graphify

Files

T

safishamsiandClaude Opus 4.8 5d0137388e Feat: opt-in GRAPHIFY_DISABLE_THINKING; correct deepseek thinking default (#1621 )

@sub4biz verified against the live DeepSeek API that deepseek-v4-flash (and
v4-pro) have thinking ENABLED by default, contradicting the built-in config's
stale "non-thinking" comment (now corrected).

The naive fix (mirror the kimi branch and force thinking off) is the wrong
call: @sub4biz's production testing on real corpora found that disabling
thinking removes a rare reasoning-leak failure — which the adaptive
extraction/labeling retry already recovers from — but trades it for far more
frequent benign truncation AND measurably lower extraction quality and file
coverage, confirmed by a blind second reviewer.

So thinking stays ON by default (quality/coverage), with a documented opt-in
`GRAPHIFY_DISABLE_THINKING=1` for users who prefer run-to-run stability. Applies
to reasoning-capable OpenAI-compatible backends at both extra_body sites
(extraction + labeling). An explicit providers.json extra_body still wins, and
the moonshot/kimi branch is unchanged (it must disable thinking or content is empty).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

2026-07-06 16:02:45 +01:00

fixtures

fix(kotlin): emit implements edge for interface delegation (by)

2026-07-04 11:26:55 +01:00

__init__.py

feat: core pipeline

2026-04-04 18:52:44 +01:00

bench_extract.py

feat: implement parallel AST extraction using ProcessPoolExecutor with benchmarking support

2026-05-02 12:54:08 +05:30

conftest.py

feat(multigraph): add runtime compatibility probe (#956 )

2026-05-22 13:22:51 +01:00

test_affected_cli.py

fix: resolve explain/affected when a source-file path matches multiple nodes (#1503 )

2026-06-27 23:57:39 +01:00

test_affected_member_seed.py

feat(ruby/affected): mixes_in edges for include/extend/prepend + method-bound callers in affected (#1668 , #1669 )

2026-07-05 11:41:18 +01:00

test_agents_platform.py

feat(install): add cross-framework agents platform (+ skills alias)

2026-06-23 17:26:49 +01:00

test_analyze.py

feat: detect circular import dependencies at file level (#961 )

2026-05-30 21:37:47 +01:00

test_anthropic_custom_endpoint.py

feat: custom endpoints via OPENAI_BASE_URL/OPENAI_MODEL and ANTHROPIC_BASE_URL/ANTHROPIC_MODEL (#1273 )

2026-06-16 01:41:15 +01:00

test_antigravity_install.py

write antigravity rules and workflows on project-scoped install

2026-06-02 23:48:54 +01:00

test_astro_extraction.py

feat(extract): add .astro support (#850 )

2026-05-13 10:07:50 -07:00

test_backend_extras.py

add anthropic extra and fix backend-missing hints for uv tool installs

2026-06-03 00:08:03 +01:00

test_benchmark.py

feat(multigraph): add runtime compatibility probe (#956 )

2026-05-22 13:22:51 +01:00

test_build_merge_hyperedges_and_prune.py

fix(build): relativize source_file across a symlinked root (#1571 follow-up)

2026-07-01 11:14:48 +01:00

test_build.py

fix(ids): legacy-id detector only inspects file-level nodes (no Go false-positive)

2026-06-28 17:52:34 +01:00

test_cache.py

fix(cache): prune orphan semantic-cache entries at end of extract (#1527 )

2026-06-29 13:14:37 +01:00

test_callflow_html.py

feat(multigraph): add runtime compatibility probe (#956 )

2026-05-22 13:22:51 +01:00

test_cargo_introspect.py

feat(extract): add opt-in --cargo crate dependency extractor

2026-06-11 15:08:36 -06:00

test_case_sensitive_resolution.py

fix(extract): case-sensitive cross-file resolution in case-sensitive languages (#1581 )

2026-07-01 15:09:42 +01:00

test_charmap_encoding.py

fix(llm): force UTF-8 encoding on _call_claude_cli subprocess + loud failure on chunk errors (#906 )

2026-05-17 11:32:38 +01:00

test_chunking.py

Fix: tolerate tiktoken special-token text in token estimation (#1685 )

2026-07-06 12:42:39 +01:00

test_claude_cli_backend.py

fix(claude-cli): deliver extraction instructions in the user turn

2026-07-02 22:29:30 +01:00

test_claude_md.py

Fix PreToolUse hook for Claude Code v2.1.117+ (Glob|Grep → Bash matcher)

2026-04-28 00:56:54 +01:00

test_cli_export.py

fix: persist cluster-only analysis sidecar

2026-07-02 22:29:29 +01:00

test_cluster.py

reduce graph update churn and stabilize community IDs

2026-05-12 02:23:51 +03:00

test_codebuddy.py

feat: add CodeBuddy platform support (#1136 )

2026-06-07 14:34:13 +01:00

test_community_hub_labels.py

fix(cluster): detect stale community labels on cluster-only re-cluster

2026-07-01 11:52:50 +01:00

test_confidence.py

v2: confidence scores on INFERRED edges, avg shown in report

2026-04-06 16:06:31 +01:00

test_corrupt_graph_json.py

test(build): add regression tests for corrupt graph.json (#1537 )

2026-07-01 10:49:43 +01:00

test_cpp_objc_cross_file_calls.py

feat(extract): cross-file member-call resolution for C++ and ObjC (#1547 , #1556 )

2026-06-30 18:30:05 +01:00

test_cpp_preprocess.py

harden ollama metadata egress and cpp path handling (F3, F5)

2026-06-02 22:23:15 +01:00

test_csharp_member_calls.py

feat(extract): C# receiver-typed member-call resolution (#1609 )

2026-07-02 23:25:54 +01:00

test_csharp_type_resolution.py

feat(csharp): namespace-aware cross-file type resolution (#1562 )

2026-06-30 19:32:10 +01:00

test_dart.py

feat(extract): SystemVerilog class-level extraction; Dart with-clause mixin fix

2026-06-11 19:52:56 +03:00

test_dedup.py

fix(dedup): warn on cross-chunk node ID collision to surface silent data loss (#1504 )

2026-07-01 10:47:10 +01:00

test_detect.py

Fix: stop silently dropping source files during discovery via two over-broad filters (#1666 )

2026-07-06 16:00:31 +01:00

test_devin.py

feat: add Devin CLI support (graphify devin install/uninstall) (#1020 )

2026-05-26 09:17:18 +01:00

test_dotnet.py

feat(extract): link XAML views to ViewModels and extract binding references (#1473 )

2026-06-26 10:23:10 +01:00

test_explain_cli.py

feat(reflect): work-memory overlay — surface learned verdicts as a graph sidecar (#1441 )

2026-06-30 11:19:54 +01:00

test_export.py

feat(reflect): work-memory overlay — surface learned verdicts as a graph sidecar (#1441 )

2026-06-30 11:19:54 +01:00

test_extract_cli.py

feat(cli): --timing flag for per-stage timings on extract and cluster-only (#1490 )

2026-06-28 16:17:21 +01:00

test_extract.py

fix(extract): route extensionless shebang scripts to their AST extractor

2026-07-06 00:09:11 +01:00

test_extraction_spec_ids.py

fix(ids): node IDs include the full repo-relative path (#1504 , #1509 )

2026-06-28 16:57:00 +01:00

test_falkordb_integration.py

feat: add FalkorDB export backend (#1175 )

2026-06-07 15:03:49 +03:00

test_file_node_id_spec.py

fix(ids): node IDs include the full repo-relative path (#1504 , #1509 )

2026-06-28 16:57:00 +01:00

test_file_slice.py

Slice oversized text documents so the whole file is extracted (#1369 )

2026-06-18 01:55:56 +01:00

test_global_graph.py

fix(global-graph): rewire edges to deduplicated external nodes (#1250 )

2026-06-11 09:36:38 +02:00

test_google_workspace.py

Harden Google Workspace gws exports (#772 )

2026-05-07 20:07:57 +01:00

test_hooks.py

perf(hooks): eliminate multi-second foreground stalls before the detached launch

2026-07-02 11:50:12 +01:00

test_hypergraph.py

fix(hyperedge): accept members/node_ids alias keys for the member list (#1561 )

2026-06-30 16:58:23 +01:00

test_id_normalization_contract.py

Unify node-ID normalization into a single source of truth (#1378 )

2026-06-18 22:55:44 +01:00

test_image_vision.py

Contain symlinked extraction inputs

2026-07-02 22:29:32 +01:00

test_import_extension_resolution.py

fix(extract): apply resolver fixups to JS/TS dynamic_import handler

2026-05-05 00:07:50 +02:00

test_incremental.py

fix(update): prune edges owned by a re-extracted file (#1521 )

2026-06-28 19:29:51 +01:00

test_indirect_dispatch_assign_return.py

feat(extract): capture assignment/return indirect_call edges (#1566 slice 2)

2026-06-30 23:26:13 +01:00

test_indirect_dispatch_getattr.py

feat(extract): capture getattr(obj, "name") indirect_call edges (#1566 slice 3)

2026-07-01 10:30:47 +01:00

test_indirect_dispatch.py

fix(extract): cross-file indirect_call survives id relativization (0.9.4 regression)

2026-07-01 11:43:05 +01:00

test_ingest.py

feat: self-improving work-memory — save-result outcomes + graphify reflect (#1441 )

2026-06-24 11:43:13 +01:00

test_install_references.py

fix: four production bugs — Windows crashes, ghost-merge collision, version probe

2026-06-13 15:13:23 +01:00

test_install_roundtrip.py

feat(skills): progressive-disclosure split for all platforms (generator + drift fence) (#1121 )

2026-06-02 20:48:13 +01:00

test_install_strings.py

fix(skillgen): host-generic /graphify install guidance (#1530 )

2026-06-29 10:01:06 +01:00

test_install_upgrade.py

fix(install): route kiro install/uninstall through shared progressive helper (#1142 )

2026-06-05 22:15:09 +01:00

test_install.py

fix: windows skill name, opencode plugin separator, doc-corpus report noise (#1635 , #1646 , #1657 )

2026-07-04 22:43:31 +01:00

test_java_type_resolution.py

feat(java): suppress java stdlib types from references edges (#1603 )

2026-07-06 01:01:53 +01:00

test_js_import_resolution.py

fix(extract): don't report deferred import() as a file cycle (#1241 )

2026-07-05 10:42:09 +01:00

test_label_retry.py

Adaptive split-and-retry for community labeling on parse failure (#1280 , #1278 )

2026-06-18 22:50:52 +01:00

test_labeling.py

Fix: salvage truncated labeling replies and account for labeling token cost (#1690 , #1694 )

2026-07-06 12:46:12 +01:00

test_language_resolvers.py

feat(ruby): type-aware member-call resolution via a resolver framework (#1499 )

2026-06-29 09:40:22 +01:00

test_languages.py

feat(java): suppress java stdlib types from references edges (#1603 )

2026-07-06 01:01:53 +01:00

test_llm_backends.py

Feat: opt-in GRAPHIFY_DISABLE_THINKING; correct deepseek thinking default (#1621 )

2026-07-06 16:02:45 +01:00

test_llm_parser.py

fix(claude-cli): deliver extraction instructions in the user turn

2026-07-02 22:29:30 +01:00

test_long_path_hashing.py

fix(detect): incremental correctness for Office sources + long paths, cache word counts (#1649 , #1655 , #1656 )

2026-07-04 22:12:47 +01:00

test_manifest_ingest.py

Parse package manifests into canonical package nodes + depends_on edges (#1377 )

2026-06-19 10:25:09 +01:00

test_mcp_ingest.py

feat: MCP config extractor (.mcp.json, claude_desktop_config.json, mcp.json)

2026-05-26 20:16:41 +01:00

test_merge_graphs_cli.py

fix: allow python@ shebang in skill detection (#1586 ) + merge-graphs mixed types (#1606 )

2026-07-02 11:25:51 +01:00

test_minhash.py

perf/fix: replace datasketch with pure-numpy MinHash; memoize detect ignore checks

2026-06-10 15:50:38 +01:00

test_multigraph_compat.py

feat(multigraph): add runtime compatibility probe (#956 )

2026-05-22 13:22:51 +01:00

test_multigraph_diagnostics.py

feat(multigraph): add runtime compatibility probe (#956 )

2026-05-22 13:22:51 +01:00

test_multilang.py

fix(rust): emit field type references for tuple structs

2026-07-01 13:45:53 +01:00

test_obsidian_dangling_member.py

fix(export): guard to_canvas against dangling community members (#1236 follow-up)

2026-07-03 18:34:41 +01:00

test_obsidian_filename_cap.py

cap obsidian/canvas filenames to avoid ENAMETOOLONG on long labels (fixes #1094 )

2026-05-31 16:41:18 +01:00

test_office_incremental.py

fix(detect): incremental correctness for Office sources + long paths, cache word counts (#1649 , #1655 , #1656 )

2026-07-04 22:12:47 +01:00

test_office_limits.py

tighten F2 and F3 from review: bounded decompression, ollama DNS + clean error

2026-06-02 22:50:33 +01:00

test_ollama_retry_cap.py

Fix: cap Ollama client-side retries so a hung request cannot multiply the stall (#1686 )

2026-07-06 12:44:47 +01:00

test_ollama.py

tighten F2 and F3 from review: bounded decompression, ollama DNS + clean error

2026-06-02 22:50:33 +01:00

test_openai_custom_endpoint.py

feat: custom endpoints via OPENAI_BASE_URL/OPENAI_MODEL and ANTHROPIC_BASE_URL/ANTHROPIC_MODEL (#1273 )

2026-06-16 01:41:15 +01:00

test_pascal.py

add Pascal regex fallback - extraction works without tree-sitter-pascal

2026-05-09 15:52:17 +01:00

test_path_cli.py

fix path/explain arrow direction and bedrock CLI guard (#846 , #849 , #853 )

2026-05-13 23:19:15 +01:00

test_paths.py

fix(resolve): test mocks no longer erase the real cross-file call graph (#1553 )

2026-06-30 16:59:16 +01:00

test_pg_introspect.py

Fix invalid virtual postgres source_file URI backslashes on Windows (#1672 )

2026-07-05 10:42:09 +01:00

test_phantom_cross_package_call.py

fix(extract): gate JS/TS cross-file calls on import evidence to kill phantom cross-package edges (#1659 )

2026-07-04 21:22:39 +01:00

test_phantom_external_import.py

fix: harden semantic extraction and kill phantom import edges (#1631 , #1638 , #1632 )

2026-07-04 03:12:23 +01:00

test_pipeline.py

v0.4.15: VS Code Copilot Chat, OpenCode/Gemini Windows fixes, .mjs/.ejs, macOS watch, god_nodes degree rename

2026-04-15 23:08:43 +01:00

test_provider_registry.py

validate custom-provider base_url and gate project-local providers (F1)

2026-06-02 22:16:58 +01:00

test_prs.py

add graphify prs: graph-aware PR dashboard with triage, worktrees, conflict detection

2026-05-16 22:36:58 +01:00

test_python_import_resolution.py

feat: add cross-language semantic contexts for Python, JS/TS, C#, and Java (#996 )

2026-05-24 20:38:10 +01:00

test_query_cli.py

feat(multigraph): add runtime compatibility probe (#956 )

2026-05-22 13:22:51 +01:00

test_querylog.py

add query logging to ~/.cache/graphify-queries.log (#1128 )

2026-06-03 21:04:01 +01:00

test_rationale.py

feat: extract rationale comments + ADR/RFC doc references from JS/TS

2026-07-06 00:45:51 +01:00

test_read_hook.py

fix(hooks): match the real file extension in the Read|Glob hook (#1463 )

2026-06-25 20:33:00 +01:00

test_reflect.py

fix(reflect): layout-ordered source resolution for overlay staleness (#1558 )

2026-06-30 12:57:33 +01:00

test_replace_or_append_section.py

Fix: exact-match section heading in _replace_or_append_section to prevent CLAUDE.md data loss (#1688 )

2026-07-06 12:36:12 +01:00

test_report.py

fix: windows skill name, opencode plugin separator, doc-corpus report noise (#1635 , #1646 , #1657 )

2026-07-04 22:43:31 +01:00

test_ruby_resolution.py

feat(ruby/affected): mixes_in edges for include/extend/prepend + method-bound callers in affected (#1668 , #1669 )

2026-07-05 11:41:18 +01:00

test_scip_ingest.py

feat(multigraph): add runtime compatibility probe (#956 )

2026-05-22 13:22:51 +01:00

test_security.py

Relativize hyperedge source_file and honour GRAPHIFY_OUT everywhere (#1418 , #1423 )

2026-06-22 17:02:29 +01:00

test_semantic_cleanup.py

fix(hyperedge): accept members/node_ids alias keys for the member list (#1561 )

2026-06-30 16:58:23 +01:00

test_semantic_fragment_sanitize.py

fix: harden semantic extraction and kill phantom import edges (#1631 , #1638 , #1632 )

2026-07-04 03:12:23 +01:00

test_semantic_id_remap_root.py

fix(build): don't crash when a node's source_file is the scan root (#1618 )

2026-07-03 00:32:24 +01:00

test_semantic_similarity.py

2026-04-06 16:06:31 +01:00

test_serve_http.py

feat(serve): optional project_path for multi-project MCP serving

2026-07-02 12:11:51 +01:00

test_serve.py

fix: guarantee per-term BFS seed diversity in query (fixes #1445 )

2026-07-03 10:14:57 +01:00

test_skill_version_warning.py

fix(cli): make skill-version warning direction-aware (#1568 )

2026-06-30 23:15:52 +01:00

test_skillgen.py

fix: windows skill name, opencode plugin separator, doc-corpus report noise (#1635 , #1646 , #1657 )

2026-07-04 22:43:31 +01:00

test_swift_cross_file_calls.py

fix(swift): resolve calls on a singleton cached into a local var (#1604 )

2026-07-02 11:46:22 +01:00

test_swift_import_resolution.py

Collapse Swift module imports to one shared node

2026-06-16 03:06:43 +01:00

test_symbol_resolution.py

fix(resolve): test mocks no longer erase the real cross-file call graph (#1553 )

2026-06-30 16:59:16 +01:00

test_terraform.py

revert: remove importorskip now that uv.lock includes tree-sitter-hcl

2026-06-05 21:46:25 +01:00

test_transcribe.py

Remove Anthropic API call from transcribe.py - agent generates Whisper prompt itself

2026-04-10 15:55:22 +01:00

test_ts_decorators.py

fix(extract): emit reference edges for TS/JS decorators

2026-07-02 22:38:29 +01:00

test_ts_generators.py

fix(extract): extract TS/JS generator functions as nodes

2026-07-02 22:38:28 +01:00

test_ts_import_require.py

fix: harden semantic extraction and kill phantom import edges (#1631 , #1638 , #1632 )

2026-07-04 03:12:23 +01:00

test_ts_inheritance.py

capture TS interface-extends and same-file class heritage (fixes #1095 )

2026-05-31 16:47:52 +01:00

test_ts_namespace.py

fix(extract): emit a node for TS namespace / module containers

2026-07-02 22:38:29 +01:00

test_ts_receiver_member_calls.py

feat(extract): TS/JS member calls on local new-binding + typed-param receivers (#1630 )

2026-07-03 16:03:18 +01:00

test_typescript_module_extensions.py

Treat .mts/.cts (TypeScript module extensions) as TypeScript

2026-07-02 22:29:31 +01:00

test_validate.py

Fix: validate_extraction crashes on non-hashable node id / edge endpoint

2026-06-24 08:54:11 +01:00

test_vue_extraction.py

fix(extract): parse .vue SFC <script> with the right grammar (#1468 )

2026-06-26 10:20:53 +01:00

test_watch.py

fix(update): reconcile removed and renamed sources

2026-07-03 10:30:27 +01:00

test_wheel_packaging.py

feat(install): add cross-framework agents platform (+ skills alias)

2026-06-23 17:26:49 +01:00

test_wiki.py

fix(wiki): portable relative markdown links so navigation works outside Obsidian (#1444 )

2026-06-27 10:19:15 +01:00

test_word_count_cache.py

fix(detect): incremental correctness for Office sources + long paths, cache word counts (#1649 , #1655 , #1656 )

2026-07-04 22:12:47 +01:00

test_zero_node_no_cache.py

fix(extract): don't cache zero-node results; warn on empty source files (#1666 )

2026-07-05 10:33:07 +01:00