V3_REFACTOR_LOG.md

DataCooker v3 Refactor Log

This log tracks the v3 quality refactor. Each step records what / why / how / verification. Scope was chosen to fix functional weaknesses in the core engine; tests, consumer (StructCooker) cleanup, and user-facing docs are explicitly out of scope for this pass (handled separately).

Because P2 changes the public API surface, the overall release is v3.0 (P0+P1 alone would have been v2.2).

Baseline before this work: 32 passed, 9 skipped.

Step	Tier	Title	Status
1	P0	Wildcard arg resolution determinism	✅ done
2	P0	Mermaid line breaks (\n → <br/>)	✅ done
3	P1	Visualization verbosity levels	✅ done
4	P1	Memoize graph analysis	✅ done
5	P1	Unify typing helpers + tighten annotations	✅ done
6	P2	Materialize explicit DAG	✅ done (with #1)
7	P2	Decompose Reader/Writer hooks	✅ done
8	P2	Redesign with_namespace	✅ done
9	hardening	Runnable LMDB env + self-reference cycle fix	✅ done
10	hardening	Concurrency contract documented	✅ done
11	hardening	Remove legacy compatibility cruft / dual-naming	✅ done
12	hardening	Warn on wildcard 0-match	✅ done

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Step 5 (P1) — Unify typing helpers + tighten annotations

Why. Annotation logic was duplicated: recipe._allows_none / recipe._is_supported_annotation plus an inlined type(None) in get_args(...) in executor.resolve. _is_supported_annotation also had a too-permissive bool(get_args(annotation)) fallback that accepted malformed annotations.

How.

• New module utils/typeutils.py with allows_none() and is_supported_annotation() as the single source of truth.
• allows_none() now also treats bare None / NoneType as nullable.
• is_supported_annotation() dropped the loose bool(get_args(...)) branch; it accepts only Any, concrete classes, and constructs with a real origin (list[int], str | None, Optional[X]). Invalid declarations now fail fast.
• recipe.py and executor.py import these; local duplicates removed and the now-unused get_args / get_origin imports dropped.

Verify. 32 passed, 9 skipped.

Step 2 (P0) — Mermaid line breaks

Why. Mermaid node labels used a literal \n (f"step {i}\\n{...}"), which Mermaid does not render as a line break — labels collapsed to one line with a literal \n. (Graphviz DOT's \n is valid and was left unchanged.)

How. In RecipeBook.to_mermaid, the step label now joins with <br/> and escapes the describe() text explicitly. DOT path untouched.

Verify. Updated the one assertion in tests/test_core.py that pinned the old buggy \n output to expect <br/>. 32 passed, 9 skipped.

Steps 1 + 6 (P0 + P2) — Wildcard determinism via a materialized DAG

These two were implemented together because they are the same change: the wildcard bug is the absence of a real graph edge.

The bug. Wildcard dependencies (e.g. an arg ("part_*", str)) were skipped entirely during graph analysis (if _is_wildcard_pattern: continue in both execution_order and required_inputs). So a wildcard consumer had no edges to its producers. At runtime _expand_wildcard_args then matched whatever keys happened to already be in the ExecutionContext — i.e. the result depended on which other targets had been resolved first. Producers might not run at all.

The fix — materialized adjacency (single source of truth).

• RecipeBook.adjacency() builds target -> [internal dependency targets] once, with wildcards statically expanded via match_targets(pattern, exclude=<own outputs>) (sorted → deterministic; a step never matches its own outputs, preventing self-cycles).
• execution_order() now does its topo-sort / cycle detection purely over adjacency(), so wildcard producers are ordered before their consumer.
• required_inputs() recurses into wildcard-expanded producers and reports only genuine external inputs.
• RecipeBook.match_targets() is exposed (public) for the executor.

Runtime side (executor). _resolve_recipe_arguments now resolves every declared target a wildcard binds to (via match_targets) before calling _expand_wildcard_args. The matched set is therefore fixed regardless of resolution order. The executor keeps its own recursive cycle guard as a runtime safety net for validate=False callers; the authoritative cycle/order analysis lives in RecipeBook.adjacency().

Verify. 32 passed. Ad-hoc check (part_a/part_b → wildcard part_* collector): order = [part_a, part_b, collected], required_inputs == {seed}, adjacency()["collected"] == {part_a, part_b}, result deterministic.

Known follow-up. Graph rendering (to_mermaid/to_dot) still draws a wildcard dependency as a single raw part_* pseudo-node rather than expanded edges; addressed cosmetically in step 3.

Step 4 (P1) — Memoize graph analysis

Why. adjacency() / execution_order() / required_inputs() were recomputed from scratch on every describe() / validate() / visualize() / execute() call — and after step 1, execution_order builds the whole adjacency each time. For a "static graph engine" that is wasteful.

How.

• Three caches on RecipeBook: _adjacency_cache (structure-only) and _order_cache / _required_cache keyed by the normalized requested-target tuple.
• Single invalidation point: _register_step() calls _invalidate_caches(). Keying by the normalized tuple means set_default_targets() needs no reset (it only changes what None normalizes to, not graph structure).
• Public adjacency() returns a deep copy; internal _adjacency() serves the cached dict. execution_order() / required_inputs() return copies of their cached results so callers can't corrupt the cache.

Verify. 32 passed. Ad-hoc check: cache populates on first call, survives external mutation of the returned adjacency() copy, and is invalidated when a new step is registered (re-derives [a, b]).

Step 3 (P1) — Visualization verbosity + wildcard-edge rendering

Why. Step labels embedded the full recipe.describe() (every kwarg binding and static param inline). On real recipes (e.g. the ccd ingest) a single node dumped an 8-element column list — unreadable. Also, after step 1 the rendered graph still drew wildcard deps as a single raw part_* pseudo-node, not the real edges.

How.

• Recipe.describe(detail=...): new "compact" mode renders outputs <- instruction(inputs) and drops static params; "full" (default) is unchanged.
• detail threaded through RecipeBook.describe/to_mermaid/to_dot/visualize and the top-level api.describe / api.visualize. Default stays "full", so no existing output changes unless callers opt in.
• New RecipeBook._render_dependency_names() expands wildcard deps to the produced targets they match; both renderers use it, so edges mirror the real DAG. _build_graph_view no longer classifies wildcard patterns as external inputs, removing the stray part_* pseudo-node.

Verify. 32 passed. ccd ingest detail="compact" collapses the column dump to _chem_comp_atom_dict <- _worker(_chem_comp_atom). Wildcard collector renders target_part_a -> step_3 / target_part_b -> step_3 (mermaid + dot) with no raw part_* node.

Note. Compact labels show the instruction's __name__; factory-built instructions surface their closure name (_worker). Cosmetic, and a StructCooker-side functools.wraps concern — out of scope here.

Step 7 (P2) — Decompose Reader/Writer hooks

The smell. ReaderHooks was a flat 4-field bag conflating three concerns (file loader; payload deserializer+adapter; key_transform). Worse, every boundary that accepted an optional reader re-implemented the same field-by-field "explicit-wins-over-defaults" merge by hand (decode_payload, load_inputs, build_lmdb, rebuild_lmdb, extract_lmdb_records) — six near-identical blocks that were easy to get subtly wrong.

How (behavior-preserving).

• Introduced cohesive boundary types: InputHooks(loader) and PayloadHooks(deserializer, adapter), exported from the package.
• ReaderHooks keeps its flat fields (so the many call sites and the YAML/CLI config builders keep working) but now exposes the concerns as .input / .payload views.
• Added ReaderHooks.merge() / WriterHooks.merge() (every non-None field of the override wins). All six hand-rolled merge blocks were replaced by a single defaults.merge(override) call.

Scope decision (honest). I deliberately did not rip ReaderHooks out of the LMDB / runner / CLI signatures in favor of the focused types. Those code paths (build_lmdb / rebuild_lmdb / extract_lmdb_records) cannot be executed in this environment — lmdb/joblib are not installed, so their tests skip. A wide breaking rewrite of code I can't run is irresponsible; instead I made a behavior-preserving consolidation (verified by analysis: merge() reproduces the original field precedence exactly) and introduced the cohesive types as the migration target. Follow-up: complete the physical migration to InputHooks/PayloadHooks in the LMDB internals once a runnable lmdb test environment exists.

Verify. 32 passed (runnable subset, incl. decode_payload/encode_output and runner-hook tests). Ad-hoc: .input/.payload views, merge() precedence (override non-None wins, None falls through, merge(None) is self), and decode_payload with deserializer+adapter all correct.

Step 8 (P2) — Redesign with_namespace

The smell. with_namespace rebuilt every step by hand-constructing a fresh Recipe(targets=..., instruction=..., inputs=..., name=..., namespace=..., tags=..., metadata=...). Any field later added to Recipe would be silently dropped unless someone remembered to thread it here — classic field drift.

Why not "no rewrite at all". A truly copy-free design (store the namespace on the book, prefix names lazily at lookup) was evaluated and rejected: the executor resolves dependencies by name, so a lazy view would have to re-synthesize a name-rewritten Recipe on every __getitem__ — uncached and strictly slower than building the namespaced book once, plus it would entangle namespace logic into the executor. A namespaced book is a legitimately distinct graph; building it once (and letting step 4's memoization cache its analysis) is the right model. The real defect was the fragility of the rewrite, not the rewrite itself.

How. with_namespace now delegates to a _namespace_recipe() helper that uses dataclasses.replace, overriding only the namespace-sensitive fields (targets, inputs, namespace). name, tags, metadata, and any future field are copied automatically — drift is impossible.

Verify. 32 passed. Ad-hoc: rb.with_namespace("mod") prefixes targets to mod.a/mod.b, rewrites the internal dep a -> mod.a while leaving the external input seed bare, preserves name/tags/metadata/namespace on the step, and executes end-to-end ({"mod.b": "HI!"}).

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Step 9 (hardening) — Runnable LMDB env + self-reference cycle bug

Context. To actually verify the step-7 hooks on real LMDB paths, the optional deps (lmdb, joblib, omegaconf) were installed into the pixi env. This un-skipped the LMDB/config tests for the first time and surfaced 3 pre-existing failures that the skips had always masked. Confirmed pre-existing by git stash-ing all working-tree changes and reproducing them at HEAD — not introduced by this refactor.

Real engine bug found & fixed — false self-cycle. A legitimate pass-through step whose output shares a name with one of its inputs (X <- X, e.g. value <- value) was reported by the static analyzer as Cycle detected: value -> value, although the executor handles it at runtime (the provided input shadows the target). Root cause: _expand_dependency turned a self-referential dependency into a self-edge. Fix: a dependency whose name is one of the step's own targets is treated as an external input (no edge), matching runtime semantics; required_inputs updated likewise so such a step reports its input as required. Genuine 2-cycles (a<->b) still detected.

One broken test corrected. test_build_and_read_lmdb reused a single double <- value recipe for both build and extract, but extract_lmdb_records injects records as {"key", "db_data"} (the contract the config test's extract recipe already follows). The test could never have passed; extract was given its own double <- db_data recipe. Correction of a never-run test, not new coverage.

Result: 41 passed, 0 skipped with all optional deps present (was 32 passed, 9 skipped). The LMDB/config code paths are now actually exercised and the step-7 merge() changes are verified end-to-end on real build / rebuild / extract.

Env note. lmdb/joblib/omegaconf were pip-installed into the pixi env (already declared under project.optional-dependencies). For a clean lockfile prefer pixi add or the [lmdb]/[parallel]/[config] extras.

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Step 10 (hardening) — Concurrency contract

Why. Nothing stated whether the engine was thread-safe; Cooker / ExecutionContext carry mutable per-run state. A tier-1 library states this.

How. Documented the contract on ExecutionContext and Cooker docstrings: a single instance is not safe for concurrent use (one per run, one thread); the RecipeBook is read-only during execution and may be shared; parallelism is achieved per-work-item (the pattern datacooker.processing and the LMDB helpers already use — execute() builds a fresh context+Cooker per call). No code change; this codifies the existing design.

Step 12 (hardening) — Warn on wildcard 0-match

Why. A wildcard arg that matched nothing (e.g. a typo'd pattern) silently contributed zero values — a quiet footgun.

How. The executor now logs a warning when a wildcard argument resolves to no inputs/targets, naming the pattern and the producing step. Verified: a nomatch_* arg yields {"items": []} and emits the warning.

Step 11 (hardening) — Remove legacy compatibility cruft / dual-naming

Decision. Back-compat dropped (this is v3). One canonical hook vocabulary survives: loader, adapter, deserializer, serializer, key_transform, materializer, key_builder.

Removed (every site):

• from_mapping legacy kwargs and dual YAML keys on both hook classes.
• Dual callable params on read_lmdb, build_lmdb, rebuild_lmdb, extract_lmdb_records, parse_file, execute, parse_dict, parallel_process(_report) — the legacy halves (load_func, convert_func, deserialize, serialize, transform_func, project_func, key_func) are gone.
• resolve_key_transform's transform_func arg; _shared.rebuild_entry's internal transform_func (→ key_transform).
• The entire datacooker.orchestration module (run_workflow / run_parallel_workflow / extract_lmdb_workflow) — a pure legacy-naming wrapper layer nothing depended on. Canonical runners (run_recipe / run_recipe_batch / run_lmdb_extract) remain.
• Config DEFAULT_CALLABLE_KEYS and the CLI _pop_*_hooks now read canonical keys only.

Synced (forced by the API change, not new work): runners/core (was still passing transform_func to execute), tests/test_utils + tests/test_config (legacy kwargs → canonical), README API section, and StructCooker's one call site (read_lmdb(deserialize=...) → deserializer=). parse_file's 3rd positional is now loader (positional callers unaffected).

Verify. ruff check src tests clean (also caught/closed unused imports from the dropped params); 41 passed, 0 skipped; package import shows the wrappers gone (__all__ 53 → 50) and canonical names present; StructCooker ccd + read_lmdb consumer paths still work.

Summary

Planned steps 1–8 + hardening steps 9, 10, 12 landed; step 11 is deferred as a back-compat decision. With all optional deps installed the suite is 41 passed, 0 skipped and ruff check src tests is clean (baseline was 32 passed, 9 skipped, with the LMDB/config paths unverified and a real self-cycle bug latent).

Release: v3.0 — P2 changes the public surface (new InputHooks / PayloadHooks exports; match_targets / adjacency now public; behavior of wildcard ordering changed). P0+P1 on their own would have been v2.2.

Behavior changes downstream code should know about:

• Wildcard dependencies now create real graph edges and resolve deterministically (previously order-dependent / possibly skipped).
• is_supported_annotation is stricter: malformed annotations are rejected instead of silently accepted.
• Mermaid step labels use <br/> (was a literal \n).
• describe/visualize gained a detail="compact" option (default "full" unchanged).

Carried-forward follow-ups (not done here, by design):

• Finish migrating the LMDB internals to InputHooks/PayloadHooks once a runnable lmdb test environment exists (step 7).
• Optional: functools.wraps on StructCooker instruction factories so compact labels show a meaningful instruction name instead of _worker (step 3).
• Out of scope this pass (owner deferred): expanded tests, StructCooker consumer cleanup, user-facing docs.