#1147 — builtin annotation nodes inflate god-node rankings:
Add _PYTHON_ANNOTATION_NOISE frozenset (str/int/bool/float/bytes/
MagicMock/Mock/AsyncMock/...) and apply it alongside
_PYTHON_TYPE_CONTAINERS in the annotation walker so scalar builtins
and test mocks are never created as nodes or emitted as edges.
Defense-in-depth guard in analyze.god_nodes filters _BUILTIN_NOISE_LABELS
so pre-existing graphs are also protected.
#1146 — package-form imports create disconnected islands:
from pkg import submod is now resolved to a file-level imports_from
edge when submod.py or submod/__init__.py exists on disk. Fix lives
in _collect_python_symbol_resolution_facts: when target resolves to
a __init__.py, each imported name is checked as a potential submodule
file and stored in _SymbolResolutionFacts.module_imports. Applied in
_apply_symbol_resolution_facts using stem-based canonical IDs.
#1145 — AST vs semantic node ID ghost duplicates:
build_from_json now runs a two-pass merge after adding all nodes:
collect AST nodes (source_location set) then find semantic ghosts
(same basename+label, no source_location). Ghosts are removed and
their IDs added to norm_to_id so all edges re-point to the AST node.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* feat: detect circular import dependencies at file level
- Add find_import_cycles() to analyze.py
- Collapses symbol nodes to parent files, builds directed file graph
- Uses nx.simple_cycles() bounded by max_cycle_length (default 5)
- Deduplicates rotations, returns shortest cycles first
- Considers both imports_from and re_exports edges
Tested on a 976-file Next.js codebase: found 4 cycles including
a known utils↔barrel circular dependency and a 4-file API cycle.
* fix: resolve import-cycle merge blockers
- use source_file-only endpoint resolution (no label fallback)
- support Graph/DiGraph orientation via edge source_file
- return structured cycle records and include self-loops
- integrate Import Cycles section into GRAPH_REPORT.md
- expand cycle tests for real-schema IDs, undirected input,
missing source_file nodes, and non-import relations
* fix(analyze): exclude npm dep-block keys from god-node selection
Extends _JSON_NOISE_LABELS in graphify/analyze.py with the six npm
package.json dependency-block keys (dependencies, devDependencies,
peerDependencies, optionalDependencies, bundledDependencies,
bundleDependencies — lowercased to match the existing .strip().lower()
comparison in _is_json_key_node).
On JS/TS corpora with non-trivial dependency counts, the dep-block key
node accumulates contains+imports edges to every package entry and was
surfacing as the top god-node in the report. The fix is a one-line
extension of the existing frozenset; no new helpers or code paths.
Includes a parametrized regression test in tests/test_analyze.py
covering all five npm keys: dependencies, devDependencies,
peerDependencies, optionalDependencies, bundledDependencies.
Validated live against rsl-siege-manager @ 6085fd66 — zero npm dep-block
keys in the top-10 god-nodes after the fix. Pre-existing failures
(Windows symlink + SQL tree-sitter): 17, unchanged.
Closes#2
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* style: drop fork-local issue refs from analyze comments
---------
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
In Python+TypeScript monorepos, the call and import resolvers match by
label across language boundaries (AuthError -> Member), producing false
positives that dominate 'Surprising Connections' due to cross-dir (+2)
and cross-community (+1) bonuses.
Expand the existing calls guard to also cover uses edges, and zero the
cross-dir and cross-community bonuses for these pairs — not just conf_bonus.
Leaves semantically_similar_to, EXTRACTED, and AMBIGUOUS edges unaffected.
5 new tests: calls suppressed, uses suppressed, semantically_similar_to
preserved, same-language INFERRED preserved, cross-language EXTRACTED preserved.
#796: add edge_data()/edge_datas() helpers in build.py that tolerate
MultiGraph/MultiDiGraph; replace all G.edges[u,v] 2-tuple call sites in
__main__.py, serve.py, wiki.py, export.py, analyze.py, benchmark.py;
fix same pattern in 10 skill file inline heredocs
#795: all 12 skill files now short-circuit on /graphify --help or -h
and print the Usage block without running any pipeline steps
#792 (hollow response): add _response_is_hollow() predicate in llm.py;
when Ollama (or any backend) returns empty/null/whitespace content or a
parsed result with no nodes/edges, rewrite finish_reason="length" so
_extract_with_adaptive_retry bisects the chunk instead of silently
dropping it; applied to _call_openai_compat, _call_claude, _call_bedrock
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- analyze.py: add seed=42 to betweenness_centrality() — eliminates non-deterministic GRAPH_REPORT.md diffs on graphs >1000 nodes (#499)
- extract.py: fix common-root inference to stop at first diverging segment not sum of all matches (#502)
- extract.py: resolve root to absolute path; post-process file node IDs to project-relative after extraction so graph.json edge endpoints are stable across machines (#502)
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- #352: add skill-kiro.md to pyproject.toml package-data
- #341: guard edge_betweenness at >5000 nodes; use approximate k=100 for suggest_questions on large graphs
- #354/#229: add Step 6b in skill.md to call to_wiki() when --wiki given (before Step 9 cleanup)
- #356: call _install_opencode_plugin() from install --platform opencode path
- #350: add cache_root param to extract() so subdirectory runs keep cache at ./graphify-out/cache/
- #230: PHP class_constant_access_expression emits references_constant edges
- #232: PHP scoped_call_expression (static method calls) emits calls edges
- #287: os.replace fallback for Windows WinError 5; graphify update exits 1 on failure; templates use graphify update . instead of python3 -c
- #348: cross-file call resolution for all languages via raw_calls + global label map pass in extract()
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Add --graphml to Usage table (was implemented but undocumented there)
- Remove early manifest save from --update merge step (Step 9 owns it; saving early meant failed pipelines left manifest ahead of graph)
- query/path/explain now check graph.json exists before running, with clear "run /graphify first" message
- --no-viz: clarify it skips both Obsidian vault and HTML (was contradictory)
style: replace all em dashes with hyphens
fix: explain hidden .graphify/ folder in skill output and README
fix: rename .graphify/ to graphify-out/ so output is visible by default
Safi