ph-code-graph

code_index and code_graph: ask a codebase about its own shape, and get back a path:start-end you can read.

One row, code-graph, registering two tools. No Node, no Rust toolchain, no submodule — tree-sitter through a Python wheel, the graph in stdlib sqlite3.

phern --patch '{insert: [{id: code-graph, name: code-graph}]}' --profile llama \
   -p "index packages/ph-core, then tell me what breaks if I change claim_slot"

The two tools

code_index(paths, glob?, forget?) parses each file through ctx.fs and records what it defines and references.

Nothing watches the filesystem. There is no daemon and no file watcher: the index changes when code_index runs, and at no other moment. So after your own edits, run it again — which is cheap by design, and cheap enough to be a habit.

Incremental in two layers, and the order matters:

1. Does this file need opening? Asked of git or jj, which already hold a content-addressed tree — ph.seams.changes. A file the version control vouches for is never read. Measured on packages/ph-core/src/ph: a re-index of 137 unchanged files went from 0.10 s to 0.03 s, with zero reads and zero hashes, on a tree_state costing 7 ms for the whole 509-file repo.
2. Is what I opened different? Asked of the file's sha256, exactly as before. Never an mtime — a checkout or a rebase moves timestamps without moving content, and re-indexing because git touched them is a cost nobody attributes correctly.

Layer 1 only decides what to open, so the guarantee layer 2 makes is untouched: a skip is always justified by somebody's content hash, never by a clock. A tree with no version control loses layer 1 and nothing else.

code_graph(mode, query?, …) answers six questions:

mode	question	what comes back
search	"something about workspace tiers"	symbols ranked by FTS5 over name + docstring
define	"where exactly is claim_slot"	every definition of that name
callers	"what calls this"	the calling symbol and the calling line
callees	"what does this call"	the definitions it reaches
impact	"what breaks if I change this"	transitive callers, ring by ring
entities	"what is big here"	definitions by span, biggest first

Every result carries path:start-line-end-line. That is the point of the package: the model finds what matters in one call, then reads exactly that.

Using it from the RLM

Nothing to do. Under Code Mode the model is handed one callable and a generated SDK listing, and every registered tool is in that listing — so these arrive as await tools.code_index(...) and await tools.code_graph(...) with no Code Mode work in this package at all. The rlm-indexed profile is rlm-stable plus this bundle and ph-text-index's:

phern --profile rlm-indexed --provider llama --model <model> --mode tui

This package registers a ph.bundles entry point, which is what lets ph-app compose that profile without depending on this distribution — and what makes an install missing it see no rlm-indexed rather than one that fails at mount.

It is a name-based graph, and it says so

A reference records the name it used, and callers/callees join on that name. Two register methods in two classes are one name to this index.

Every answer that could be ambiguous carries definitions — how many places that name is defined — and the rendered text says so outright when it is above one, so the model sees the ambiguity instead of being handed one of the possibilities. mode=define is how it disambiguates.

Resolving properly means an import graph, scope, and per-language type inference. In the Rust/Node CodeGraph that is 29,708 lines of TypeScript, and this package deliberately did not port it. Name-based matching answers most of what an agent actually asks and reports where it cannot — which is a better trade than a resolved graph for one language.

Why Python-native, and not a wrapper

The obvious plan was to submodule the Rust/Node CodeGraph and wrap its kernel with maturin. The investigation said no, for three reasons in increasing order of importance:

1. codegraph-kernel is a #[napi] crate — crate-type = ["cdylib"] against napi/napi-derive. maturin builds PyO3/cffi extensions; wrapping it means forking the crate to rewrite its boundary.
2. It is only an extractor. Its whole export surface is extract_file, contract_info, grammar_info and two cfnptr helpers — "tree-sitter parse+extract with one JS boundary crossing per file", in its own words. It also has a complete TS/WASM fallback, so it is an accelerator, not the core.
3. The intelligence is TypeScript: resolution/ 29,708 lines, extraction/ 25,612, mcp/ 13,940, graph/ 6,023, db/ 5,475 — 112,612 against the kernel's 25,242. Wrapping the kernel gets a parser and leaves the product behind.

And the parser is the part Python already has. tree-sitter-language-pack 1.16 ships 26 languages compiled into a 3.7 MB wheel, working offline (python, ts/tsx/js, rust, go, java, csharp, c, cpp, ruby, php, swift, kotlin, scala, dart, lua, r, and more), with 371 available and the long tail fetched on demand — which this row never triggers implicitly.

Why sqlite3 and not pyturso

pH's session log runs on turso, so this is the exception and the reason is measured. Against a real 40 MB CodeGraph database (11,396 nodes, 36,830 edges), pyturso served indexed lookups, joins and aggregates correctly, and then:

• FTS5 is absent — a CREATE VIRTUAL TABLE … USING fts5 is invisible to it, shadow tables included. That is search.
• Recursive CTEs are not yet supported — that is impact.
• json_extract silently returns NULL where SQLite returns the value: 0.95 against None, same rows, same expression. A wrong answer with no error is worse than a missing feature.

Two of the six modes here are exactly the two turso cannot serve. Stdlib sqlite3 (SQLite 3.45, FTS5 compiled in) costs no dependency and does all six. If turso grows both, _store.py changes one import.

Extraction: two passes, and why

• process(), the pack's intelligence layer — definitions with kinds, the file's imports, docstrings and comments. What it will not give is references: SymbolInfo says a function exists, never who calls it.
• the tags query, tree-sitter's own tags.scm per language — the data GitHub's code navigation is built on. @definition.* and, crucially, @reference.call.

Measured over packages/ph-core/src/ph: 136 files and 1.58 MiB through process() in 219 ms, through the tags query in 108 ms. Indexing this repository's core takes 2.0 s end to end including the SQLite writes, and 0.1 s when nothing has changed. Parsing twice is worth more than the parse it saves.

Four details that are easy to get wrong, each handled once in _extract and each pinned by a test:

• ProcessConfig spans are 0-based while tree-sitter points are 0-based and every line pH shows a model is 1-based. Normalized on the way out, so nothing downstream has to remember which pass a number came from. Getting this wrong is an off-by-one pointer, which is what makes a model stop trusting a tool.
• SymbolInfo.doc is always None. The pack does not populate it — measured against a file full of docstrings. Trusting it would have shipped an index with an empty doc column and a search mode matching names only. The prose is on two other channels: result.docstrings, which carries the pack's own associated_item, and result.comments for doc comments (Rust ///, TypeScript block comments, Go //). Those have no association, so the rule is positional and narrow — the comment's last line must be immediately above the definition's first.
• A comment node's span.end_line can be one past the line it occupies, because Rust's /// node includes its trailing newline. Trusting it missed the definition directly below and matched one a blank line away. The line count comes from the comment's own text instead.
• TypeScript's tags query is half the story. Its grammar extends javascript's and upstream splits the queries to match, so class, function and call live in the javascript query — a .ts file matched against the typescript query alone yields two tags and no calls. INHERITS fixes that.

Per-language caveats

Both are pinned by tests, so they are known shapes rather than surprises:

• C has definitions but no call references. Its tags query ships no @reference.* captures at all, so callers/callees are empty for C while search, define and entities work.
• A bare Ruby send is invisible. helper without parentheses parses as an identifier rather than a call, so only helper() becomes an edge.

Only reference.call is stored. The tags queries also emit reference.type, reference.class and more; each is a real relationship, but folding them in would make callers return every place that merely mentions a type.

Where things live

• the index: $PH_CACHE/code-graph/<digest of the workspace root>.db — the cache root because it is rebuildable from the source, and keyed by root so two checkouts do not answer each other's questions. path: in the row's config overrides it.
• the grammars: $PH_CACHE/tree-sitter, set by the row at mount.

That second one is not housekeeping. The pack materializes even its bundled grammars into a writable cache on first use — the wheel ships them as an archive, not as loadable libraries — and it fails hard when that directory cannot be created, rather than falling back to the wheel. Its own default is $XDG_CACHE_HOME/…, which is right on a laptop and wrong in a container with a read-only HOME; both measured. So the row hands over the root pH already designates for rebuildable artifacts, and refuses at mount with a MountRefusal sentence — not a pathlib traceback — when even that is unwritable.

TREE_SITTER_LANGUAGE_PACK_CACHE_DIR still wins if an operator set it: their spelling is what makes the variable mean anything.

One consequence worth expecting: the first index on a cold grammar cache pays for materializing the grammar. Measured on packages/ph-core/src/ph, that is 9 s cold against 2 s warm, and 0.1 s when nothing changed.

Provision it on purpose rather than during someone's turn:

/code-graph status     # how many grammars are ready, and where they live
/code-graph install    # load each one now, naming any that will not

A command, not a tool — a person asks the harness to provision, and it costs no model turn. phern doctor reports the same path and the index's state without mounting an agent. It matters less here than for ph-text-index, whose model is a download rather than an unpack, but the question should have one answer per plugin asked the same way.

The skill

The package installs a code-graph skill, so an RLM under progressive disclosure sees one line in its catalog and can read the page when it needs it — index first, ask the question you actually have, then read the narrow thing; and that a name-based graph reports ambiguity rather than resolving it.

Registered by the row rather than found by a directory scan, so it arrives exactly when the tools do and leaves with them — skills-progressive ships an empty paths on purpose, because a skill is something a distribution installs deliberately (I7).

Tests

tests/test_code_graph.py runs the real parser and the real SQLite index. Three things it pins deliberately:

• line spans against the file — every span is checked by slicing the actual source at it, not against an expected number, because a pointer that is off by one still looks plausible in a diff;
• the enclosing-symbol rule — a call inside a nested closure belongs to the closure, not the 40-line function around it;
• incrementality — a second index pass over an unchanged tree parses nothing and a touched-but-unmodified file stays unchanged.