codenib.scip_interface

Language-specific SCIP indexing and decoding.

The public classes stay lazy so importing an LSP-shaped provider does not load the optional igraph runtime or every language backend.

Modules:

Name	Description
lsp_occurrence_index	Exact position index for LSP-shaped navigation over decoded SCIP data.
rust_analyzer	Helpers for invoking rust-analyzer consistently.
scip_decode_core	Thin Python wrapper around the codenib_core pybind11 extension.
scip_decode_csharp	SCIP decoder for C# projects indexed by scip-dotnet.
scip_decode_go	SCIP decoder for Go projects.
scip_decode_java	SCIP decoder for JVM projects indexed by scip-java.
scip_decode_php	SCIP decoder for PHP projects indexed by scip-php.
scip_decode_python	SCIP decoder for Python projects.
scip_decode_ruby	SCIP decoder for Ruby projects indexed by scip-ruby.
scip_decode_rust	SCIP decoder for Rust projects.
scip_decode_ts
scip_decode_utils	Shared normalization helpers for SCIP TextFormat decoders.
scip_indexer_base	Base class for SCIP indexers across different languages.
scip_indexer_csharp	SCIP indexer for C# projects using scip-dotnet.
scip_indexer_go	SCIP indexer for Go projects using scip-go.
scip_indexer_java	SCIP indexers for JVM projects using scip-java.
scip_indexer_php	SCIP-backed PHP graph routes using scip-php.
scip_indexer_python	SCIP indexer for Python projects using scip-python.
scip_indexer_ruby	SCIP-backed Ruby graph routes using scip-ruby.
scip_indexer_rust	SCIP indexer for Rust projects using rust-analyzer.
scip_indexer_ts	SCIP indexer for TypeScript and JavaScript projects using scip-typescript.
scip_pb2	Generated protocol buffer code.

Classes:

Name	Description
SCIPLocation	Repository-relative location returned by the occurrence index.
SCIPOccurrence	One SCIP symbol occurrence with an exact half-open source range.
SCIPOccurrenceIndex	Resolve exact source positions to SCIP definitions and references.
SCIPCSharpGraphDecoder	Decode scip-dotnet TextFormat output into CodeGraph.
SCIPJavaGraphDecoder	Decode scip-java TextFormat output into CodeGraph.
SCIPPHPGraphDecoder	Decode scip-php TextFormat output into CodeGraph.
SCIPPythonGraphDecoder	Decoder for Python SCIP indices.
SCIPRubyGraphDecoder	Decode scip-ruby TextFormat output into CodeGraph.
SCIPRustGraphDecoder	Decoder for Rust SCIP indices.
SCIPTypeScriptGraphDecoder
SCIPIndexerBase	Abstract base class for SCIP indexers.
SCIPCSharpIndexer	Run scip-dotnet for the active C# graph backend.
SCIPJavaIndexer	Run scip-java for Java and JVM candidate routes.
SCIPKotlinIndexer	Candidate scip-java indexer for Kotlin projects.
SCIPScalaIndexer	Candidate scip-java indexer for Scala projects.
PHPHybridIndexer	Active PHP graph route: SCIP for Composer projects, LSP fallback otherwise.
SCIPPHPIndexer	Pure scip-php route used by candidate gates and the active hybrid route.
SCIPPythonIndexer	SCIP indexer for Python projects.
RubyHybridIndexer	Active Ruby graph route: prepared scip-ruby bundles, LSP fallback otherwise.
SCIPRubyIndexer	Pure scip-ruby route used by candidate gates and active hybrid routing.
SCIPRustIndexer	SCIP indexer for Rust projects.
SCIPTypeScriptIndexer	SCIP indexer for TypeScript and JavaScript projects.

SCIPLocation dataclass

SCIPLocation(
    file_path: str,
    start_line: int,
    start_character: int,
    end_line: int,
    end_character: int,
)

Repository-relative location returned by the occurrence index.

SCIPOccurrence dataclass

SCIPOccurrence(
    file_path: str,
    start_line: int,
    start_character: int,
    end_line: int,
    end_character: int,
    symbol: str,
    symbol_roles: int = 0,
)

One SCIP symbol occurrence with an exact half-open source range.

SCIPOccurrenceIndex

SCIPOccurrenceIndex(
    occurrences: Iterable[SCIPOccurrence], *, position_encoding: str = "UTF8"
)

Resolve exact source positions to SCIP definitions and references.

Source code in codenib/scip_interface/lsp_occurrence_index.py

def __init__(
    self,
    occurrences: Iterable[SCIPOccurrence],
    *,
    position_encoding: str = "UTF8",
) -> None:
    self.position_encoding = str(position_encoding or "UTF8")
    self.occurrences = tuple(occurrences)
    by_file: dict[str, list[int]] = {}
    by_symbol: dict[tuple[str, str], list[int]] = {}
    for index, occurrence in enumerate(self.occurrences):
        by_file.setdefault(occurrence.file_path, []).append(index)
        key = self._symbol_key(occurrence.file_path, occurrence.symbol)
        by_symbol.setdefault(key, []).append(index)
    self._by_file = {
        file_path: tuple(
            sorted(
                indexes,
                key=lambda item: self.occurrences[item].span_key,
            )
        )
        for file_path, indexes in by_file.items()
    }
    self._by_symbol = {key: tuple(indexes) for key, indexes in by_symbol.items()}

SCIPCSharpGraphDecoder

SCIPCSharpGraphDecoder(index_file_path, project_root=None)

Bases: SCIPJavaGraphDecoder

Decode scip-dotnet TextFormat output into CodeGraph.

Source code in codenib/scip_interface/scip_decode_java.py

def __init__(self, index_file_path, project_root=None):
    self.index_file_path = index_file_path
    self.project_root = Path(project_root) if project_root else None
    self.code_graph = CodeGraph(project_root)
    self.indexed_directories: set[str] = set()
    self.symbols: dict[str, _SymbolInfo] = {}
    self.definition_lines: dict[str, list[_DefinitionInfo]] = {}
    self.logger = get_logger(__name__)
    register_scip_logger(__name__)

SCIPJavaGraphDecoder

SCIPJavaGraphDecoder(index_file_path, project_root=None)

Decode scip-java TextFormat output into CodeGraph.

Source code in codenib/scip_interface/scip_decode_java.py

def __init__(self, index_file_path, project_root=None):
    self.index_file_path = index_file_path
    self.project_root = Path(project_root) if project_root else None
    self.code_graph = CodeGraph(project_root)
    self.indexed_directories: set[str] = set()
    self.symbols: dict[str, _SymbolInfo] = {}
    self.definition_lines: dict[str, list[_DefinitionInfo]] = {}
    self.logger = get_logger(__name__)
    register_scip_logger(__name__)

SCIPPHPGraphDecoder

SCIPPHPGraphDecoder(index_file_path, project_root=None)

Bases: SCIPJavaGraphDecoder

Decode scip-php TextFormat output into CodeGraph.

Source code in codenib/scip_interface/scip_decode_java.py

def __init__(self, index_file_path, project_root=None):
    self.index_file_path = index_file_path
    self.project_root = Path(project_root) if project_root else None
    self.code_graph = CodeGraph(project_root)
    self.indexed_directories: set[str] = set()
    self.symbols: dict[str, _SymbolInfo] = {}
    self.definition_lines: dict[str, list[_DefinitionInfo]] = {}
    self.logger = get_logger(__name__)
    register_scip_logger(__name__)

SCIPPythonGraphDecoder

SCIPPythonGraphDecoder(index_file_path, project_root=None)

Decoder for Python SCIP indices.

Parses decoded SCIP index files and builds a CodeGraph representing: - Classes - Methods and fields within classes - Module-level functions - References between symbols

Parameters:

Name	Type	Description	Default
index_file_path		Path to the decoded SCIP index file	required
project_root		Root directory of the Python project	None

Methods:

Name	Description
decode	Decode the SCIP index and build the CodeGraph.
save_graph	Save the code graph to a file.

Source code in codenib/scip_interface/scip_decode_python.py

def __init__(self, index_file_path, project_root=None):
    """
    Initialize the Python SCIP decoder.

    Args:
        index_file_path: Path to the decoded SCIP index file
        project_root: Root directory of the Python project
    """
    self.index_file_path = index_file_path
    self.project_root = project_root
    self.code_graph = CodeGraph(project_root)
    self.indexed_directories = set()
    self.logger = get_logger(__name__)
    register_scip_logger(__name__)

decode

decode()

Decode the SCIP index and build the CodeGraph.

Returns:

Name	Type	Description
CodeGraph		The constructed code graph

Source code in codenib/scip_interface/scip_decode_python.py

def decode(self):
    """
    Decode the SCIP index and build the CodeGraph.

    Returns:
        CodeGraph: The constructed code graph
    """
    self.logger.info(f"Starting SCIP Python decode from {self.index_file_path}")
    try:
        with open(self.index_file_path, "r") as f:
            content = f.read()
    except Exception as e:
        self.logger.error(f"Error reading SCIP index file: {e}")
        raise

    # Parse documents
    document_blocks = re.findall(
        r"documents\s*{(.*?)(?=documents\s*{|$)", content, re.DOTALL
    )

    # Add the root node to the graph
    self.code_graph.add_root_node(ROOT_NODE)

    # Process all documents. Batch edge insertion: per-edge add_edges is
    # O(E^2) (igraph reindexes each call); buffering flushes once as O(E).
    with self.code_graph.batch_edges():
        for document in document_blocks:
            self._process_document(document)

    self._fix_unified_names()
    return self.code_graph

save_graph

save_graph(output_path)

Save the code graph to a file.

Parameters:

Name	Type	Description	Default
output_path		Path where the graph should be saved	required

Source code in codenib/scip_interface/scip_decode_python.py

def save_graph(self, output_path):
    """
    Save the code graph to a file.

    Args:
        output_path: Path where the graph should be saved
    """
    self.code_graph.save_graph(output_path)

SCIPRubyGraphDecoder

SCIPRubyGraphDecoder(index_file_path, project_root=None)

Bases: SCIPJavaGraphDecoder

Decode scip-ruby TextFormat output into CodeGraph.

Source code in codenib/scip_interface/scip_decode_ruby.py

def __init__(self, index_file_path, project_root=None):
    super().__init__(index_file_path, project_root=project_root)
    self._file_definition_keys: dict[tuple[str, str], str] = {}
    self._display_names_by_graph_key: dict[str, str] = {}
    self._source_lines_by_file: dict[str, tuple[str, ...] | None] = {}

SCIPRustGraphDecoder

SCIPRustGraphDecoder(index_file_path, project_root=None)

Decoder for Rust SCIP indices.

Parses decoded SCIP index files and builds a CodeGraph representing: - Structs as classes - Traits as classes - Impl blocks and their methods - Free functions - References between symbols

Parameters:

Name	Type	Description	Default
index_file_path		Path to the decoded SCIP index file	required
project_root		Root directory of the Rust project	None

Methods:

Name	Description
decode	Decode the SCIP index and build the CodeGraph.
save_graph	Save the code graph to a file.

Source code in codenib/scip_interface/scip_decode_rust.py

def __init__(self, index_file_path, project_root=None):
    """
    Initialize the Rust SCIP decoder.

    Args:
        index_file_path: Path to the decoded SCIP index file
        project_root: Root directory of the Rust project
    """
    self.index_file_path = index_file_path
    self.project_root = Path(project_root) if project_root else None
    self.code_graph = CodeGraph(project_root)
    self.indexed_directories = set()
    self.logger = get_logger(__name__)
    # Register this module for SCIP debug logging
    register_scip_logger(__name__)

    # Internal workspace crate names (loaded lazily on first document)
    self.internal_crates = None

decode

decode()

Decode the SCIP index and build the CodeGraph.

Returns:

Name	Type	Description
CodeGraph		The constructed code graph

Source code in codenib/scip_interface/scip_decode_rust.py

def decode(self):
    """
    Decode the SCIP index and build the CodeGraph.

    Returns:
        CodeGraph: The constructed code graph
    """
    self.logger.info(f"Starting SCIP Rust decode from {self.index_file_path}")
    try:
        with open(self.index_file_path, "r") as f:
            content = f.read()
    except Exception as e:
        self.logger.error(f"Error reading SCIP index file: {e}")
        raise

    # Parse documents
    document_blocks = re.findall(
        r"documents\s*{(.*?)(?=documents\s*{|$)", content, re.DOTALL
    )

    # Add the root node to the graph
    self.code_graph.add_root_node(ROOT_NODE)

    # Process all documents. Batch edge insertion: per-edge add_edges is
    # O(E^2) (igraph reindexes each call); buffering flushes once as O(E).
    with self.code_graph.batch_edges():
        for document in document_blocks:
            self._process_document(document)

    return self.code_graph

save_graph

save_graph(output_path)

Save the code graph to a file.

Parameters:

Name	Type	Description	Default
output_path		Path where the graph should be saved	required

Source code in codenib/scip_interface/scip_decode_rust.py

def save_graph(self, output_path):
    """
    Save the code graph to a file.

    Args:
        output_path: Path where the graph should be saved
    """
    self.code_graph.save_graph(output_path)

SCIPTypeScriptGraphDecoder

SCIPTypeScriptGraphDecoder(index_file_path, project_root=None)

Source code in codenib/scip_interface/scip_decode_ts.py

def __init__(self, index_file_path, project_root=None):
    self.index_file_path = index_file_path
    self.project_root = project_root
    self.code_graph = CodeGraph(project_root)
    self.indexed_directories = set()
    self.logger = get_logger(__name__)
    # Register this module for SCIP debug logging
    register_scip_logger(__name__)

    # Track actual file paths from documents to fix index file handling
    self.document_file_paths = set()

    # Track project's own SCIP package names to filter external refs
    self._project_packages = set()

SCIPIndexerBase

SCIPIndexerBase(
    project_root: str | Path,
    output_dir: str | Path | None = None,
    exclude_patterns: list | None = None,
    profiler: Profiler | None = None,
    language: str = "unknown",
    decoder_backend: str | None = None,
)

Bases: ABC

Abstract base class for SCIP indexers.

This class provides common functionality for all SCIP indexers, while allowing language-specific implementations to customize the indexing process.

Parameters:

Name	Type	Description	Default
project_root	str | Path	Root directory of the project to index	required
output_dir	str | Path | None	Directory to store output files	None
exclude_patterns	list | None	List of patterns to exclude from indexing	None
profiler	Profiler | None	Profiler instance for performance tracking	None
language	str	Language being indexed (for logging)	'unknown'
decoder_backend	str | None	Which decoder to use when process_index runs. "serial" (default) uses the pure-Python per-language decoder; "core" uses the C++ pybind decoder from core/.	None

Methods:

Name	Description
generate_index	Generate SCIP index for the project.
decode_index	Decode the SCIP index with the packaged protobuf descriptor.
process_index	Process the decoded SCIP index into a more usable format.
run_pipeline	Run the complete SCIP indexing pipeline: generate, decode, and process.
clear_cache	Clear cache files at different levels.

Source code in codenib/scip_interface/scip_indexer_base.py

def __init__(
    self,
    project_root: Union[str, Path],
    output_dir: Optional[Union[str, Path]] = None,
    exclude_patterns: Optional[List] = None,
    profiler: Optional[Profiler] = None,
    language: str = "unknown",
    decoder_backend: Optional[str] = None,
):
    """
    Initialize the SCIP indexer.

    Args:
        project_root: Root directory of the project to index
        output_dir: Directory to store output files
        exclude_patterns: List of patterns to exclude from indexing
        profiler: Profiler instance for performance tracking
        language: Language being indexed (for logging)
        decoder_backend: Which decoder to use when ``process_index`` runs.
            ``"serial"`` (default) uses the pure-Python per-language decoder;
            ``"core"`` uses the C++ pybind decoder from ``core/``.
    """
    self.project_root = Path(project_root).absolute()
    self.language = language
    self.decoder_backend = self._resolve_backend(decoder_backend)

    if output_dir:
        self.output_dir = Path(output_dir).absolute()
    else:
        self.output_dir = temp_state_dir() / self.project_root.name

    # Create output directory if it doesn't exist
    os.makedirs(self.output_dir, exist_ok=True)

    # Set paths for index files in the output directory
    self.index_file = self.output_dir / "index.scip"
    self.decoded_file = self.output_dir / "index.decoded"
    self.graph_file = self.output_dir / "graph.pkl"
    self.lsp_index_file = self.output_dir / "lsp_index.pkl"
    self.exclude_patterns = exclude_patterns if exclude_patterns else []
    self._target_dir: str | None = None
    self.profiler = profiler or Profiler(f"scip_{language}_indexer")

    # Path to the scip.proto file (shared across all indexers)
    self.module_dir = Path(__file__).parent
    self.proto_file = self.module_dir / "scip.proto"

generate_index

generate_index(**kwargs) -> bool

Generate SCIP index for the project.

Parameters:

Name	Type	Description	Default
**kwargs		Language-specific options	{}

Returns:

Name	Type	Description
bool	bool	True if index generation was successful, False otherwise

Source code in codenib/scip_interface/scip_indexer_base.py

def generate_index(self, **kwargs) -> bool:
    """
    Generate SCIP index for the project.

    Args:
        **kwargs: Language-specific options

    Returns:
        bool: True if index generation was successful, False otherwise
    """
    if not self._check_indexer_available():
        return False

    # Build the command
    cmd = self._build_index_command(**kwargs)

    logger.debug(f"Running command: {' '.join(cmd)}")

    # Run the command
    with self.profiler.section("generate_index") as section:
        try:
            # For Rust projects, override the repository toolchain so SCIP
            # generation uses CodeNib's selected rust-analyzer version.
            env = None
            if self.language == "rust":
                import os

                from .rust_analyzer import rust_toolchain

                env = os.environ.copy()
                env["RUSTUP_TOOLCHAIN"] = rust_toolchain()

            subprocess.run(
                cmd,
                check=True,
                cwd=self.project_root,
                capture_output=True,
                text=True,
                env=env,
            )
            success = True
        except subprocess.CalledProcessError as e:
            logger.error(f"Error generating SCIP index: {e}")
            if e.stdout:
                logger.error(f"stdout: {e.stdout}")
            if e.stderr:
                logger.error(f"stderr: {e.stderr}")
            success = False

    duration = section.duration

    if success:
        logger.info(f"Successfully generated SCIP index at {self.index_file}")
        logger.info(f"⏱️  Index generation took: {duration:.2f} seconds")
        return True
    else:
        logger.error(f"❌ Index generation failed after {duration:.2f} seconds")
        return False

decode_index

decode_index() -> bool

Decode the SCIP index with the packaged protobuf descriptor.

Returns:

Name	Type	Description
bool	bool	True if decoding was successful, False otherwise

Source code in codenib/scip_interface/scip_indexer_base.py

def decode_index(self) -> bool:
    """
    Decode the SCIP index with the packaged protobuf descriptor.

    Returns:
        bool: True if decoding was successful, False otherwise
    """
    if not self.index_file.exists():
        logger.error(f"Index file not found at {self.index_file}")
        return False

    try:
        from google.protobuf.message import DecodeError
        from google.protobuf.text_format import MessageToString

        from .scip_pb2 import Index
    except ImportError:
        logger.error("SCIP decoding requires protobuf. Install `codenib[graph]`.")
        return False

    try:
        with self.profiler.section("decode_index") as section:
            payload = self.index_file.read_bytes()
            if not payload:
                raise DecodeError("SCIP index is empty")
            index = Index()
            index.ParseFromString(payload)
            self.decoded_file.write_text(
                MessageToString(index, as_utf8=True),
                encoding="utf-8",
            )
        duration = section.duration

        logger.info(f"Successfully decoded SCIP index to {self.decoded_file}")
        logger.info(f"⏱️  Index decoding took: {duration:.2f} seconds")
        return True
    except (OSError, DecodeError) as e:
        logger.error(f"Error decoding SCIP index: {e}")
        return False

process_index

process_index(output_file: str | None = None) -> CodeGraph | None

Process the decoded SCIP index into a more usable format.

Parameters:

Name	Type	Description	Default
output_file	str | None	Path to write the processed data to	None

Returns:

Name	Type	Description
CodeGraph	CodeGraph | None	Processed graph object

Source code in codenib/scip_interface/scip_indexer_base.py

def process_index(
    self, output_file: Optional[str] = None
) -> Union[CodeGraph, None]:
    """
    Process the decoded SCIP index into a more usable format.

    Args:
        output_file: Path to write the processed data to

    Returns:
        CodeGraph: Processed graph object
    """
    if not self.decoded_file.exists():
        logger.error(f"Decoded index file not found at {self.decoded_file}")
        return None

    try:
        logger.info(
            f"Starting SCIP index processing (backend={self.decoder_backend})..."
        )
        with self.profiler.section("process_index.decode") as section:
            decoder = self._make_decoder(
                str(self.decoded_file), project_root=self.project_root
            )
            graph: CodeGraph = decoder.decode()
        duration = section.duration
        graph = self._filter_project_graph(graph)

        from .lsp_occurrence_index import SCIPOccurrenceIndex

        with self.profiler.section("process_index.build_lsp_occurrence_index"):
            occurrence_index = SCIPOccurrenceIndex.from_decoded_file(
                self.decoded_file,
                path_filter=(
                    self._path_allowed
                    if self._target_dir or self.exclude_patterns
                    else None
                ),
            )
        graph.lsp_occurrence_index = occurrence_index

        # Build line-range indexes once the graph is fully assembled.
        # Must happen before save_graph so the indexes are persisted.
        with self.profiler.section("process_index.build_range_indexes"):
            graph.build_range_indexes()

        if output_file:
            with self.profiler.section("process_index.save_graph") as save_section:
                output_path = Path(output_file)
                graph.save_graph(str(output_path))
                occurrence_index.save(output_path.with_name("lsp_index.pkl"))
            save_duration = save_section.duration
            logger.info(f"Saved processed SCIP index to {output_path}")
            logger.info(f"⏱️  Graph saving took: {save_duration:.2f} seconds")

        n_nodes = graph.graph.vcount()
        n_edges = graph.graph.ecount()
        logger.info(
            f"✅ Graph created successfully ({n_nodes} nodes, {n_edges} edges)"
        )
        if n_nodes <= 1:
            logger.warning(
                "⚠️  Graph has no symbol nodes — the SCIP index may be empty. "
                "Check that the indexer produced valid output."
            )
        logger.info(f"⏱️  Index processing took: {duration:.2f} seconds")
        return graph

    except Exception as e:
        logger.error(f"Error processing SCIP index: {e}")
        return None

run_pipeline

run_pipeline(
    output_file: str | None = None,
    skip_level: str | None = None,
    *,
    reset_profiler: bool = True,
    report_profile: bool = True,
    **kwargs
) -> CodeGraph | None

Run the complete SCIP indexing pipeline: generate, decode, and process.

Parameters:

Name	Type	Description	Default
output_file	str | None	Path to write the processed data to (if None, uses self.graph_file)	None
skip_level	str | None	Cache/skip level - 'graph', 'decode', 'raw', or None - 'graph': Check if graph.pkl exists, load and return it if found - 'decode': Check if index.decoded exists, skip to processing if found - 'raw': Check if index.scip exists, skip to decoding if found - None: Run full pipeline from scratch (default)	None
reset_profiler	bool	Clear profiler stats before running the pipeline	True
report_profile	bool	Emit profiler summary automatically after the run	True
**kwargs		Language-specific options passed to generate_index	{}

Returns:

Name	Type	Description
CodeGraph	CodeGraph | None	Processed graph object

Source code in codenib/scip_interface/scip_indexer_base.py

def run_pipeline(
    self,
    output_file: Optional[str] = None,
    skip_level: Optional[str] = None,
    *,
    reset_profiler: bool = True,
    report_profile: bool = True,
    **kwargs,
) -> Union[CodeGraph, None]:
    """
    Run the complete SCIP indexing pipeline: generate, decode, and process.

    Args:
        output_file: Path to write the processed data to (if None, uses self.graph_file)
        skip_level: Cache/skip level - 'graph', 'decode', 'raw', or None
            - 'graph': Check if graph.pkl exists, load and return it if found
            - 'decode': Check if index.decoded exists, skip to processing if found
            - 'raw': Check if index.scip exists, skip to decoding if found
            - None: Run full pipeline from scratch (default)
        reset_profiler: Clear profiler stats before running the pipeline
        report_profile: Emit profiler summary automatically after the run
        **kwargs: Language-specific options passed to generate_index

    Returns:
        CodeGraph: Processed graph object
    """
    # Use default graph file if output_file not specified
    if output_file is None:
        output_file = str(self.graph_file)
    self._target_dir = _normalize_rel_path(kwargs.pop("target_dir", None))

    # Check graph cache if skip_level is 'graph'
    if skip_level == "graph" and self.graph_file.exists():
        logger.info(f"Loading cached graph from {self.graph_file}")
        try:
            from ..graph.code_graph import CodeGraph

            graph = CodeGraph.load_graph(str(self.graph_file))
            if self.lsp_index_file.is_file():
                from .lsp_occurrence_index import SCIPOccurrenceIndex

                graph.lsp_occurrence_index = SCIPOccurrenceIndex.load(
                    self.lsp_index_file
                )
            elif self.decoded_file.is_file():
                from .lsp_occurrence_index import SCIPOccurrenceIndex

                graph.lsp_occurrence_index = SCIPOccurrenceIndex.from_decoded_file(
                    self.decoded_file,
                    path_filter=(
                        self._path_allowed
                        if self._target_dir or self.exclude_patterns
                        else None
                    ),
                )
                graph.lsp_occurrence_index.save(self.lsp_index_file)
            if self._target_dir or self.exclude_patterns:
                graph = self._filter_project_graph(graph)
                graph.build_range_indexes()
                if output_file:
                    graph.save_graph(output_file)
                    if hasattr(graph, "lsp_occurrence_index"):
                        graph.lsp_occurrence_index.save(
                            Path(output_file).with_name("lsp_index.pkl")
                        )
            logger.info(
                "✅ Successfully loaded cached graph "
                f"({len(graph.graph.vs)} nodes, "
                f"{len(graph.graph.es)} edges)"
            )
            return graph
        except Exception as e:
            logger.warning(
                f"Failed to load cached graph: {e}. Proceeding with pipeline..."
            )

    # Determine what needs to be generated based on what exists
    if skip_level in ("graph", "decode") and self.decoded_file.exists():
        logger.info(
            f"Found existing decoded file at "
            f"{self.decoded_file}, skipping generation and decode"
        )
        should_generate_index = False
        should_decode_index = False
    elif skip_level in ("graph", "decode", "raw") and self.index_file.exists():
        logger.info(
            f"Found existing raw index at {self.index_file}, skipping generation"
        )
        should_generate_index = False
        should_decode_index = True
    else:
        should_generate_index = True
        should_decode_index = True

    if reset_profiler:
        self.profiler.reset()

    try:
        # Generate the index if needed
        if should_generate_index:
            logger.info("Generating SCIP index")
            if not self.generate_index(**kwargs):
                # The indexer reported failure but the index
                # file may still have been written
                # (e.g. scip-typescript crashes during cleanup after emitting index.scip).
                # Continue if the file exists.
                if not self.index_file.exists():
                    return None
                logger.warning(
                    "Index generation returned failure but %s exists; continuing.",
                    self.index_file,
                )

        # Decode the index if needed
        if should_decode_index:
            if not self.index_file.exists():
                logger.error(
                    f"Index file not found at {self.index_file}, cannot decode"
                )
                return None
            logger.info("Decoding SCIP index")
            if not self.decode_index():
                return None

        # Process the index and save graph
        graph = self.process_index(output_file)

        if graph:
            logger.info(
                "✅ Graph created successfully "
                f"({len(graph.graph.vs)} nodes, "
                f"{len(graph.graph.es)} edges)"
            )

        return graph
    finally:
        if report_profile:
            self.profiler.report(reset=reset_profiler)

clear_cache

clear_cache(level: str = 'all') -> bool

Clear cache files at different levels.

Parameters:

Name	Type	Description	Default
level	str	Preserve cache up to this pipeline stage, remove above. Pipeline: raw (index.scip) → decode (index.decoded) → graph (graph.pkl) - 'graph': keep everything (raw + decoded + graph) - 'decode': keep raw + decoded, remove graph - 'raw': keep raw, remove decoded + graph - 'all': remove all cache files (default)	'all'

Returns:

Name	Type	Description
bool	bool	True if cache clearing was successful, False otherwise

Source code in codenib/scip_interface/scip_indexer_base.py

def clear_cache(self, level: str = "all") -> bool:
    """
    Clear cache files at different levels.

    Args:
        level: Preserve cache up to this pipeline stage, remove above.
            Pipeline: raw (index.scip) → decode (index.decoded) → graph (graph.pkl)
            - 'graph': keep everything (raw + decoded + graph)
            - 'decode': keep raw + decoded, remove graph
            - 'raw': keep raw, remove decoded + graph
            - 'all': remove all cache files (default)

    Returns:
        bool: True if cache clearing was successful, False otherwise
    """
    try:
        files_to_remove = []

        if level == "graph":
            files_to_remove = []
            logger.info("Clearing cache: keeping up to graph (nothing to remove)")
        elif level == "decode":
            files_to_remove = [self.graph_file, self.lsp_index_file]
            logger.info("Clearing cache: keeping up to decode, removing graph")
        elif level == "raw":
            files_to_remove = [
                self.decoded_file,
                self.graph_file,
                self.lsp_index_file,
            ]
            logger.info("Clearing cache: keeping raw, removing decoded + graph")
        elif level == "all":
            files_to_remove = [
                self.index_file,
                self.decoded_file,
                self.graph_file,
                self.lsp_index_file,
            ]
            logger.info("Clearing all cache files")
        else:
            logger.error(
                f"Invalid cache level: {level}. Must be 'graph', 'decode', 'raw', or 'all'"
            )
            return False

        # Remove the specified files
        for file_path in files_to_remove:
            if file_path.exists():
                file_path.unlink()
                logger.info(f"Removed {file_path}")
            else:
                logger.debug(f"File does not exist, skipping: {file_path}")

        logger.info("✅ Cache cleared successfully")
        return True

    except Exception as e:
        logger.error(f"Error clearing cache: {e}")
        return False

SCIPCSharpIndexer

SCIPCSharpIndexer(
    project_root: str | Path,
    output_dir: str | Path | None = None,
    exclude_patterns: list | None = None,
    profiler: Profiler | None = None,
    decoder_backend: str | None = None,
)

Bases: SCIPIndexerBase

Run scip-dotnet for the active C# graph backend.

Source code in codenib/scip_interface/scip_indexer_csharp.py

def __init__(
    self,
    project_root: Union[str, Path],
    output_dir: Optional[Union[str, Path]] = None,
    exclude_patterns: Optional[List] = None,
    profiler: Optional[Profiler] = None,
    decoder_backend: Optional[str] = None,
):
    super().__init__(
        project_root=project_root,
        output_dir=output_dir,
        exclude_patterns=exclude_patterns,
        profiler=profiler,
        language="csharp",
        decoder_backend=decoder_backend,
    )

SCIPJavaIndexer

SCIPJavaIndexer(
    project_root: str | Path,
    output_dir: str | Path | None = None,
    exclude_patterns: list | None = None,
    profiler: Profiler | None = None,
    decoder_backend: str | None = None,
    scip_language: str = "java",
)

Bases: SCIPIndexerBase

Run scip-java for Java and JVM candidate routes.

Source code in codenib/scip_interface/scip_indexer_java.py

def __init__(
    self,
    project_root: Union[str, Path],
    output_dir: Optional[Union[str, Path]] = None,
    exclude_patterns: Optional[List] = None,
    profiler: Optional[Profiler] = None,
    decoder_backend: Optional[str] = None,
    scip_language: str = "java",
):
    self.scip_language = scip_language
    super().__init__(
        project_root=project_root,
        output_dir=output_dir,
        exclude_patterns=exclude_patterns,
        profiler=profiler,
        language=scip_language,
        decoder_backend=decoder_backend,
    )

SCIPKotlinIndexer

SCIPKotlinIndexer(
    project_root: str | Path,
    output_dir: str | Path | None = None,
    exclude_patterns: list | None = None,
    profiler: Profiler | None = None,
    decoder_backend: str | None = None,
)

Bases: SCIPJavaIndexer

Candidate scip-java indexer for Kotlin projects.

Source code in codenib/scip_interface/scip_indexer_java.py

def __init__(
    self,
    project_root: Union[str, Path],
    output_dir: Optional[Union[str, Path]] = None,
    exclude_patterns: Optional[List] = None,
    profiler: Optional[Profiler] = None,
    decoder_backend: Optional[str] = None,
):
    super().__init__(
        project_root=project_root,
        output_dir=output_dir,
        exclude_patterns=exclude_patterns,
        profiler=profiler,
        decoder_backend=decoder_backend,
        scip_language="kotlin",
    )

SCIPScalaIndexer

SCIPScalaIndexer(
    project_root: str | Path,
    output_dir: str | Path | None = None,
    exclude_patterns: list | None = None,
    profiler: Profiler | None = None,
    decoder_backend: str | None = None,
)

Bases: SCIPJavaIndexer

Candidate scip-java indexer for Scala projects.

Source code in codenib/scip_interface/scip_indexer_java.py

def __init__(
    self,
    project_root: Union[str, Path],
    output_dir: Optional[Union[str, Path]] = None,
    exclude_patterns: Optional[List] = None,
    profiler: Optional[Profiler] = None,
    decoder_backend: Optional[str] = None,
):
    super().__init__(
        project_root=project_root,
        output_dir=output_dir,
        exclude_patterns=exclude_patterns,
        profiler=profiler,
        decoder_backend=decoder_backend,
        scip_language="scala",
    )

PHPHybridIndexer

PHPHybridIndexer(
    project_root: str | Path,
    output_dir: str | Path | None = None,
    exclude_patterns: list | None = None,
    profiler: Profiler | None = None,
    decoder_backend: str | None = None,
)

Active PHP graph route: SCIP for Composer projects, LSP fallback otherwise.

Source code in codenib/scip_interface/scip_indexer_php.py

def __init__(
    self,
    project_root: Union[str, Path],
    output_dir: Optional[Union[str, Path]] = None,
    exclude_patterns: Optional[List] = None,
    profiler: Optional[Profiler] = None,
    decoder_backend: Optional[str] = None,
):
    self.project_root = Path(project_root).absolute()
    self.output_dir = (
        Path(output_dir).absolute()
        if output_dir
        else temp_state_dir() / self.project_root.name
    )
    self.exclude_patterns = exclude_patterns or []
    self.profiler = profiler
    self.decoder_backend = decoder_backend
    self._delegate = self._preferred_delegate()
    self._sync_delegate_attrs()

SCIPPHPIndexer

SCIPPHPIndexer(
    project_root: str | Path,
    output_dir: str | Path | None = None,
    exclude_patterns: list | None = None,
    profiler: Profiler | None = None,
    decoder_backend: str | None = None,
)

Bases: SCIPIndexerBase

Pure scip-php route used by candidate gates and the active hybrid route.

Source code in codenib/scip_interface/scip_indexer_php.py

def __init__(
    self,
    project_root: Union[str, Path],
    output_dir: Optional[Union[str, Path]] = None,
    exclude_patterns: Optional[List] = None,
    profiler: Optional[Profiler] = None,
    decoder_backend: Optional[str] = None,
):
    self._index_via_docker = False
    self._index_root: Path | None = None
    super().__init__(
        project_root=project_root,
        output_dir=output_dir,
        exclude_patterns=exclude_patterns,
        profiler=profiler,
        language="php",
        decoder_backend=decoder_backend,
    )

SCIPPythonIndexer

SCIPPythonIndexer(
    project_root: str | Path,
    output_dir: str | Path | None = None,
    exclude_patterns: list | None = None,
    profiler: Profiler | None = None,
    decoder_backend: str | None = None,
)

Bases: SCIPIndexerBase

SCIP indexer for Python projects.

Uses a scip-python executable already available on PATH when possible. The historical managed Conda environment remains a fallback for development and CI environments that do not expose the tool directly.

Parameters:

Name	Type	Description	Default
project_root	str | Path	Root directory of the Python project	required
output_dir	str | Path | None	Directory to store output files	None
exclude_patterns	list | None	List of patterns to exclude from indexing	None
profiler	Profiler | None	Profiler instance for performance tracking	None
decoder_backend	str | None	"serial" (default) or "core".	None

Methods:

Name	Description
generate_index	Generate SCIP index for the Python project.
run_pipeline	Run Python pipeline while ignoring non-Python kwargs.

Source code in codenib/scip_interface/scip_indexer_python.py

def __init__(
    self,
    project_root: Union[str, Path],
    output_dir: Optional[Union[str, Path]] = None,
    exclude_patterns: Optional[List] = None,
    profiler: Optional[Profiler] = None,
    decoder_backend: Optional[str] = None,
):
    """
    Initialize the Python SCIP indexer.

    Args:
        project_root: Root directory of the Python project
        output_dir: Directory to store output files
        exclude_patterns: List of patterns to exclude from indexing
        profiler: Profiler instance for performance tracking
        decoder_backend: ``"serial"`` (default) or ``"core"``.
    """
    super().__init__(
        project_root=project_root,
        output_dir=output_dir,
        exclude_patterns=exclude_patterns,
        profiler=profiler,
        language="python",
        decoder_backend=decoder_backend,
    )

    # Conda environment configuration
    self.conda_env_name = "scip-env"
    self.env_file = self.module_dir / "scip-environment.yml"
    self._direct_indexer_path: Optional[str] = None

generate_index

generate_index(
    cwd: str | None = None,
    project_name: str | None = None,
    target_dir: str | None = None,
    **kwargs
) -> bool

Generate SCIP index for the Python project.

Uses the resolved PATH executable, with Conda as a compatibility fallback.

Parameters:

Name	Type	Description	Default
cwd	str | None	Working directory (defaults to project_root)	None
project_name	str | None	Project name to use in the index	None
target_dir	str | None	Optional subdirectory to target for indexing	None
**kwargs		Additional arguments (ignored)	{}

Returns:

Name	Type	Description
bool	bool	True if index generation was successful, False otherwise

Source code in codenib/scip_interface/scip_indexer_python.py

def generate_index(
    self,
    cwd: Optional[str] = None,
    project_name: Optional[str] = None,
    target_dir: Optional[str] = None,
    **kwargs,
) -> bool:
    """
    Generate SCIP index for the Python project.

    Uses the resolved PATH executable, with Conda as a compatibility
    fallback.

    Args:
        cwd: Working directory (defaults to project_root)
        project_name: Project name to use in the index
        target_dir: Optional subdirectory to target for indexing
        **kwargs: Additional arguments (ignored)

    Returns:
        bool: True if index generation was successful, False otherwise
    """
    if not self._check_indexer_available():
        return False

    cmd = self._build_index_command(
        cwd=cwd or str(self.project_root),
        project_name=project_name,
        target_dir=target_dir,
    )

    logger.debug(f"Running command: {' '.join(cmd)}")

    with self.profiler.section("generate_index") as section:
        with self._temporary_exclude_config():
            if self._direct_indexer_path:
                success = self._run_direct(cmd, self.project_root)
            else:
                success = self._run_in_conda_env(cmd, self.project_root)
    duration = section.duration

    if success:
        logger.info(f"Successfully generated SCIP index at {self.index_file}")
        logger.info(f"Index generation took: {duration:.2f} seconds")
        return True
    else:
        logger.error(f"Index generation failed after {duration:.2f} seconds")
        # Remove partial index file so pipeline does not continue with broken data
        if self.index_file.exists():
            self.index_file.unlink()
            logger.info("Removed partial index file")
        return False

run_pipeline

run_pipeline(
    output_file: str | None = None,
    skip_level: str | None = None,
    *,
    reset_profiler: bool = True,
    report_profile: bool = True,
    **kwargs
)

Run Python pipeline while ignoring non-Python kwargs.

Source code in codenib/scip_interface/scip_indexer_python.py

def run_pipeline(
    self,
    output_file: Optional[str] = None,
    skip_level: Optional[str] = None,
    *,
    reset_profiler: bool = True,
    report_profile: bool = True,
    **kwargs,
):
    """
    Run Python pipeline while ignoring non-Python kwargs.
    """
    # Pop kwargs from other languages
    kwargs.pop("config_path", None)
    kwargs.pop("exclude_vendored_libraries", None)
    kwargs.pop("infer_tsconfig", None)
    kwargs.pop("yarn_workspaces", None)
    kwargs.pop("pnpm_workspaces", None)
    kwargs.pop("npm_workspaces", None)
    kwargs.pop("compdb_path", None)
    kwargs.pop("show_compiler_diagnostics", None)

    return super().run_pipeline(
        output_file=output_file,
        skip_level=skip_level,
        reset_profiler=reset_profiler,
        report_profile=report_profile,
        **kwargs,
    )

RubyHybridIndexer

RubyHybridIndexer(
    project_root: str | Path,
    output_dir: str | Path | None = None,
    exclude_patterns: list | None = None,
    profiler: Profiler | None = None,
    decoder_backend: str | None = None,
)

Active Ruby graph route: prepared scip-ruby bundles, LSP fallback otherwise.

Source code in codenib/scip_interface/scip_indexer_ruby.py

def __init__(
    self,
    project_root: Union[str, Path],
    output_dir: Optional[Union[str, Path]] = None,
    exclude_patterns: Optional[List] = None,
    profiler: Optional[Profiler] = None,
    decoder_backend: Optional[str] = None,
):
    self.project_root = Path(project_root).absolute()
    self.output_dir = (
        Path(output_dir).absolute()
        if output_dir
        else temp_state_dir() / self.project_root.name
    )
    self.exclude_patterns = exclude_patterns or []
    self.profiler = profiler
    self.decoder_backend = decoder_backend
    self._delegate = self._preferred_delegate()
    self._sync_delegate_attrs()

SCIPRubyIndexer

SCIPRubyIndexer(
    project_root: str | Path,
    output_dir: str | Path | None = None,
    exclude_patterns: list | None = None,
    profiler: Profiler | None = None,
    decoder_backend: str | None = None,
)

Bases: SCIPIndexerBase

Pure scip-ruby route used by candidate gates and active hybrid routing.

Source code in codenib/scip_interface/scip_indexer_ruby.py

def __init__(
    self,
    project_root: Union[str, Path],
    output_dir: Optional[Union[str, Path]] = None,
    exclude_patterns: Optional[List] = None,
    profiler: Optional[Profiler] = None,
    decoder_backend: Optional[str] = None,
):
    super().__init__(
        project_root=project_root,
        output_dir=output_dir,
        exclude_patterns=exclude_patterns,
        profiler=profiler,
        language="ruby",
        decoder_backend=decoder_backend,
    )

SCIPRustIndexer

SCIPRustIndexer(
    project_root: str | Path,
    output_dir: str | Path | None = None,
    exclude_patterns: list | None = None,
    profiler: Profiler | None = None,
    decoder_backend: str | None = None,
)

Bases: SCIPIndexerBase

SCIP indexer for Rust projects.

Uses the rust-analyzer tool to generate SCIP indices for Rust codebases. rust-analyzer scip generates a SCIP index from Rust source code.

Parameters:

Name	Type	Description	Default
project_root	str | Path	Root directory of the Rust project (must contain Cargo.toml)	required
output_dir	str | Path | None	Directory to store output files (defaults to /tmp/project_name)	None
exclude_patterns	list | None	List of patterns to exclude from indexing	None
profiler	Profiler | None	Profiler instance for performance tracking	None
decoder_backend	str | None	"serial" (default) or "core".	None

Methods:

Name	Description
generate_index	Generate SCIP index for the Rust project.
run_pipeline	Run Rust pipeline while ignoring Python-specific kwargs.

Source code in codenib/scip_interface/scip_indexer_rust.py

def __init__(
    self,
    project_root: Union[str, Path],
    output_dir: Optional[Union[str, Path]] = None,
    exclude_patterns: Optional[List] = None,
    profiler: Optional[Profiler] = None,
    decoder_backend: Optional[str] = None,
):
    """
    Initialize the Rust SCIP indexer.

    Args:
        project_root: Root directory of the Rust project (must contain Cargo.toml)
        output_dir: Directory to store output files (defaults to /tmp/project_name)
        exclude_patterns: List of patterns to exclude from indexing
        profiler: Profiler instance for performance tracking
        decoder_backend: ``"serial"`` (default) or ``"core"``.
    """
    super().__init__(
        project_root=project_root,
        output_dir=output_dir,
        exclude_patterns=exclude_patterns,
        profiler=profiler,
        language="rust",
        decoder_backend=decoder_backend,
    )

generate_index

generate_index(
    config_path: str | None = None, exclude_vendored_libraries: bool = False
) -> bool

Generate SCIP index for the Rust project.

Parameters:

Name	Type	Description	Default
config_path	str | None	Path to a JSON configuration file for customizing cargo behavior	None
exclude_vendored_libraries	bool	Exclude code from vendored libraries from the index	False

Returns:

Name	Type	Description
bool	bool	True if index generation was successful, False otherwise

Source code in codenib/scip_interface/scip_indexer_rust.py

def generate_index(
    self,
    config_path: Optional[str] = None,
    exclude_vendored_libraries: bool = False,
) -> bool:
    """
    Generate SCIP index for the Rust project.

    Args:
        config_path: Path to a JSON configuration file for customizing cargo behavior
        exclude_vendored_libraries: Exclude code from vendored libraries from the index

    Returns:
        bool: True if index generation was successful, False otherwise
    """
    # Check if Cargo.toml exists
    cargo_toml = self.project_root / "Cargo.toml"
    if not cargo_toml.exists():
        logger.error(
            f"Cargo.toml not found at {cargo_toml}. "
            "This doesn't appear to be a Rust project."
        )
        return False

    return super().generate_index(
        config_path=config_path,
        exclude_vendored_libraries=exclude_vendored_libraries,
    )

run_pipeline

run_pipeline(
    output_file: str | None = None,
    skip_level: str | None = None,
    *,
    reset_profiler: bool = True,
    report_profile: bool = True,
    **kwargs
)

Run Rust pipeline while ignoring Python-specific kwargs.

Source code in codenib/scip_interface/scip_indexer_rust.py

def run_pipeline(
    self,
    output_file: Optional[str] = None,
    skip_level: Optional[str] = None,
    *,
    reset_profiler: bool = True,
    report_profile: bool = True,
    **kwargs,
):
    """
    Run Rust pipeline while ignoring Python-specific kwargs.
    """
    kwargs.pop("project_name", None)
    kwargs.pop("target_dir", None)
    kwargs.pop("cwd", None)

    return super().run_pipeline(
        output_file=output_file,
        skip_level=skip_level,
        reset_profiler=reset_profiler,
        report_profile=report_profile,
        **kwargs,
    )

SCIPTypeScriptIndexer

SCIPTypeScriptIndexer(
    project_root: str | Path,
    output_dir: str | Path | None = None,
    exclude_patterns: list | None = None,
    profiler: Profiler | None = None,
    decoder_backend: str | None = None,
)

Bases: SCIPIndexerBase

SCIP indexer for TypeScript and JavaScript projects.

Uses the scip-typescript tool to generate SCIP indices for TypeScript/JavaScript codebases.

Parameters:

Name	Type	Description	Default
project_root	str | Path	Root directory of the TypeScript/JavaScript project	required
output_dir	str | Path | None	Directory to store output files (defaults to ~/.codenib/{project_name})	None
exclude_patterns	list | None	List of patterns to exclude from indexing	None
profiler	Profiler | None	Profiler instance for performance tracking	None
decoder_backend	str | None	"serial" (default) or "core".	None

Methods:

Name	Description
generate_index	Generate SCIP index for the TypeScript/JavaScript project.
run_pipeline	Run TypeScript pipeline with language-specific defaults.

Source code in codenib/scip_interface/scip_indexer_ts.py

def __init__(
    self,
    project_root: Union[str, Path],
    output_dir: Optional[Union[str, Path]] = None,
    exclude_patterns: Optional[List] = None,
    profiler: Optional[Profiler] = None,
    decoder_backend: Optional[str] = None,
):
    """
    Initialize the TypeScript SCIP indexer.

    Args:
        project_root: Root directory of the TypeScript/JavaScript project
        output_dir: Directory to store output files
            (defaults to ~/.codenib/{project_name})
        exclude_patterns: List of patterns to exclude from indexing
        profiler: Profiler instance for performance tracking
        decoder_backend: ``"serial"`` (default) or ``"core"``.
    """
    super().__init__(
        project_root=project_root,
        output_dir=output_dir,
        exclude_patterns=exclude_patterns,
        profiler=profiler,
        language="typescript",
        decoder_backend=decoder_backend,
    )

generate_index

generate_index(
    project_name: str | None = None,
    infer_tsconfig: bool = False,
    yarn_workspaces: bool = False,
    pnpm_workspaces: bool = False,
    npm_workspaces: bool = False,
    patched_tsconfig: str | None = None,
) -> bool

Generate SCIP index for the TypeScript/JavaScript project.

Parameters:

Name	Type	Description	Default
project_name	str | None	Project name (not used by scip-typescript)	None
infer_tsconfig	bool	Infer tsconfig for JavaScript projects without tsconfig.json	False
yarn_workspaces	bool	Enable Yarn workspaces support	False
pnpm_workspaces	bool	Enable pnpm workspaces support	False
npm_workspaces	bool	Enable npm workspaces support	False
patched_tsconfig	str | None	Path to a patched tsconfig file to use	None

Returns:

Name	Type	Description
bool	bool	True if index generation was successful, False otherwise

Source code in codenib/scip_interface/scip_indexer_ts.py

def generate_index(
    self,
    project_name: Optional[str] = None,
    infer_tsconfig: bool = False,
    yarn_workspaces: bool = False,
    pnpm_workspaces: bool = False,
    npm_workspaces: bool = False,
    patched_tsconfig: Optional[str] = None,
) -> bool:
    """
    Generate SCIP index for the TypeScript/JavaScript project.

    Args:
        project_name: Project name (not used by scip-typescript)
        infer_tsconfig: Infer tsconfig for JavaScript projects without tsconfig.json
        yarn_workspaces: Enable Yarn workspaces support
        pnpm_workspaces: Enable pnpm workspaces support
        npm_workspaces: Enable npm workspaces support
        patched_tsconfig: Path to a patched tsconfig file to use

    Returns:
        bool: True if index generation was successful, False otherwise
    """
    # Guardrail: if no explicit ts/js config exists, force infer mode.
    has_tsconfig = (self.project_root / "tsconfig.json").exists()
    has_jsconfig = (self.project_root / "jsconfig.json").exists()
    if not infer_tsconfig and not has_tsconfig and not has_jsconfig:
        infer_tsconfig = True
        logger.info(
            "No tsconfig.json/jsconfig.json in %s; forcing infer_tsconfig=True",
            self.project_root,
        )

    return super().generate_index(
        project_name=project_name,
        infer_tsconfig=infer_tsconfig,
        yarn_workspaces=yarn_workspaces,
        pnpm_workspaces=pnpm_workspaces,
        npm_workspaces=npm_workspaces,
        patched_tsconfig=patched_tsconfig,
    )

run_pipeline

run_pipeline(
    output_file: str | None = None,
    skip_level: str | None = None,
    *,
    reset_profiler: bool = True,
    report_profile: bool = True,
    **kwargs
)

Run TypeScript pipeline with language-specific defaults.

If neither tsconfig.json nor jsconfig.json exists, enable --infer-tsconfig automatically unless caller explicitly sets it.

Source code in codenib/scip_interface/scip_indexer_ts.py

def run_pipeline(
    self,
    output_file: Optional[str] = None,
    skip_level: Optional[str] = None,
    *,
    reset_profiler: bool = True,
    report_profile: bool = True,
    **kwargs,
):
    """
    Run TypeScript pipeline with language-specific defaults.

    If neither tsconfig.json nor jsconfig.json exists, enable
    --infer-tsconfig automatically unless caller explicitly sets it.
    """
    # Drop Python-specific kwargs that may be forwarded by callers.
    kwargs.pop("target_dir", None)
    kwargs.pop("cwd", None)

    # Auto-select workspace mode when not explicitly provided.
    workspace_flags = ("yarn_workspaces", "pnpm_workspaces", "npm_workspaces")
    has_workspace_mode = any(kwargs.get(flag) for flag in workspace_flags)
    if not has_workspace_mode:
        # pnpm defines workspaces in pnpm-workspace.yaml (not package.json),
        # so check for it independently.
        has_pnpm_workspace_yaml = (
            self.project_root / "pnpm-workspace.yaml"
        ).exists()

        has_pkg_workspaces = False
        package_json = self.project_root / "package.json"
        if package_json.exists():
            try:
                payload = json.loads(package_json.read_text(encoding="utf-8"))
                has_pkg_workspaces = bool(payload.get("workspaces"))
            except Exception:
                pass

        if has_pnpm_workspace_yaml and shutil.which("pnpm"):
            kwargs["pnpm_workspaces"] = True
            logger.info("Detected pnpm workspace in %s", self.project_root)
        elif has_pkg_workspaces:
            if (self.project_root / "yarn.lock").exists() and shutil.which("yarn"):
                kwargs["yarn_workspaces"] = True
                logger.info("Detected yarn workspace in %s", self.project_root)
            else:
                kwargs["npm_workspaces"] = True
                logger.info("Detected npm workspace in %s", self.project_root)

    # Only enable --infer-tsconfig when no tsconfig/jsconfig exists.
    if "infer_tsconfig" not in kwargs:
        has_tsconfig = (self.project_root / "tsconfig.json").exists()
        has_jsconfig = (self.project_root / "jsconfig.json").exists()
        if not has_tsconfig and not has_jsconfig:
            kwargs["infer_tsconfig"] = True
            logger.info(
                "No tsconfig.json/jsconfig.json; enabling infer_tsconfig for %s",
                self.project_root,
            )
        else:
            kwargs["infer_tsconfig"] = False
            logger.info(
                "Using existing tsconfig/jsconfig for %s", self.project_root
            )

    kwargs = self._normalize_workspace_kwargs(kwargs)

    # Determine whether index generation will actually run.
    # and dependency installation / tsconfig patching
    needs_generate = True
    if skip_level == "graph" and self.graph_file.exists():
        needs_generate = False
    elif skip_level in ("graph", "decode") and self.decoded_file.exists():
        needs_generate = False
    elif skip_level in ("graph", "decode", "raw") and self.index_file.exists():
        needs_generate = False

    if needs_generate:
        self._install_dependencies()
        patched_tsconfig = self._ensure_allow_js()
        if patched_tsconfig is not None:
            kwargs["patched_tsconfig"] = str(patched_tsconfig)
    else:
        logger.info(
            "Skipping dependency install and tsconfig patching (cached artifacts exist)"
        )

    logger.info("TypeScript run_pipeline kwargs: %s", kwargs)
    try:
        return super().run_pipeline(
            output_file=output_file,
            skip_level=skip_level,
            reset_profiler=reset_profiler,
            report_profile=report_profile,
            **kwargs,
        )
    finally:
        self._cleanup_patched_tsconfig()