Abdullah d68d6012bd feat: add R language extractor ...

(cherry picked from commit 250395de31)

2026-09-21 19:10:13 +01:00

..

fixtures

feat: add R language extractor

2026-09-21 19:10:13 +01:00

__init__.py

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bench_extract.py

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bench_query_scoring.py

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conftest.py

test: isolate backend-detection tests from the developer's environment

2026-09-10 23:04:40 +01:00

test_affected_cli.py

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test_affected_member_seed.py

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test_agents_platform.py

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test_analyze.py

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test_anthropic_custom_endpoint.py

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test_antigravity_install.py

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test_apm_fallback_version.py

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test_architecture_doc.py

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test_astro_extraction.py

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test_astro_import_ids.py

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test_atomic_canvas_export.py

fix(export): write graph.canvas and Obsidian notes atomically

2026-09-05 01:18:59 +01:00

test_atomic_version_stamp.py

fix(install): write .graphify_version atomically via os.replace

2026-09-05 01:18:59 +01:00

test_atomic_writes.py

Guard os_replace_with_fallback against src equal to dst

2026-09-12 17:36:09 +01:00

test_backend_env_isolation.py

test: isolate backend-detection tests from the developer's environment

2026-09-10 23:04:40 +01:00

test_backend_extras.py

release: 0.9.61 — fix Python 3.12/3.13 breakage from 0.9.60

2026-09-12 22:23:00 +01:00

test_benchmark_raw_graph.py

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test_benchmark.py

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test_build_merge_dedup_scope.py

Scope deduplication during incremental merges

2026-09-11 22:46:15 +01:00

test_build_merge_hyperedges_and_prune.py

fix: support Python 3.14 optional dependencies

2026-09-12 21:33:43 +01:00

test_build_merge_shrink_guard.py

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test_build.py

Import Iterable in build.py, the annotations already use it

2026-09-10 14:03:22 +01:00

test_builtin_global_type_refs.py

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test_cache.py

Use the replace fallback for AST cache writes

2026-09-12 17:36:09 +01:00

test_callflow_html.py

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test_cargo_introspect.py

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test_carried_hyperedge_remap.py

test: route carried-hyperedge dedup through a re-extracted chunk (#3503)

2026-09-11 22:51:35 +01:00

test_case_sensitive_resolution.py

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test_charmap_encoding.py

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test_chunking.py

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test_cjs_module_extension.py

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test_claude_cli_backend.py

fix(claude-cli): tolerate a diagnostic preamble before the JSON envelope

2026-09-05 21:55:34 +01:00

test_claude_md.py

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test_cli_broken_pipe.py

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test_cli_export.py

Compare partition structure, not just the node id set, for staleness

2026-09-17 11:01:38 +01:00

test_cli_help.py

fix(cli): list prs, provider, and export formats in --help

2026-08-29 19:32:51 +01:00

test_cluster.py

test(cluster): add the self-loop cohesion_score regressions #3558 described

2026-09-14 18:55:31 +01:00

test_cobol_extractor.py

feat: add COBOL language extractor

2026-09-21 18:04:14 +01:00

test_codebuddy.py

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test_community_hub_labels.py

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test_community_labels_skill.py

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test_confidence.py

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test_corrupt_graph_json.py

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test_cpp_nested_and_cli.py

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test_cpp_objc_cross_file_calls.py

Add a regression test for the god node guard on the fallback

2026-09-17 11:03:41 +01:00

test_cpp_preprocess.py

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test_cross_extension_reexport_self_cycle.py

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test_cross_language_call_resolution.py

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test_cross_repo_external_call_guards.py

fix(merge): respect C# type visibility across repos

2026-09-13 17:47:56 +01:00

test_cross_repo_member_calls.py

feat(merge): finish member calls across a repo boundary (#3152)

2026-09-02 14:58:01 +01:00

test_cross_repo_shared_types.py

test(merge): pin that a shared type links even when the declarations drift (#3007)

2026-08-24 14:12:53 +01:00

test_csharp_call_site_generic_args.py

fix(extract): collapse byte-identical duplicate edges at emission (#3251)

2026-09-05 01:18:59 +01:00

test_csharp_enum_members.py

feat(csharp): emit a node per enum member (#3063)

2026-08-25 15:45:06 +01:00

test_csharp_field_generic_args.py

fix(csharp): walk generic type arguments in field position

2026-08-21 16:50:25 +01:00

test_csharp_generic_callsites.py

fix(csharp): resolve unqualified generic call sites, Get<int>(...) (#3406)

2026-09-09 11:30:27 +01:00

test_csharp_interface_dispatch.py

feat(csharp): link interface methods to their single implementation (#3003)

2026-08-24 13:22:09 +01:00

test_csharp_member_calls.py

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test_csharp_member_nodes.py

feat(csharp): emit a member node per property (#3006)

2026-08-24 14:08:25 +01:00

test_csharp_object_creation.py

fix(csharp): emit calls edges for object creation expressions (#2997)

2026-08-24 13:17:23 +01:00

test_csharp_partial_classes.py

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test_csharp_type_resolution.py

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test_dart.py

Add source_location to Dart extraction

2026-09-07 20:21:35 +01:00

test_dedup_remaps_hyperedges.py

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test_dedup_survivor_richness.py

fix(dedup): pick the richer duplicate as survivor and keep the losers' fields (#3372)

2026-09-09 11:30:29 +01:00

test_dedup.py

Add negative control test for an ordinary ASCII path

2026-09-14 18:49:17 +01:00

test_definition_file_portability.py

fix(build): make definition_file portable, like its sibling source_file (#3223)

2026-09-02 03:05:59 +01:00

test_detect.py

fix: bare plural "tokens" in a prose file is no longer treated as a secret

2026-09-13 17:47:53 +01:00

test_devin.py

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test_dotnet.py

fix(razor): resolve @inject types across files (#3187)

2026-08-29 18:38:33 +01:00

test_duplicate_annotation_edges.py

fix(extract): collapse byte-identical duplicate edges at emission (#3251)

2026-09-05 01:18:59 +01:00

test_elixir_import_resolution.py

fix(elixir): guard nested-module capture and same-file contains clobber (#3603 follow-up)

2026-09-16 15:37:30 +01:00

test_evidence_binding.py

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test_explain_cli.py

Stop path::Symbol from shadowing a literal :: label

2026-09-11 23:58:31 +01:00

test_export_control_characters.py

fix(export): a control character in a label must not abort the export (#2897)

2026-08-20 16:09:00 +01:00

test_export_path_length.py

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test_export.py

fix(export): complete the vis-network crash fix and pin the tooltip XSS boundary (#3699, #3686 follow-ups)

2026-09-20 18:07:23 +01:00

test_external_stub_endpoints.py

fix(build): mint typed external stubs for undeclared import endpoints (#2873)

2026-09-16 16:20:01 +01:00

test_extract_cache_location.py

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test_extract_cli.py

fix(extract): scope fresh semantic results to dispatched files (#2926)

2026-08-21 19:21:20 +01:00

test_extract_code_only_cli.py

fix(extract): rescan code with --force --code-only (#3125)

2026-08-28 01:20:57 +01:00

test_extract.py

feat: add R language extractor

2026-09-21 19:10:13 +01:00

test_extraction_spec_ids.py

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test_extractors_registry.py

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test_falkordb_integration.py

test(falkordb): skip when the port answers but is not FalkorDB

2026-08-27 20:20:16 +01:00

test_file_label_disambiguation.py

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test_file_node_id_spec.py

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test_file_slice.py

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test_forwarding_review_findings.py

fix: preserve export cycles and legacy declaration facts

2026-09-05 21:55:33 +01:00

test_gemini_hook.py

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test_global_add_tag_inference.py

Never infer an empty repo tag for global add

2026-09-10 14:03:22 +01:00

test_global_graph.py

fix(build): offset community ids per input in merge-graphs (#3014)

2026-08-25 18:09:25 +01:00

test_go_builtin_call_targets.py

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test_go_interface_methods.py

fix(go): extract method requirements declared in an interface body

2026-09-20 13:59:25 +01:00

test_go_qualified_resolution.py

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test_god_nodes_cli.py

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test_god_nodes_exclude_hubs.py

fix(analyze): god_nodes honours exclude_hubs_percentile (#3205)

2026-09-02 14:49:03 +01:00

test_google_workspace.py

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test_hollow_chunks_arm_shrink_guard.py

fix(extract): hollow, unparseable and omitting chunks count as incomplete (#3105)

2026-08-28 01:20:27 +01:00

test_home_sandbox.py

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test_hook_chain_survives_skip.py

fix(hooks): a graphify skip must not terminate the whole git hook (#2986)

2026-09-06 16:17:37 +01:00

test_hook_guard_token_match.py

fix(cli): hook-guard search detection matches executed commands, not prose (#3121)

2026-08-30 15:11:40 +01:00

test_hook_guard.py

fix(cli): hook-guard search detection matches executed commands, not prose (#3121)

2026-08-30 15:11:40 +01:00

test_hook_out_of_project_paths.py

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test_hook_strict.py

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test_hooks.py

fix(hooks): resolve the output dir from GRAPHIFY_OUT in the sh gates, not a literal graphify-out/

2026-09-14 18:49:21 +01:00

test_hyperedge_member_shapes.py

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test_hyperedge_roundtrip.py

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test_hypergraph.py

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test_id_normalization_contract.py

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test_ignore_file_encoding.py

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test_image_vision.py

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test_import_extension_resolution.py

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test_import_self_loops.py

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test_imported_export_forwarding.py

fix: resolve explicit named exports through imported bindings

2026-09-05 21:55:33 +01:00

test_incomplete_build_guard.py

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test_incremental_mtime_collision.py

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test_incremental.py

fix: resolve generic Rust self calls

2026-09-18 15:16:09 +01:00

test_indirect_call_arrow_single_param_shadow.py

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test_indirect_call_block_scoped_shadow.py

Add regression tests for block scoped let/const shadowing

2026-09-20 13:59:26 +01:00

test_indirect_call_catch_binding_shadow.py

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test_indirect_call_external_import_shadow.py

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test_indirect_call_for_of_binding_shadow.py

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test_indirect_call_function_expression_shadow.py

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test_indirect_call_nested_closure_shadow.py

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test_indirect_dispatch_assign_return.py

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test_indirect_dispatch_getattr.py

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test_indirect_dispatch.py

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test_inferred_confidence_rubric.py

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test_ingest.py

fix(ingest): make memory-doc filenames unique so concurrent saves do not overwrite

2026-09-05 01:18:59 +01:00

test_inherited_field_receivers.py

fix(engine): resolve fields declared on a superclass for receivers in a subclass (#3151)

2026-08-29 16:14:47 +01:00

test_injection_sentinel_coverage.py

fix(llm): defang any <|token|> chat-template marker, not an enumerated few (#3183)

2026-08-30 15:11:24 +01:00

test_install_references.py

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test_install_roundtrip.py

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test_install_strings.py

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test_install_upgrade.py

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test_install_version_stamp.py

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test_install_version_warning.py

fix(install): actionable stale-skill warning; back up a diverged SKILL.md (#3144)

2026-08-30 15:11:40 +01:00

test_install.py

Use the replace fallback for skill install writes

2026-09-12 17:36:09 +01:00

test_issue_3405_python_resolution.py

Fix Python nested function resolution

2026-09-09 17:20:54 +01:00

test_issue_3472_source_file_collision.py

Fix same-file source path collision during merge

2026-09-10 22:44:39 +01:00

test_java_enum_members.py

fix(java): attach enum body members to the enum, not the file

2026-09-20 13:59:25 +01:00

test_java_member_calls.py

fix(engine): resolve fields declared on a superclass for receivers in a subclass (#3151)

2026-08-29 16:14:47 +01:00

test_java_type_resolution.py

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test_js_callback_calls.py

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test_js_destructured_export.py

Add a regression test for unexported require destructures

2026-09-14 18:49:19 +01:00

test_js_dynamic_import_affected.py

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test_js_dynamic_imports.py

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test_js_exported_fn_call_resolution.py

fix(js): resolve calls inside exported functions, incl. aliased imports (#3346)

2026-09-12 21:31:34 +01:00

test_js_exported_scalar_bindings.py

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test_js_import_resolution.py

fix(imports): pick workspace exports by importer platform, runtime before types

2026-09-12 21:31:35 +01:00

test_js_module_level_anonymous_calls.py

Add regression tests for module level anonymous calls

2026-09-13 17:47:55 +01:00

test_js_this_member_expressions.py

fix(js): keep this.X = function members in every enclosing-function form (#3408)

2026-09-09 11:30:28 +01:00

test_jsconfig_baseurl.py

fix(extract): invalidate tsconfig alias/baseUrl caches per run (#2917)

2026-08-21 16:49:55 +01:00

test_kotlin_grammar.py

test(kotlin): cover companion members + incremental persistence (#1698 follow-up)

2026-09-17 11:09:52 +01:00

test_kotlin_object_literal.py

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test_label_retry.py

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test_labeling.py

test(labeling): keep the no-backend test hermetic against the claude-cli fallback

2026-09-10 22:45:31 +01:00

test_language_resolvers.py

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test_languages.py

fix(verilog): link a module instantiation to the local definition, not a phantom

2026-09-20 13:59:25 +01:00

test_llm_backends.py

fix: label via an installed claude CLI, and stop pinning a path that expires

2026-09-10 22:44:40 +01:00

test_llm_parser_reasoning.py

fix(llm): gate the reasoning-JSON winner on sanitized content, not raw value (#2882)

2026-08-20 15:44:56 +01:00

test_llm_parser.py

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test_long_path_hashing.py

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test_loose_sibling_import_resolution.py

Fix loose sibling module import resolution

2026-09-09 17:20:56 +01:00

test_lua_import.py

test: cover bare require() imports edges for Lua (#3320)

2026-09-13 17:47:57 +01:00

test_manifest_ingest.py

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test_manifest_tomli_required.py

fix(manifest): require tomli on Py3.10 and fail loud when missing

2026-09-05 01:19:09 +01:00

test_markdown_code_spans.py

fix(watch): keep code-span mention edges through a rebuild over an existing graph

2026-09-16 14:50:54 +01:00

test_mcp_ingest.py

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test_merge_chunks_validation.py

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test_merge_graphs_cli.py

test(merge): pin same-order community-offset byte-reproducibility (#3014)

2026-08-25 18:09:58 +01:00

test_minhash.py

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test_multigraph_compat.py

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test_multigraph_diagnostics.py

fix(diagnostics): separate external reference edges

2026-09-17 11:01:37 +01:00

test_multilang.py

fix(rust): extract module-level static and const declarations

2026-09-10 22:44:38 +01:00

test_no_dedup_flag.py

test(extract): assert --no-dedup graph invariant, not just kwarg propagation (#2881)

2026-08-20 16:13:45 +01:00

test_node_id_canonical.py

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test_non_regular_files.py

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test_non_string_node_ids.py

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test_objc_category_interfaces.py

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test_objc_field_table_remap.py

fix(objc): remap the field->type table keys with the ids they hold (#3150)

2026-08-29 16:14:29 +01:00

test_objc_member_calls.py

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test_objc_property_ivar_receivers.py

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test_obsidian_dangling_member.py

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test_obsidian_filename_cap.py

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test_obsidian_unicode_tags.py

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test_obsidian_vault_migration.py

fix(export): adopt a pre-manifest vault's own notes instead of orphaning them (#2863)

2026-08-21 19:22:21 +01:00

test_ocaml.py

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test_office_incremental.py

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test_office_limits.py

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test_ollama_retry_cap.py

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test_ollama.py

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test_openai_custom_endpoint.py

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test_out_dir_evidence.py

fix(detect): probe every out subdirectory under an entry budget, not the first 20

2026-09-09 17:20:57 +01:00

test_oversized_document_slicing.py

fix(llm): bisect PDF slices on extracted text; reconcile splittable-PDF tests (#2906)

2026-08-21 16:57:29 +01:00

test_owned_type_sources.py

fix(resolution): require owned sources for type-use edges

2026-09-05 21:13:54 +01:00

test_package_json_subpath_imports.py

fix(js): resolve Node subpath imports via package.json imports

2026-09-07 19:02:18 +01:00

test_partial_cache.py

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test_partial_extraction_warning.py

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test_pascal_call_scoping.py

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test_pascal_resolution.py

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test_pascal.py

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test_path_cli.py

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test_paths.py

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test_pdf_slicing.py

fix(llm): bisect PDF slices on extracted text; reconcile splittable-PDF tests (#2906)

2026-08-21 16:57:29 +01:00

test_pdf_token_estimate.py

fix(llm): estimate PDF tokens from the extracted text, not the container (#2903)

2026-08-21 16:50:44 +01:00

test_pg_introspect.py

fix(postgres): carry tree-sitter-sql in the postgres extra and surface grammar errors

2026-08-25 15:44:52 +01:00

test_phantom_cross_package_call.py

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test_phantom_external_import.py

Add an end to end regression test for the reporter's exact repro

2026-09-17 11:01:38 +01:00

test_php_object_creation.py

test(php): escape namespace backslashes in object-creation fixtures (#3115)

2026-08-29 16:15:58 +01:00

test_php_type_resolution.py

Prefer the alias for a PHP use import edge's target

2026-09-09 17:20:56 +01:00

test_pipeline.py

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test_provider_registry.py

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test_prs.py

fix(mcp): prevent PR subprocess stdin hangs

2026-09-05 21:55:35 +01:00

test_prune_sweeps_orphans.py

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test_python_decorators.py

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test_python_import_resolution.py

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test_python_parse_memoization.py

perf(resolution): parse each Python file once across both resolution passes

2026-09-11 22:46:27 +01:00

test_python_underscore_resolution.py

Fix Python leading-underscore method/function id collision

2026-09-05 21:55:32 +01:00

test_query_cli.py

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test_query_induced_edges.py

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test_query_mcp_direction.py

fix(serve): traverse the MCP query_graph undirected so a seed with no outgoing edges reaches its callers

2026-09-07 18:42:56 +01:00

test_query_names_its_graph.py

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test_querylog.py

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test_r_extractor.py

feat: add R language extractor

2026-09-21 19:10:13 +01:00

test_rationale.py

Fix module docstring extraction when a leading comment precedes it

2026-09-05 21:13:53 +01:00

test_read_hook.py

Add regression tests for the guard hook timeouts

2026-09-13 17:47:54 +01:00

test_reflect.py

…

test_relation_collapse_precedence.py

fix(build): preserve higher confidence on same-relation edge collision (#3703)

2026-09-21 18:04:04 +01:00

test_replace_or_append_section.py

…

test_report_gap_thresholds.py

Update thin community tests for the corrected count

2026-09-14 18:49:20 +01:00

test_report.py

Surface unclassified files in GRAPH_REPORT.md

2026-09-12 17:36:10 +01:00

test_resolve_memoization.py

perf(resolution): memoize Path.resolve() across the symbol-resolution passes

2026-09-11 22:46:36 +01:00

test_ruby_resolution.py

fix: resolve inherited Ruby member calls

2026-09-16 14:43:05 +01:00

test_rust_self_member_calls.py

fix: resolve generic Rust self calls

2026-09-18 15:16:09 +01:00

test_scala_self_type.py

…

test_scip_ingest.py

…

test_search_hook.py

Add regression tests for the guard hook timeouts

2026-09-13 17:47:54 +01:00

test_security.py

…

test_semantic_cache_basename_recovery.py

Add regression test for dangling edge pruning consistency

2026-09-14 18:52:06 +01:00

test_semantic_cache_out_root.py

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test_semantic_cleanup.py

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test_semantic_fragment_sanitize.py

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test_semantic_id_remap_root.py

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test_semantic_similarity.py

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test_serve_http.py

Route get_node through the same resolver as get_neighbors

2026-08-29 18:38:05 +01:00

test_serve.py

fix: address Python 3.14 review findings

2026-09-12 21:35:25 +01:00

test_settings_merge.py

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test_skill_version_warning.py

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test_skillgen.py

chore(lock): sync uv.lock for the #3490 dependency-floor bumps; fix stale skillgen windows test

2026-09-12 21:49:56 +01:00

test_source_key_memoization.py

perf(resolution): memoize source-key resolution in the id-disambiguation pass

2026-09-11 22:46:36 +01:00

test_sourceless_call_targets.py

fix(extract): skip calls to sourceless stubs

2026-09-13 17:47:54 +01:00

test_src_layout_import_resolution.py

…

test_stale_prune.py

…

test_stat_index_husk.py

fix(cache): the atexit stat-index flush must not resurrect a deleted corpus (#2974)

2026-08-28 01:18:04 +01:00

test_stat_index_portability.py

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test_swift_builtin_noise.py

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test_swift_computed_properties.py

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test_swift_cross_file_calls.py

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test_swift_import_resolution.py

…

test_swift_protocol_requirements.py

fix(swift): extract method requirements declared in a protocol body

2026-09-20 13:59:25 +01:00

test_symbol_resolution.py

…

test_terraform_modules.py

feat(terraform): resolve local module sources and directory topology

2026-09-15 18:01:35 +01:00

test_terraform.py

fix(terraform): redact secret-named attribute values before they hit the graph (#3644 follow-up)

2026-09-18 15:21:04 +01:00

test_trailing_newline_not_a_syntax_error.py

Add tests for newline char at EOF fix

2026-09-12 17:39:27 +01:00

test_transcribe.py

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test_tree_html.py

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test_ts_decorators.py

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test_ts_generators.py

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test_ts_import_require.py

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test_ts_import_type_arguments.py

test(ts): de-flake the normalizer scaling test that reddened v8 CI

2026-09-20 18:53:35 +01:00

test_ts_inheritance.py

fix(extract): emit inherits edge for JavaScript class extends (#1790)

2026-08-30 15:48:40 +01:00

test_ts_namespace.py

…

test_ts_new_expression_calls.py

fix(ts): resolve new_expression constructor calls (#3116)

2026-08-27 20:57:16 +01:00

test_ts_parse_warning.py

…

test_ts_receiver_member_calls.py

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test_type_only_import_cycles.py

fix(ts): type-only imports no longer manufacture Import Cycles (#3123)

2026-08-29 16:16:09 +01:00

test_typescript_enum_members.py

feat(typescript): emit a node per enum member (#3064)

2026-08-25 15:45:33 +01:00

test_typescript_module_extensions.py

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test_uninstall_scope.py

…

test_unmapped_at_alias_resolution.py

fix: resolve unmapped @/ imports in JS projects

2026-09-06 16:17:38 +01:00

test_unverified_semantic_shrink.py

fix: protect against unverified semantic node loss (#3203)

2026-08-30 15:12:10 +01:00

test_validate.py

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test_vbnet_extractor.py

feat: add VB.NET language extractor

2026-09-21 19:06:50 +01:00

test_vue_extraction.py

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test_walk_python_tree_iterative.py

perf(resolution): walk the Python tree iteratively, not via recursive yield-from

2026-09-11 22:46:26 +01:00

test_watch_manifest_location.py

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test_watch.py

test(watch): drop two broken #3695 symlink tests that never trigger fail-closed (#3697 follow-up)

2026-09-20 15:07:29 +01:00

test_wheel_packaging.py

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test_wiki_link_filename_parity.py

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test_wiki_truncation_indicator.py

fix(wiki): say when a god-node relation group was truncated (#3127)

2026-08-30 15:11:23 +01:00

test_wiki.py

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test_word_count_cache.py

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test_zero_node_no_cache.py

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