mneme-graph 3.1.0__tar.gz

mneme_graph-3.1.0/.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+.pytest_cache/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+htmlcov/
+.mypy_cache/
+.ruff_cache/
+
+# Virtual envs
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Node
+node_modules/
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+pnpm-debug.log*
+.pnpm-store/
+*.tsbuildinfo
+
+# TypeScript
+*.js.map
+*.d.ts.map
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+.DS_Store
+
+# OS
+Thumbs.db
+desktop.ini
+
+# mneme local
+.mneme/
+*.local.json
+vault-test/
+benchmarks/results/
+benchmarks/_runs/
+benchmarks/*/output/
+benchmarks/*/result.json
+benchmarks/*/hardware.json
+
+# Secrets
+.env.local
+.env.*.local
+secrets/
+*.key
+*.pem
+
+# Build artifacts
+*.tgz
+*.whl

mneme_graph-3.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: mneme-graph
+Version: 3.1.0
+Summary: Local code knowledge graph for mneme: tree-sitter extraction, atomic GraphStore, confidence-labelled nodes.
+Author: Onour Impram
+License: Apache-2.0
+Keywords: ast,code-graph,knowledge-graph,mneme,tree-sitter
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.11
+Requires-Dist: mneme-core<4,>=3.0.0
+Requires-Dist: tree-sitter-javascript>=0.21
+Requires-Dist: tree-sitter-python>=0.21
+Requires-Dist: tree-sitter-typescript>=0.21
+Requires-Dist: tree-sitter>=0.21
+Provides-Extra: dev
+Requires-Dist: mypy>=1.10; extra == 'dev'
+Requires-Dist: pytest-cov>=5.0; extra == 'dev'
+Requires-Dist: pytest>=8.2; extra == 'dev'
+Requires-Dist: ruff>=0.4.7; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# mneme-graph
+
+Local code knowledge graph for mneme. Extracts GraphNode/GraphEdge from Python
+source files via tree-sitter. Derived and rebuildable — the ground truth is
+always the source files; `graph.json` is a derived artifact.
+
+Part of the [mneme](https://github.com/TheGoatPsy/mneme) memory engine.
+
+## Scope (v1)
+
+This package is deliberately small and honest about its limits.
+
+- **Python only.** Extraction uses tree-sitter for Python source. TypeScript,
+  JavaScript, Rust, and other languages are not yet supported.
+- **`calls` resolution is heuristic.** A call edge resolves to a local
+  function/method by unqualified name within the same vault, with `INFERRED`
+  confidence. There is no cross-file binding or precise symbol resolution; a
+  call with no local name match points at an `<external>` node (`EXTRACTED`).
+- **Derived, never source of truth.** `graph.json` is rebuilt from source on
+  every `build`; the source files remain the ground truth.
+
+### Deferred (not implemented yet)
+
+- Community detection / clustering.
+- Pull-request impact analysis.
+- Entity canonicalization and a merge queue (to avoid ghost-duplicate nodes
+  across renames and aliases).
+- Multi-language extraction.
+
+These are roadmap items, not present capabilities.

mneme_graph-3.1.0/README.md

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+# mneme-graph
+
+Local code knowledge graph for mneme. Extracts GraphNode/GraphEdge from Python
+source files via tree-sitter. Derived and rebuildable — the ground truth is
+always the source files; `graph.json` is a derived artifact.
+
+Part of the [mneme](https://github.com/TheGoatPsy/mneme) memory engine.
+
+## Scope (v1)
+
+This package is deliberately small and honest about its limits.
+
+- **Python only.** Extraction uses tree-sitter for Python source. TypeScript,
+  JavaScript, Rust, and other languages are not yet supported.
+- **`calls` resolution is heuristic.** A call edge resolves to a local
+  function/method by unqualified name within the same vault, with `INFERRED`
+  confidence. There is no cross-file binding or precise symbol resolution; a
+  call with no local name match points at an `<external>` node (`EXTRACTED`).
+- **Derived, never source of truth.** `graph.json` is rebuilt from source on
+  every `build`; the source files remain the ground truth.
+
+### Deferred (not implemented yet)
+
+- Community detection / clustering.
+- Pull-request impact analysis.
+- Entity canonicalization and a merge queue (to avoid ghost-duplicate nodes
+  across renames and aliases).
+- Multi-language extraction.
+
+These are roadmap items, not present capabilities.

mneme_graph-3.1.0/mneme_graph/__init__.py

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+"""mneme-graph: local code knowledge graph with confidence-labelled nodes.
+
+Derives a rebuildable graph from source files via tree-sitter extraction.
+The ground truth is always the source files; graph.json is a derived artifact
+that can be deleted and rebuilt identically from the same source.
+
+Public surface:
+
+    from mneme_graph.schema import GraphNode, GraphEdge, ConfidenceLabel
+    from mneme_graph.store import GraphStore
+    from mneme_graph.extractor.python_extractor import extract_file
+"""
+
+__version__ = "0.2.0"
+__all__ = ["__version__"]

mneme_graph-3.1.0/mneme_graph/analytics.py

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+"""Derived and inferred analytics over the extracted mneme code graph.
+
+All functions in this module are PURE: they operate on list[GraphNode] and
+list[GraphEdge], never mutate their inputs, perform no IO, make no network
+calls, and are fully deterministic.
+
+Confidence-label invariant
+--------------------------
+Nodes and edges stored in the graph carry ``confidence="EXTRACTED"`` because
+they were directly observed from source-code ASTs.  The outputs of this
+module are one level removed:
+
+* ``Community`` objects are **INFERRED** — connected-component membership is
+  derived from structural patterns, not directly observable in any single
+  source location.
+* ``MergeCandidate`` objects are **AMBIGUOUS** — duplicate detection is based
+  on heuristics (same name/kind/path, different ``line_start``); the evidence
+  is present but may be contradictory or incomplete.
+* ``ImpactResult`` and ``apply_merge`` return plain node/edge data; callers
+  retain whatever confidence labels the underlying objects carry.
+"""
+
+from __future__ import annotations
+
+from collections import deque
+from collections.abc import Iterable
+from dataclasses import dataclass, field
+
+from .schema import ConfidenceLabel, GraphEdge, GraphNode
+
+# ---------------------------------------------------------------------------
+# Community detection (connected components)
+# ---------------------------------------------------------------------------
+
+_COMMUNITY_EDGE_KINDS = frozenset({"calls", "inherits", "imports"})
+
+
+@dataclass(frozen=True)
+class Community:
+    """A connected component in the undirected graph projection.
+
+    Attributes:
+        community_id  Lexicographically smallest ``node_id`` in the component.
+        node_ids      Sorted tuple of all ``node_id`` values in the component.
+        confidence    Always ``"INFERRED"`` — membership is derived, not
+                      directly observed.
+    """
+
+    community_id: str
+    node_ids: tuple[str, ...]
+    confidence: ConfidenceLabel = field(default="INFERRED")
+
+
+def detect_communities(
+    nodes: list[GraphNode],
+    edges: list[GraphEdge],
+) -> list[Community]:
+    """Return connected components over the undirected projection of *nodes*.
+
+    Only edges whose ``kind`` is in ``{"calls", "inherits", "imports"}`` are
+    considered; ``"defines"`` edges are ignored.  Edges that reference a
+    ``node_id`` not present in *nodes* are silently ignored.  Every node in
+    *nodes* participates: an isolated node becomes a singleton community.
+
+    Output is sorted by ``community_id``; ``node_ids`` within each community
+    is sorted.  Calling this function twice with the same inputs produces
+    identical results.
+    """
+    node_ids: set[str] = {n.node_id for n in nodes}
+
+    # Build undirected adjacency list (only within known nodes).
+    adj: dict[str, list[str]] = {nid: [] for nid in node_ids}
+    for edge in edges:
+        if edge.kind not in _COMMUNITY_EDGE_KINDS:
+            continue
+        if edge.src_id not in node_ids or edge.dst_id not in node_ids:
+            continue
+        adj[edge.src_id].append(edge.dst_id)
+        adj[edge.dst_id].append(edge.src_id)
+
+    # BFS to find connected components.
+    visited: set[str] = set()
+    communities: list[Community] = []
+
+    for start in sorted(node_ids):  # deterministic traversal order
+        if start in visited:
+            continue
+        component: list[str] = []
+        queue: deque[str] = deque([start])
+        visited.add(start)
+        while queue:
+            current = queue.popleft()
+            component.append(current)
+            for neighbour in adj[current]:
+                if neighbour not in visited:
+                    visited.add(neighbour)
+                    queue.append(neighbour)
+        sorted_ids = tuple(sorted(component))
+        communities.append(
+            Community(
+                community_id=sorted_ids[0],
+                node_ids=sorted_ids,
+            )
+        )
+
+    return sorted(communities, key=lambda c: c.community_id)
+
+
+# ---------------------------------------------------------------------------
+# PR impact analysis (reverse BFS)
+# ---------------------------------------------------------------------------
+
+
+@dataclass(frozen=True)
+class ImpactResult:
+    """Result of a PR impact query.
+
+    Attributes:
+        changed   Sorted tuple of ``changed_node_ids`` that actually exist in
+                  *nodes* (unknown ids are silently dropped).
+        affected  Sorted tuple of ``(node_id, distance)`` pairs — nodes
+                  reachable upstream from the changed set, excluding the
+                  changed nodes themselves.  Sorted by ``(distance, node_id)``.
+    """
+
+    changed: tuple[str, ...]
+    affected: tuple[tuple[str, int], ...]
+
+
+def pr_impact(
+    nodes: list[GraphNode],
+    edges: list[GraphEdge],
+    changed_node_ids: Iterable[str],
+    *,
+    max_depth: int | None = None,
+) -> ImpactResult:
+    """Return the nodes transitively affected by changes to *changed_node_ids*.
+
+    Edge semantics: ``src -> dst`` means "``src`` depends on ``dst``".
+    Changing ``dst`` therefore affects ``src``.  The traversal follows edges
+    in the reverse direction (``dst -> src``), i.e. it finds all nodes that
+    (directly or transitively) depend on any changed node.
+
+    Args:
+        nodes:             Full node list; defines the valid node universe.
+        edges:             Full edge list.
+        changed_node_ids:  Seed set.  Ids not found in *nodes* are ignored.
+        max_depth:         Maximum hop distance to explore (``None`` = unbounded).
+
+    Returns:
+        ``ImpactResult`` with ``changed`` and ``affected`` fields.
+    """
+    node_ids: set[str] = {n.node_id for n in nodes}
+    changed_set: set[str] = {nid for nid in changed_node_ids if nid in node_ids}
+
+    # Build reverse adjacency: dst -> list[src] (who depends on dst?).
+    rev_adj: dict[str, list[str]] = {nid: [] for nid in node_ids}
+    for edge in edges:
+        if edge.src_id in node_ids and edge.dst_id in node_ids:
+            rev_adj[edge.dst_id].append(edge.src_id)
+
+    # BFS from changed_set, traversing reverse edges.
+    distance: dict[str, int] = {}
+    queue: deque[str] = deque()
+    for nid in sorted(changed_set):  # deterministic seed order
+        distance[nid] = 0
+        queue.append(nid)
+
+    while queue:
+        current = queue.popleft()
+        current_dist = distance[current]
+        next_dist = current_dist + 1
+        if max_depth is not None and next_dist > max_depth:
+            continue
+        for upstream in rev_adj[current]:
+            if upstream not in distance:
+                distance[upstream] = next_dist
+                queue.append(upstream)
+
+    affected: list[tuple[str, int]] = sorted(
+        [(nid, dist) for nid, dist in distance.items() if nid not in changed_set],
+        key=lambda t: (t[1], t[0]),
+    )
+
+    return ImpactResult(
+        changed=tuple(sorted(changed_set)),
+        affected=tuple(affected),
+    )
+
+
+def changed_nodes_for_paths(
+    nodes: list[GraphNode],
+    paths: Iterable[str],
+) -> list[str]:
+    """Return sorted, deduplicated ``node_id`` values for nodes in *paths*.
+
+    Args:
+        nodes:  Full node list to search.
+        paths:  Iterable of ``source_path`` strings to match against.
+
+    Returns:
+        Sorted list of matching ``node_id`` values.
+    """
+    path_set: set[str] = set(paths)
+    return sorted({n.node_id for n in nodes if n.source_path in path_set})
+
+
+# ---------------------------------------------------------------------------
+# Ghost-duplicate / merge candidate detection
+# ---------------------------------------------------------------------------
+
+
+@dataclass(frozen=True)
+class MergeCandidate:
+    """A set of nodes that appear to represent the same logical symbol.
+
+    Ghost duplicates arise when ``line_start`` drift causes the extractor to
+    assign a new ``node_id`` to a symbol that has not meaningfully changed.
+    Only **local** nodes (``source_path != "<external>"``) are considered.
+
+    Attributes:
+        key       ``(source_path, name, kind)`` grouping key.
+        node_ids  Sorted tuple of duplicate ``node_id`` values (len >= 2).
+        confidence  Always ``"AMBIGUOUS"`` — the heuristic may be wrong.
+    """
+
+    key: tuple[str, str, str]
+    node_ids: tuple[str, ...]
+    confidence: ConfidenceLabel = field(default="AMBIGUOUS")
+
+
+def find_merge_candidates(nodes: list[GraphNode]) -> list[MergeCandidate]:
+    """Detect ghost-duplicate local nodes sharing ``(source_path, name, kind)``.
+
+    External nodes (``source_path == "<external>"``) are excluded because
+    their ``node_id`` is already content-addressed without ``line_start`` and
+    so they cannot produce duplicates by design.
+
+    FIX 3: A group is only a merge candidate when its nodes span at least two
+    DISTINCT ``content_hash`` values.  Nodes that share ``(source_path, name,
+    kind)`` but have the SAME ``content_hash`` were extracted from the same
+    file version — they are legitimately distinct symbols (e.g. two methods
+    both named ``render`` in different classes) and must NOT be flagged.  A
+    real ghost-duplicate (PA3) arises only across different file versions,
+    which necessarily have different content hashes.
+
+    Returns candidates sorted by ``key``; ``node_ids`` within each candidate
+    is sorted.
+    """
+    # Map key -> list of (node_id, content_hash) pairs.
+    groups: dict[tuple[str, str, str], list[tuple[str, str]]] = {}
+    for node in nodes:
+        if node.source_path == "<external>":
+            continue
+        key = (node.source_path, node.name, str(node.kind))
+        groups.setdefault(key, []).append((node.node_id, node.content_hash))
+
+    candidates: list[MergeCandidate] = []
+    for key, id_hash_pairs in groups.items():
+        distinct_hashes = {chash for _, chash in id_hash_pairs}
+        # Only emit a candidate when nodes span >= 2 distinct content_hash values
+        # (cross-version ghost duplicate).  Same content_hash = same file version
+        # = legitimately distinct symbols within that version → NOT a candidate.
+        if len(distinct_hashes) < 2:
+            continue
+        deduped_ids = sorted({nid for nid, _ in id_hash_pairs})
+        if len(deduped_ids) >= 2:
+            candidates.append(
+                MergeCandidate(
+                    key=key,
+                    node_ids=tuple(deduped_ids),
+                )
+            )
+
+    return sorted(candidates, key=lambda c: c.key)
+
+
+# ---------------------------------------------------------------------------
+# Merge application
+# ---------------------------------------------------------------------------
+
+
+def _resolve_canonical(node_id: str, canonical_map: dict[str, str]) -> str:
+    """Follow canonical_map transitively until fixpoint, handling cycles.
+
+    For a simple chain (no cycle) the terminal id (not in canonical_map) is
+    returned.  For a cycle (or a rho-shaped chain whose tail enters a cycle)
+    the lexicographically smallest id among the cycle members is returned so
+    that exactly one node in the cycle survives apply_merge.
+    """
+    seen_list: list[str] = []
+    seen_set: set[str] = set()
+    current = node_id
+    while current in canonical_map:
+        if current in seen_set:
+            # Cycle detected — current is the entry point we've looped back to.
+            # The cycle members are the suffix of seen_list starting from current.
+            cycle_start = seen_list.index(current)
+            cycle_members = seen_list[cycle_start:]
+            return min(cycle_members)
+        seen_list.append(current)
+        seen_set.add(current)
+        current = canonical_map[current]
+    # No cycle — current is the terminal (not in canonical_map).
+    return current
+
+
+def apply_merge(
+    nodes: list[GraphNode],
+    edges: list[GraphEdge],
+    canonical_map: dict[str, str],
+) -> tuple[list[GraphNode], list[GraphEdge]]:
+    """Apply a duplicate-to-canonical mapping, returning new (nodes, edges).
+
+    *canonical_map* maps ``duplicate_node_id -> canonical_node_id``.
+
+    Rules:
+    * Nodes whose ``node_id`` is a key in *canonical_map* (and is not itself
+      the canonical target after transitive resolution) are dropped.
+    * Every edge's ``src_id`` and ``dst_id`` are rewritten through the map
+      (transitively resolved).
+    * After rewriting, a new ``edge_id`` is derived via ``GraphEdge.make``;
+      duplicate edges are deduplicated (last writer wins on same ``edge_id``).
+    * Self-loops introduced by merging (``src_id == dst_id``) are dropped.
+    * The original *nodes* and *edges* lists are never mutated.
+    * Output lists are deterministically sorted (nodes by ``node_id``, edges
+      by ``edge_id``).
+
+    Transitive resolution: if the map contains ``a -> b`` and ``b -> c`` then
+    ``a`` resolves to ``c``.  Cycles in the map are broken at the first
+    repeated node (the node keeps its current id).
+    """
+    # Resolve each key to its ultimate canonical target.
+    resolved: dict[str, str] = {
+        dup: _resolve_canonical(dup, canonical_map) for dup in canonical_map
+    }
+
+    # Non-canonical node ids: keys whose resolved target differs from themselves.
+    non_canonical: set[str] = {dup for dup, canon in resolved.items() if dup != canon}
+
+    # Filter nodes: drop non-canonical duplicates.
+    new_nodes: list[GraphNode] = sorted(
+        [n for n in nodes if n.node_id not in non_canonical],
+        key=lambda n: n.node_id,
+    )
+
+    # FIX 1: surviving node ids — only nodes actually present in new_nodes.
+    surviving_node_ids: set[str] = {n.node_id for n in new_nodes}
+
+    # Rewrite and deduplicate edges.
+    seen_edge_ids: dict[str, GraphEdge] = {}
+    for edge in edges:
+        new_src = resolved.get(edge.src_id, edge.src_id)
+        new_dst = resolved.get(edge.dst_id, edge.dst_id)
+        if new_src == new_dst:
+            # Drop self-loops created by merging.
+            continue
+        # FIX 1: drop edges whose rewritten endpoint is not in the surviving set.
+        if new_src not in surviving_node_ids or new_dst not in surviving_node_ids:
+            continue
+        new_edge = GraphEdge.make(
+            src_id=new_src,
+            dst_id=new_dst,
+            kind=edge.kind,
+            confidence=edge.confidence,
+            valid_at=edge.valid_at,
+        )
+        seen_edge_ids[new_edge.edge_id] = new_edge
+
+    new_edges: list[GraphEdge] = sorted(seen_edge_ids.values(), key=lambda e: e.edge_id)
+
+    return new_nodes, new_edges