java-codebase-rag 0.6.1__py3-none-any.whl → 0.6.2__py3-none-any.whl

java_codebase_rag/cli.py

@@ -6,6 +6,7 @@ from __future__ import annotations
 import argparse
 import asyncio
 import json
+import os
 import pprint
 import shutil
 import sys
@@ -930,5 +931,21 @@ def main(argv: list[str] | None = None) -> int:
         return 2
 
 
+def _console_script_main() -> None:
+    """Real CLI entry: terminate without interpreter finalization.
+
+    A pyarrow/lance worker thread (loaded via lancedb in lifecycle commands) can
+    outlive CPython finalization in a one-shot CLI subprocess and trip
+    ``PyGILState_Release`` (SIGABRT, exit -6). Flushing + ``os._exit`` skips that
+    racy teardown — the command has already done its work and emitted its result.
+    ``main()`` stays return-based so in-process test callers (``cli.main(...)``)
+    keep working.
+    """
+    rc = main()
+    sys.stdout.flush()
+    sys.stderr.flush()
+    os._exit(rc)
+
+
 if __name__ == "__main__":
-    raise SystemExit(main())
+    _console_script_main()

java_codebase_rag/config.py

@@ -52,14 +52,36 @@ _DEFAULT_EMBEDDING_MODEL = "sentence-transformers/all-MiniLM-L6-v2"
 _UNRESOLVED_VAR_RE = re.compile(r"\$(\w+|\{[^}]+\})")
 
 
-def maybe_expand_embedding_model_path(value: str) -> str:
-    """Expand ``~`` and ``$VAR`` when *value* is path-shaped.
+def maybe_expand_embedding_model_path(
+    value: str,
+    *,
+    config_dir: Path | None = None,
+    source_root: Path | None = None,
+    source: SettingSource | None = None,
+) -> str:
+    """Expand ``~`` / ``$VAR`` for path-shaped values and resolve relatives to absolute.
 
     Path-shape: starts with ``/``, ``./``, ``../``, ``~``, or contains ``$``.
     Plain ``org/name`` (hub id) does not match and is passed through unchanged.
 
-    Used for ``embedding.model`` after precedence resolution and for runtime
-    ``SBERT_MODEL`` reads (e.g. MCP) so the string matches ``ResolvedOperatorConfig``.
+    Relative resolution mirrors :func:`_resolve_index_dir_path` so a committed
+    config is portable regardless of process CWD:
+
+    * YAML values (``source == "yaml"``) resolve against ``config_dir`` (the
+      directory holding ``.java-codebase-rag.yml``).
+    * CLI / env values resolve against ``source_root``.
+
+    Only a result that still starts with ``./`` or ``../`` *after* ``~`` /
+    ``$VAR`` expansion is re-based — so hub ids (``org/name``), absolute paths,
+    ``~/``-expanded paths, and an env var that already yielded an absolute path
+    are all left untouched.
+
+    When no base is supplied (the runtime ``SBERT_MODEL`` read via
+    :func:`resolved_sbert_model_for_process_env`), relative resolution is
+    skipped: the value is returned ``expandvars`` / ``expanduser``-expanded but
+    not re-based, matching the prior best-effort behavior. The main resolution
+    path (:func:`resolve_operator_config`) supplies a base, so the absolute path
+    it stores is what downstream loaders receive.
     """
     needs_expand = value.startswith(("/", "./", "../", "~")) or "$" in value
     if not needs_expand:
@@ -70,9 +92,31 @@ def maybe_expand_embedding_model_path(value: str) -> str:
             f"java-codebase-rag: path-shaped model string contains unresolved variable: {expanded}",
             file=sys.stderr,
         )
+    if expanded.startswith(("./", "../")):
+        base = _embedding_model_base(
+            source=source, config_dir=config_dir, source_root=source_root
+        )
+        if base is not None:
+            return str((base / expanded).resolve())
     return expanded
 
 
+def _embedding_model_base(
+    *,
+    source: SettingSource | None,
+    config_dir: Path | None,
+    source_root: Path | None,
+) -> Path | None:
+    """Base directory for a relative ``embedding.model``.
+
+    Mirrors :func:`_resolve_index_dir_path`: YAML values anchor on the config
+    file's directory; CLI / env values anchor on the resolved ``source_root``.
+    """
+    if source == "yaml":
+        return config_dir
+    return source_root
+
+
 def resolved_sbert_model_for_process_env(import_time_default: str) -> str:
     """``SBERT_MODEL`` from the process environment, with the same expansion as YAML/CLI resolution.
 
@@ -387,7 +431,12 @@ def resolve_operator_config(
         yaml_path=("embedding", "model"),
         default=_DEFAULT_EMBEDDING_MODEL,
     )
-    model = maybe_expand_embedding_model_path(model)
+    model = maybe_expand_embedding_model_path(
+        model,
+        config_dir=config_dir,
+        source_root=root,
+        source=model_src,
+    )
     device, device_src = _pick_optional_device(
         cli_val=cli_embedding_device,
         env_key="SBERT_DEVICE",

java_codebase_rag/installer.py

@@ -759,6 +759,11 @@ def generate_yaml_config(
         else:
             config["embedding"].pop("model", None)
 
+    # Seed cross-service resolution safe-by-default: only evidence-backed cross-service
+    # edges survive (see _is_brownfield_sourced in build_ast_graph). setdefault preserves
+    # an explicit user choice (e.g. `auto`) on re-run update.
+    config.setdefault("cross_service_resolution", "brownfield_only")
+
     # Keys NOT written by installer (preserved if present):
     # - source_root (config.py resolves from walk-up discovery)
     # - index_dir (config.py defaults to <source_root>/.java-codebase-rag)
@@ -1250,9 +1255,14 @@ def run_update(
         print("Skipping index update.")
         return EXIT_PARTIAL if has_artifact_failures else EXIT_SUCCESS
 
-    # Resolve configuration
+    # Resolve configuration. Pass source_root=None so the YAML ``source_root``
+    # field is honored exactly like increment/init/reprocess — passing the
+    # discovered config dir here routes resolve_operator_config into the
+    # explicit-override branch that SKIPS the YAML field, which made `update`
+    # point cocoindex at the config dir (no Java) against the real index and
+    # mass-delete it. Discovery still runs against the CLI's cwd.
     try:
-        cfg = resolve_operator_config(source_root=project_root, cli_index_dir=None)
+        cfg = resolve_operator_config(source_root=None, cli_index_dir=None)
         index_dir = cfg.index_dir
     except Exception as e:
         print(f"\nWarning: Failed to resolve configuration: {e}")

{java_codebase_rag-0.6.1.dist-info → java_codebase_rag-0.6.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: java-codebase-rag
-Version: 0.6.1
+Version: 0.6.2
 Summary: MCP server for semantic + structural search over Java codebases
 Author: HumanBean17
 License-Expression: MIT

{java_codebase_rag-0.6.1.dist-info → java_codebase_rag-0.6.2.dist-info}/RECORD

@@ -7,7 +7,6 @@ index_common.py,sha256=HT6FKHFJ084eFvd3fR1j8z8gf4eWoPHVW8GXLpw464I,285
 java_index_flow_lancedb.py,sha256=MH9iTNF6HDHDTt5Jn7TOVE5hQ4WUPNt7PlQoh1tuh9o,13212
 java_index_v1_common.py,sha256=nF1KrSqboF_RRvWerG9knRRFmWwsrG_CvhgnsoZ8KqA,1154
 java_ontology.py,sha256=71bCLDNvMy0SpZPzSR5apJ0qJXNd6y5ggkLdBEw_PFo,16682
-kuzu_queries.py,sha256=9bQzrU311AOw_BcUp_KSGiZgPVSaLSU7y63XfcT_vqI,90137
 ladybug_queries.py,sha256=912j9VAYDjcU4ReVorWQ6R4DZl0tteKic-Pqu0jyBS0,90837
 mcp_hints.py,sha256=3swh05LSiWur3tm3-yssndBsLxIxFhy501kBtJI8jJ0,42509
 mcp_v2.py,sha256=o94GJI7j6dLJDIA3R_1ZiQhjzQfMAEW3etdeZYnHOUc,80637
@@ -17,20 +16,18 @@ search_lancedb.py,sha256=scG6HBUrsgIeSWFrGcLcGdhWv1qODOx4JOBMAlLDY_E,36793
 server.py,sha256=Js3XDpV7ThAtj352StH6QdhHutf1D5qUkbR-8k3jO8g,31303
 java_codebase_rag/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
 java_codebase_rag/_fdlimit.py,sha256=WroFdfSNbcriKok6q8znTf74dqlznxea_1Fd5bHl_3o,1930
-java_codebase_rag/cli.py,sha256=a5IFLWAsh77mfLv1Z9OdpvLaYvj4i0KR3_kLtL-ans8,34156
+java_codebase_rag/cli.py,sha256=HkzCP8-G3WlCzoXcVCI2K3forDOMpTmUSoxgx3jbKk4,34774
 java_codebase_rag/cli_format.py,sha256=arU7P9W6Fvm7X_wzR1wJ8EfyxK1rDP_ESEhdA0ub4Mo,2579
 java_codebase_rag/cli_progress.py,sha256=9jCqEagYOXs32SYVA31_sOCrONvYy7cl1CrdBD2Pg44,3168
-java_codebase_rag/config.py,sha256=Gn3LgxkTOtAvsL-3U2Xn7atOIhyOT2aGmY8SBBTLoQg,16975
-java_codebase_rag/installer.py,sha256=DlBuVVWbHXgcjaQkuXUeT9fNdmk7XZefVT3zzw47k18,45965
+java_codebase_rag/config.py,sha256=bfwYI4R8PU9YV_M4r8-03iaUZ_0TW-qN_NuhIsDXy2M,18769
+java_codebase_rag/installer.py,sha256=sE0l85K_o291PdpF1vpesefR9VgdvvVeARXrpTxa30A,46689
 java_codebase_rag/lance_optimize.py,sha256=MzACYlgwxmkJCK64qQLyIAdizSq5BARqaMYSZONlc1I,6069
 java_codebase_rag/pipeline.py,sha256=UcgluFAW9Ghnas8u40x45bVic0mQv6rjzcliDKsnYJI,11936
 java_codebase_rag/install_data/agents/explorer-rag-enhanced.md,sha256=APl9d-No12qZNZLjU7mwNRwxHIgnT3ZtQZiD4clWlyU,14413
 java_codebase_rag/install_data/skills/explore-codebase/SKILL.md,sha256=pIM-Xdwq_fXkhhBJCdb-fA2nes5c_mMPcdUXb7Adyxo,12040
-java_codebase_rag-0.6.1.dist-info/licenses/LICENSE,sha256=gxvtiHtuviR_q8ZAjWw-QTcF3DyPzg6ZY-lQrr8OPpw,1068
-user_rag/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
-user_rag/cli.py,sha256=TVcyfzwvmdYXJW6KrEYTKMHm7z2JSXMmz2uB-8kkjxY,5604
-java_codebase_rag-0.6.1.dist-info/METADATA,sha256=aPiLbGD8xE-P3B_RI9gx7VuqrTd-VUriZ--ZPYNK02I,16934
-java_codebase_rag-0.6.1.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
-java_codebase_rag-0.6.1.dist-info/entry_points.txt,sha256=mVVQJa0n73OWfhHXYCDoPRrWin_LJhH2Rn0CkJ2iax4,101
-java_codebase_rag-0.6.1.dist-info/top_level.txt,sha256=syQgi8XPBwY2ws_NZ1uRCxTf_s41NpshwEHNdcdnk3A,245
-java_codebase_rag-0.6.1.dist-info/RECORD,,
+java_codebase_rag-0.6.2.dist-info/licenses/LICENSE,sha256=gxvtiHtuviR_q8ZAjWw-QTcF3DyPzg6ZY-lQrr8OPpw,1068
+java_codebase_rag-0.6.2.dist-info/METADATA,sha256=X92kaZ5TbEacz0sznWtUtpYEJvBdWIXX0s8MlqOeRyg,16934
+java_codebase_rag-0.6.2.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
+java_codebase_rag-0.6.2.dist-info/entry_points.txt,sha256=wsPZwot0Ui4JI3TIgW8LcbN8bNtKFbwQAlHAAJXfYgQ,117
+java_codebase_rag-0.6.2.dist-info/top_level.txt,sha256=syQgi8XPBwY2ws_NZ1uRCxTf_s41NpshwEHNdcdnk3A,245
+java_codebase_rag-0.6.2.dist-info/RECORD,,

java_codebase_rag-0.6.2.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+java-codebase-rag = java_codebase_rag.cli:_console_script_main
+java-codebase-rag-mcp = server:main

java_codebase_rag-0.6.1.dist-info/entry_points.txt

@@ -1,3 +0,0 @@
-[console_scripts]
-java-codebase-rag = java_codebase_rag.cli:main
-java-codebase-rag-mcp = server:main