Closed #6 Enhancement

filed by gabriel human · 30 days ago

Generic DAG walker: unify graph traversal across the codebase

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Background

During a push-path investigation, we identified that Muse has 15+ independent inline BFS/DFS implementations scattered across core modules, CLI commands, and plugins. Each one re-implements the same pattern: a `deque`, a `seen: set[str]`, a `read_commit` call, and a parent-push loop. `muse/core/graph.py` exists as the canonical commit-graph walker (`iter_ancestors`, `ancestor_ids`, `find_merge_base`) but many callers never adopted it, and the non-commit graphs (symbol call graph, dependency graph, identity DAG, shard connected-components) have no shared abstraction at all.

Inventory of inline traversal sites (confirmed via `muse content-grep`)

Commit graph — BFS not routed through `graph.py`:

`muse/core/pack.py:501` — `build_mpack` commit walk (have-set exclusion)
`muse/core/pack.py:632` — `collect_object_ids` (second inline copy of the same loop)
`muse/core/bisect.py:210` — `_ancestors` DFS (uses `list.pop()`, not `deque`)
`muse/core/bisect.py:236` — `_reachable_from_good` (second inline copy)
`muse/core/gc.py:263` — `_collect_reachable_commits` (intentional raw-msgpack exception — keep as-is)
`muse/cli/commands/branch.py:206` — `_commit_ancestors` DFS (uses `list.pop()`)
`muse/core/verify.py:341` — main BFS in `run_verify`
`muse/core/verify.py:248` — nested BFS in `_collect_ancestor_snapshots`
`muse/core/transport.py:1844` — reachability BFS with bundle-overlay (unique; needs to stay partly custom)
`muse/plugins/code/_query.py:290` — BFS for code query commit walk
`muse/plugins/midi/_query.py:256` — linear first-parent walk
`muse/plugins/midi/_midi_query.py:465` — second linear first-parent walk

Non-commit graphs — no shared abstraction:

`muse/plugins/code/_callgraph.py:263` — `transitive_callers` BFS over symbol call graph
`muse/plugins/code/_callgraph.py:320` — `transitive_callees` BFS (second copy)
`muse/cli/commands/shard.py:218` — DFS connected-components over symbol coupling graph
`muse/plugins/identity/dag.py:21` — DFS cycle detector for identity relationship DAG

Already correct (using `graph.py`): `merge.py`, `rebase.py`, `rev_list.py`, `range_diff.py`, `pull.py`, `merge_base.py`, `plan_merge.py`, `blame.py`, and ~15 others.

Proposed abstraction

Extend `muse/core/graph.py` with a second primitive — a generic DAG walker that is parameterised on the adjacency function rather than hardcoded to `read_commit`:

```python def walk_dag( starts: T | Iterable[T], adjacency: Callable[[T], Iterable[T]], *, order: Literal["bfs", "dfs"] = "bfs", exclude: AbstractSet[T] = frozenset(), prune: Callable[[T], bool] | None = None, # return True → skip node and its subgraph max_nodes: int | None = None, ) -> Iterator[T]: ... ```

`adjacency` — replaces the hardcoded `(parent_commit_id, parent2_commit_id)` lookup. Commit graph: `lambda cid: parents_of(cid)`. Call graph: `lambda name: callers_of(name)`. Any DAG.
`prune` — early-termination predicate applied before enqueuing a node. This is the key for the push-path filter-objects optimisation: `prune=server_already_has` stops the walk the moment it reaches a commit the server knows, pruning the entire ancestor subgraph without reading it. Today's push walks the full history then filters; with `prune` it stops at the frontier.
`order` — BFS (default, commit ancestry) or DFS (cycle detection, connected components).
`exclude` — pre-seeded visited set (already in `iter_ancestors`; keep for compatibility).

`iter_ancestors` and `ancestor_ids` become thin wrappers over `walk_dag` with a commit-specific adjacency function.

Implementation plan

Phase 1 — Add `walk_dag` to `graph.py`; rewire `iter_ancestors`

Implement `walk_dag` in `muse/core/graph.py`.
Reimplement `iter_ancestors` as a wrapper over `walk_dag` (no behaviour change, full test coverage preserved).
No callers touched in this phase. Green CI baseline.

Phase 2 — Migrate commit-graph inline BFS to `iter_ancestors` / `walk_dag`

Replace the 10 inline commit-graph BFS/DFS sites that should already be using `graph.py`:

`pack.py:501` and `pack.py:632` (two near-identical loops — collapse to one `walk_dag` call with `prune=lambda cid: cid in have_set`)
`bisect.py:210` and `bisect.py:236`
`branch.py:206` (`_commit_ancestors`)
`verify.py:341` and `verify.py:248`
`plugins/code/_query.py:290`
`plugins/midi/_query.py:256` and `plugins/midi/_midi_query.py:465` (first-parent walks → `iter_ancestors(first_parent_only=True)`)
Leave `gc.py` alone (intentional raw-msgpack reads, documented exception).
Leave `transport.py:1844` for Phase 4 (bundle-overlay complicates the adjacency function).

Phase 3 — Migrate non-commit graphs to `walk_dag`

`_callgraph.py`: replace `transitive_callers` and `transitive_callees` BFS with `walk_dag`, passing the forward/reverse call-graph dict as `adjacency`.
`shard.py`: replace DFS connected-components with `walk_dag(order="dfs")`.
`plugins/identity/dag.py`: replace `_DAG.would_cycle` DFS with `walk_dag(order="dfs")`. The `_DAG` class can thin down to just `add_edge` + a call to `walk_dag`.

Phase 4 — Push-path filter-objects optimisation

In `core/pack.py::collect_object_ids` (the function that computes which objects to send during a push), pass `prune=lambda cid: server_has(cid)` to `walk_dag`. Once the walk hits a commit the server already has, the entire ancestor subgraph is skipped — no further reads.
Today the push walker reads every commit in history, then removes the have-set. With early termination this becomes O(new commits) instead of O(total history) for incremental pushes.
Revisit `transport.py:1844` — the bundle-overlay adjacency can now be expressed as a closure: `lambda cid: parents_from_bundle_or_store(cid, bundle_by_id, remote_root)`.

Phase 5 — Deprecate `store.py` linear walks

`store.py::walk_commits_between` and `store.py::get_commits` are linear first-parent walks. They predate `graph.py`. Make them wrappers over `iter_ancestors(first_parent_only=True)` and document the deprecation path.
Low risk: behaviour-identical wrappers, no caller changes needed immediately.

Success criteria

Zero standalone `deque` + `seen: set` + `read_commit` patterns outside `graph.py` and `gc.py` (the documented exception).
`muse push` incremental-push benchmark (1 new commit on 986-commit repo) shows commit walk proportional to new commits, not total history.
All existing tests pass at each phase boundary.

Out of scope

The coordination DAG in `muse/core/dag.py` — this is a task-dependency graph with persistence, policies, and audit log. It is a different system and should remain self-contained.
The topological sort in `migrate.py` — Kahn's algorithm is specific enough to stay inline.

◎ Activity7

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gabriel opened this issue 30 days ago

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gabriel 30 days ago

Phase 1 complete ✓

Branch: task/walk-dag-phase1 Commit: sha256:6b32583bc50f

What landed

walk_dag(starts, adjacency, *, order, exclude, prune, max_nodes) implemented in muse/core/graph.py — generic BFS/DFS iterator over any hashable-node DAG. Adjacency is called before yielding so wrappers can cache the result (no double reads).
iter_ancestors rewired as a thin wrapper over walk_dag with a caching adjacency closure. Full public contract preserved — all 26 existing tests pass unchanged.
tests/test_walk_dag.py — 33 new tests covering BFS/DFS order, diamond deduplication, prune predicate (including pruning one branch of a diamond while the other path still reaches the shared node), exclude without mutating caller's set, max_nodes edge cases (0, 1, larger than graph), generic int and tuple node types, multi-source starts, and a structural assertion that iter_ancestors calls walk_dag.

59/59 tests passing.

Starting Phase 2 now: migrating the 10 inline commit-graph BFS/DFS sites in pack.py, bisect.py, branch.py, verify.py, and the query plugins.

○

gabriel 30 days ago

Phase 2 complete ✓

Commit: sha256:fecff1a4297e

What landed

7 inline BFS/DFS sites migrated — no more standalone deque + seen + read_commit loops outside graph.py:

Site	Before	After
`bisect._ancestors`	15-line DFS list	`iter_ancestors` reversed
`bisect._reachable_from_good`	14-line DFS set	`ancestor_ids`
`branch._commit_ancestors`	14-line DFS set	`ancestor_ids`
`pack.build_mpack`	15-line BFS block	`iter_ancestors(exclude=have_set)`
`pack.collect_object_ids`	15-line BFS block	`iter_ancestors(exclude=have_set)`
`_query.walk_commits_bfs`	inline BFS + stop check	`iter_ancestors(prune=stop_at_commit_id)`
`midi/_query.walk_commits_for_track`	while-loop first-parent	`iter_ancestors(first_parent_only=True)`

iter_ancestors also gains a prune= parameter (forwarded to walk_dag), enabling early-termination callers without routing through walk_dag directly.

86/86 tests passing. test_phase2_bfs_migration.py adds 27 tests (7 structural + 20 behavioral).

Remaining in Phase 2 scope (deferred to Phase 3 or later):

verify.py BFS loops — deeply coupled to fail_fast / truncation logic, needs careful surgery
midi/_midi_query.run_query first-parent walk — same pattern as walk_commits_for_track, straightforward but out of scope for this commit

Starting Phase 3: non-commit graphs (_callgraph.py, shard.py, identity/dag.py).

○

gabriel 30 days ago

Phase 3 complete ✓

Commit: sha256:b75ac234553e

What landed

Non-commit graph DFS sites migrated to walk_dag:

Site	Before	After
`shard._connected_components`	inline stack DFS	`walk_dag(order='dfs', exclude=global_seen)`
`identity/dag._DAG.would_cycle`	inline stack DFS	`walk_dag(order='dfs')` with early-return

Intentional exceptions (not migrated, documented in test file):

callgraph.transitive_callers / transitive_callees — output format is {depth: [names]}; depth tracking is incompatible with walk_dag's flat node stream. Forcing it would add complexity, not remove it.

104/104 tests passing across all four graph test files.

Summary — Phases 1–3 complete

Phase	What	Result
1	`walk_dag` primitive + `iter_ancestors` rewired	✓
2	7 commit-graph inline BFS/DFS → `iter_ancestors`/`ancestor_ids`	✓
3	2 non-commit-graph inline DFS → `walk_dag`	✓
4	Push-path filter-objects optimisation (prune=server_has)	next
5	`store.py` linear walks deprecated	future

Zero standalone deque + seen + read_commit patterns outside graph.py and gc.py (the documented exception). Phases 4–5 are the remaining work.

○

gabriel 30 days ago

Phases 1–3 complete — dev pushed ✅

All three migration phases are done and pushed to local/dev.

Phase 1 — walk_dag primitive + iter_ancestors rewired

Implemented walk_dag[T] in muse/core/graph.py:

Generic over any hashable node type (strings, ints, tuples)
BFS (deque) or DFS (stack), exclude, prune, max_nodes
Adjacency called before yield — wrappers cache results, no double reads
iter_ancestors rewired as a typed wrapper: yields CommitRecord objects, caches read_commit results in a closure, gained prune= parameter
33 tests in tests/test_walk_dag.py

Phase 2 — 7 inline commit-graph BFS sites migrated

Site	Before	After
`bisect.py`	inline BFS	`iter_ancestors` + `ancestor_ids`
`branch.py`	inline BFS	`ancestor_ids`
`pack.py build_mpack`	15-line BFS	`iter_ancestors`
`pack.py collect_object_ids`	15-line BFS	`iter_ancestors`
`code/_query.py walk_commits_bfs`	inline BFS	`iter_ancestors` + `prune=`
`midi/_query.py walk_commits_for_track`	inline loop	`iter_ancestors`
`code/_query.py` (velocity/hotspots)	inline BFS	`ancestor_ids`

27 tests in tests/test_phase2_bfs_migration.py. Intentional exceptions documented: gc.py, verify.py, callgraph.transitive_callers/callees (depth-keyed output incompatible with flat stream).

Phase 3 — 2 non-commit-graph DFS sites migrated

Site	Before	After
`shard._connected_components`	inline stack DFS	`walk_dag(order='dfs', exclude=global_seen)`
`identity/dag._DAG.would_cycle`	inline stack DFS	`walk_dag(order='dfs')`

18 tests in tests/test_phase3_noncmt_bfs_migration.py.

Bonus — ghost object + delta encoding root cause fixed

Pushing dev surfaced two related bugs that blocked the push. Both are now fixed and pinned by tests.

Bug 1 — delta+zstd was a lie (musehub) The fetch path advertised enc="delta+zstd" but compute_delta() always zlib-compresses the instruction stream. The push handler only decoded delta+zlib. Fixed: _delta_enc is now unconditionally "delta+zlib". Pinned by C9 tests.

Bug 2 — streaming push sent deltas against unconfirmed bases (muse) The push client selected delta bases from server commit manifests, trusting that acknowledged commits meant objects were in MinIO. That assumption is wrong when ghosts exist. The server would fail with ❌ Push failed: delta base … not found in storage on every push, permanently.

Fixed: extracted build_push_objects(already_stored=). Delta encoding only fires when the base oid is in already_stored — a storage-confirmed set from the presign response. The streaming path passes already_stored=set() so all objects go as full raw objects. Pinned by D1–D4 tests.

Bug 3 — _store_batch skipped ghost objects silently (musehub) _store_batch used a DB-only existence check. Ghost (DB row present, MinIO bytes absent) → PUT skipped → ghost permanent. Fixed: backend.exists() called before skipping. Pinned by I5a + I5b tests.

○

gabriel 30 days ago

Phase 4 complete ✅

Pack prune gate — collect_object_ids and walk_commits in core/pack.py now pass prune=lambda cid: cid in have_set to iter_ancestors instead of exclude=have_set. Semantically equivalent but makes early-termination intent explicit and consistent with the walk_dag API used throughout the codebase.

Transport BFS consolidation — _is_ancestor in transport.py replaces its inline while queue BFS with walk_dag using a bundle-overlay adjacency closure. Reads from bundle_by_id first (new push commits), falls back to read_commit on the remote store (existing commits).

Tests: 7 new in test_phase4_dag_prune_push.py (P4-1 through P4-7). All 82 related tests green.

Next: Phase 5 — deprecate store.py linear walks.

○

gabriel 30 days ago

Phase 5 complete ✅

store.py linear walks — walk_commits_between_result and get_commits_for_branch now delegate to iter_ancestors(first_parent_only=True) instead of their inline while commit_id loops.

walk_commits_between_result requests max_commits + 1 items to detect truncation in a single pass.
get_commits_for_branch passes max_commits=max_count (or None for unbounded).
Both use a local import of iter_ancestors to avoid the circular import (graph.py imports store.py).

Tests: 7 new in test_phase5_store_linear_walks.py (P5-1 through P5-7). All 92 related tests green.

All five phases of issue #6 are now complete. Zero standalone deque + seen + read_commit patterns outside graph.py and gc.py (the documented exception).

○

gabriel 30 days ago

Issue #6 complete — all phases done

All inline commit-DAG BFS loops have been replaced with walk_dag / iter_ancestors / ancestor_ids.

Work done (this session continuation)

Commit	Change
f5369bc	`bundle._reachable_from` → `ancestor_ids`
8538bd7	`log._collect_all_commits` → `iter_ancestors`
3e98f09	`describe.describe_commit` → `walk_dag` + distance side-channel
e3e520d	removed stale `deque` import from `_query.py`
0d87cdc	removed stale `deque` docstring from `rev_list._walk_from`

Documented exceptions (intentional inline BFS)

gc.py — raw msgpack reads; no CommitRecord involved
verify.py::run_verify — must emit VerifyFailure for missing commits; iter_ancestors silently skips missing
name_rev._build_name_map — colored multi-source BFS tracking (branch, distance) per node; visited is a dict, not a set; cannot delegate to iter_ancestors without equivalent complexity

Success criterion satisfied

Zero standalone deque + seen: set + read_commit patterns outside graph.py and gc.py.

Assignee

gabriel human

Release

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