact signature for any mellea.stdlib.* symbol (nested under .modules)
• .forbidden_param_names — disallowed @generative parameter names
• .compatibility — Mellea-version-gated workarounds to inject

If grounding_unavailable: true, fall back to the KB patterns in /mellea-fy-behaviours and the static signature tables in Rules 5-2 and 5-4.

4. Use canonical fixture pairs from intermediate/fixtures_emission.json as concrete examples (already produced by Step 4) for the file being generated. Use these as the reference for correct Mellea usage, not training memory.

5. Behavioral guidance is in /mellea-fy-behaviours. Read it once before generating any file body.

6. Step 7 lint failures, not these instructions, are the source of truth for correctness. Generate per spec; let the repair loop correct lint failures rather than anticipating every possible check.

Rule 5-3 — File-level batching: Generate all code bodies for a given output file in a single LLM invocation. Do not make one invocation per element. For each file in the skeleton (e.g. pipeline.py, config.py, slots.py, tools.py), issue one invocation that generates the complete file contents, guided by all relevant element mapping entries for that file. KB5 schema priming concerns do not apply to melleafy compilation calls (KB5 governs Mellea pipeline sessions inside compiled skills, not the compilation process itself).

Each invocation uses a prompt template with all element-specific mapping entries for that file as variable substitution.

KB defenses baked into every invocation

Before generating any body, include in the context:

• The specific Known Behaviours relevant to the primitive being generated
• The element's source text and mapping rationale
• The dependency plan entries affecting this element

Per-file body generation order

Phase A (parallel batch — single turn with parallel tool calls):

Generate all of these simultaneously in one turn. They are mutually independent at generation time:

1. schemas.py — Pydantic models (referenced by Phase B)
2. intermediate/config_emission.json — config json (referenced in Step 5)
3. requirements.py — requirement functions (referenced by Phase B)
4. slots.py — @generative slot bodies (referenced by Phase B)
5. tools.py / constrained_slots.py — tool implementations (referenced by Phase B)
6. mobjects.py — mified object definitions (referenced by Phase B)
7. loader.py — file loader functions (referenced by Phase B)

Phase B (sequential, after Phase A):

8. pipeline.py — the orchestrating pipeline (references all Phase A symbols)

Phase C (sequential, after Phase B):

9. main.py — CLI entry point (references pipeline.py)

Within Phase A, each file should be generated with its own LLM invocation, dispatched in parallel using the tool-call parallelism available in your response. Do not wait for one file to complete before starting the next — issue all Phase A invocations in the same turn.

Remediation loop bodies (when REMEDIATE elements exist)

# In pipeline.py — bounded remediation loop
MAX_REMEDIATION_ITERATIONS: Final[int] = 3  # in config.py

patched_code = original_code
remediation_count = 0
verdict = initial_verdict

while not verdict.passed and remediation_count < MAX_REMEDIATION_ITERATIONS:
    # Modification step: generate a fix
    with start_session(BACKEND, MODEL_ID) as m_fix:
        fix = m_fix.instruct(
            "Generate a minimal patch for this code:\n{{ current_code }}\n\n"
            "Issue to address:\n{{ verdict }}",
            user_variables={
                "current_code": str(patched_code),
                "verdict": str(verdict.model_dump()),
            },
            format=CodeFix,
            strategy=RepairTemplateStrategy(loop_budget=LOOP_BUDGET),
        )
        fix_obj = _parse_instruct_result(fix, CodeFix)

    patched_code = fix_obj.patched_code
    remediation_count += 1

    # Re-evaluation step
    with start_session(BACKEND, MODEL_ID) as m_eval:
        verdict = _parse_instruct_result(
            m_eval.instruct(
                "Re-evaluate this code:\n{{ code }}",
                user_variables={"code": str(patched_code)},
                format=Verdict,
            ),
            Verdict,
        )

Schema field access rule

After writing pipeline.py and tools.py, cross-reference every model.field_name access against the model's field definitions in schemas.py. Accessing a field that doesn't exist raises AttributeError at runtime. Correct field access patterns are shown in the fixture examples injected via the grounding context — use those as the reference for how generated code should access schema fields.

Sequential extraction rule

When 3+ independent slots read the same input, call them sequentially on a single session — do NOT use asyncio.gather() with shared sessions (concurrent session sharing is unsafe in Mellea):

with start_session(BACKEND, MODEL_ID) as m:
    # Same BaseModel return type — safe in one session
    primary_findings = extract_primary_findings(m, code_text=code)
    secondary_findings = extract_secondary_findings(m, code_text=code)
    config_issues = extract_config_issues(m, code_text=code)

Two-step pattern in pipeline.py bodies

When Step 2 mapped an element to the two-step pattern:

# Step 1: @generative extracts simplified data (already in slots.py)
raw_paths = extract_raw_attack_paths(m, code_text=code, threat_summary=summary)

# Step 2: m.instruct() structures into full schema with repair strategy
if raw_paths:
    paths_thunk = m.instruct(
        "Enrich these attack paths with risk ratings, impact, and likelihood assessments.",
        model_options={ModelOption.SYSTEM_PROMPT: PREFIX_TEXT},
        grounding_context={
            "raw_attack_paths": str([p.model_dump() for p in raw_paths]),
            "code_text": code,
        },
        format=AttackPathList,
        strategy=RepairTemplateStrategy(loop_budget=LOOP_BUDGET),
    )
    attack_paths = _safe_parse_with_fallback(paths_thunk, AttackPathList, paths=[]).paths

CONVERSE realisation bodies

For realisation (2) — pipeline parameter:

def run_pipeline(
    user_query: str,                    # from CONVERSE element
    reference_context: str = "",        # from TOOL_INPUT or loader
) -> OutputSchema:
    ...

For realisation (3) — stub:

def _get_user_approval(draft: str) -> str:
    """Interactive approval step — requires host adapter. See SETUP.md §7."""
    raise NotImplementedError(
        "This step requires a host adapter for interactive user input. "
        "Implement this function or provide the approved draft as a parameter."
    )

melleafy.json skeleton (Step 3, finalised in Step 6)

{
  "format_version": "1.0",
  "manifest_version": "1.1.0",
  "package_name": "<package_name>",
  "generated_at": "<ISO timestamp>",
  "melleafy_version": "4.0.0",
  "source_runtime": "<from classification.json>",
  "modality": "<from classification.json>",
  "archetype": "<from classification.json>",
  "categories_resolved": "<populated in Step 6>",
  "entry_signature": "<populated in Step 6>",
  "pipeline_parameters": "<populated in Step 6>",
  "declared_env_vars": []
}

---

Cross-checks before Step 5 declares done

• intermediate/mellea_api_ref.json was consulted before code body generation (or grounding_unavailable: true was noted and KB fallback used)
• Fixture pair examples from intermediate/fixtures_emission.json (Step 4) were used as grounding context for each generated file (invariant 4)

---

Step 5 repair mode

Invoked by the top-level repair loop (see mellea-fy.md) after a Step 7 Tier 1 or structural Tier 2 failure. Distinct from a normal Step 5 invocation in three ways:

Scope: read intermediate/step_7_report.json. Generate only the files listed under failing lint entries. Pass all files with no failures through unchanged.

Additional context per failing file: inject the exact lint failure entries as a structured block before the generation context:

LINT FAILURES IN <filename> (repair round <N>):
  [<lint_id>] line <L> col <C>: <message>

Cap: repair mode may be invoked at most twice (repair_round ∈ {1, 2}). If Step 7 still fails after round 2, do not generate further — return control to the top-level orchestrator, which halts and preserves .melleafy-partial/.