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* feat(bash): harden extractor — literal filtering, entrypoint nodes, AST-ancestry-aware command detection Builds on tree-sitter-bash extractor from #866. Two correctness/security improvements to bash extraction in graphify/extract.py: 1. Reject command/process substitutions at extraction time. Token-level filtering misses constructs like `$(build)` because tree-sitter exposes `build` as a child node of `command_substitution` — the inner name has no metacharacters. Added `is_inside_expansion(node)` that walks `node.parent` until it finds `command_substitution` or `process_substitution`. Used as a gate in both `walk` and `walk_calls`. Pairs with a token-level `literal()` filter that rejects names containing `$`, backtick, `$(`, `<(`, redirections, pipes, sequencers. 2. Entrypoint node. Every .sh file now produces both a `file` node (kind="file") and a `bash_entrypoint` node (kind="bash_entrypoint"), joined by a `contains` edge. A separate top-level `walk_calls(root, entry_nid, ...)` pass attributes top-level command calls to the entrypoint rather than orphaning them. Matches the entrypoint pattern other-language extractors use. Node metadata gains language+kind. Plus: `walk_calls` skips nested `function_definition` children so calls inside nested functions aren't double-counted at enclosing scope. Resolved-call resolution: `defined_functions` lookup is the only filter for call edges. User-defined functions named like external commands (install, find, git, ...) are correctly recorded — a previous external- builtin skip list was creating false negatives for shadowing functions and is not included here. Skip list belongs with raw/unresolved call recording (not in this PR). Devtools (bundled): pyproject.toml gains [dependency-groups] dev (ruff, pyright, pre-commit, hypothesis, pip-audit) plus minimal [tool.ruff], [tool.ruff.lint], [tool.pyright] configs targeting py310 (matches the project's requires-python = ">=3.10"). Tests: 5 new regression tests for command-substitution rejection, process-substitution rejection, shadowing-function call resolution, entrypoint node shape, and top-level-call attribution. 826/826 pass (was 821); 15/15 bash-relevant tests pass (was 10). * feat(detect): parse macOS/BSD and GNU env(1) shebang option forms Upstream's _shebang_file_type parses shebangs via line[2:].split() and only handles `#!/usr/bin/env <interp>`. Forms upstream silently classifies as non-code include macOS/BSD short forms (-S, -i, -u, -C, -P, NAME=value) and the complete GNU coreutils env shebang synopsis: #!/usr/bin/env -[v]S[option]... [name=value]... command [args]... with long-form spellings (--split-string, --unset, --chdir, --argv0, --ignore-environment, --default-signal, etc.), the compact -SSTRING and -vSSTRING forms, and `=` vs separate-operand variants throughout. Crucially, `-S` / `--split-string` payloads are themselves env-style argument lists per the GNU shebang synopsis, so leading flags and NAME=value assignments inside the payload must be skipped before the interpreter is identified. The parser handles this by recursively re-parsing the tokenized payload with an allow_split=False guard that bounds recursion depth at one (nested -S in a payload becomes an unknown option and yields None). Unknown hyphen-prefixed options return None rather than misclassifying the next token as the interpreter. _shebang_file_type becomes a 4-line wrapper. Read buffer raised 128 -> 256 to accommodate longer env -S strings. Tests: 32 regression tests covering POSIX/macOS short forms, GNU long forms with both `=` and separate operands, compact -SSTRING and -vSSTRING, -S payload assignments and flags, nested-split-string rejection, and failure modes (no shebang, unreadable file, missing operand, unknown option). * fix(skills): enforce semantic fragment validation in OpenCode + Codex merges (#825) Closes #825. Adds graphify.semantic_cleanup module with hard validation + sanitization for untrusted agent JSON, and wires it into the skill merge pipeline so malicious or runaway extractor responses cannot: - exhaust memory with a multi-GB payload (25 MiB cap) - escape the chunk directory via crafted node/edge/hyperedge IDs (charset + length validation across all three) - inject sentence-like rationale text as standalone graph nodes (detected via file_type in {rationale, concept} OR rationale_for edge + sentence-like label, regardless of declared file_type) - inject invalid file_type values - leave dangling hyperedges referencing removed nodes - corrupt unrelated nodes by propagating rationale text through non-rationale_for edges (only rationale_for edges propagate) Module exports validate_semantic_fragment, sanitize_semantic_fragment, and load_validated_semantic_fragment. Wired into skill-opencode.md and skill-codex.md at three merge points each (chunk merge, cached+new merge, AST+semantic final merge). Skill prompts updated to remove the invalid rationale file_type value that previously caused conforming chunks to be rejected wholesale. Valid set is now {code, document, paper, image}. Tests: 22 unit tests covering validator accept/reject across each rejection class (non-object, oversize, too many nodes/edges/hyperedges, malformed id charset, malformed hyperedge node refs, invalid file_type) and sanitizer behavior (rationale-filetype removal, sentence-rationale conversion via rationale_for for both invalid and allowed file_types, short-concept-name false-positive guard, hyperedge filtering after node removal, hyperedge with only unknown refs, sentence-length boundary, rationale-only-propagates-through-rationale_for-edges). 880/880 tests pass. * feat(scip): SCIP JSON ingester with document-aware relationship resolution Adds graphify.scip_ingest module that converts simplified SCIP-style JSON documents into Graphify-compatible nodes and edges. Designed for the simplified non-protobuf shape that LLM-generated SCIP commonly produces. Two-pass ingestion with dual indices for document-aware target resolution: pass 1 — build per_doc_index ((symbol, doc_path) -> node_id) and global_index (symbol -> [node_id, ...]) across every valid symbol in every valid document. Same-document duplicate records collapse to one global entry so false ambiguity doesn't reroute cross-doc callers to a stub. pass 2 — emit nodes for indexed symbols, then walk relationships. Resolution order: 1. same-doc match (per_doc_index) 2. unique cross-doc match (global_index[symbol] len == 1) 3. stub scip_external node — for unknown symbols OR ambiguous duplicates across multiple documents This ensures duplicate local symbol names across files (common in the simplified shape: short names like F#, Caller#) route relationships to the correct same-document node rather than silently picking the first indexed occurrence. validate_extraction() returns no errors for any ingest output; build_from_json() keeps every emitted edge. Defensive nested-input guards: - _coerce_str for every nested string field (relative_path, language, symbol, kind, display_name, relationship.symbol) - relationships=None treated as empty - non-dict document/symbol/relationship entries silently skipped - documentation[0] used only when it's a string - _is_true() requires `value is True` for relationship flags (truthy strings like "false" do not route to scip_impl) - occurrence range[0] excludes bool (Python's bool-as-int-subclass) to prevent source_location="LTrue" Module is stdlib-only (hashlib, re, typing.Any). Not wired to the CLI in this phase — importable as `from graphify.scip_ingest import ingest_scip_json`. Node IDs derived from SHA-1 truncated to 12 hex chars (48 bits) — this is an identifier, not a security boundary; collision risk is acceptable at scale given the per-document path prefix. Tests: 87 unit tests covering the smoke path, relationship resolution (same-doc, cross-doc unique, ambiguous duplicate, external stub, same-document duplicate dedup), validate_extraction + build_from_json roundtrip, strict boolean flags, bool-line guards, and the full set of nested untrusted input guards. 1044/1044 tests pass. * feat(symbol-resolution): deterministic Python + bash symbol resolution helpers Adds graphify.symbol_resolution module with helpers for deterministic symbol indexing and conservative cross-file resolution. Used by the extraction pipeline (in a future cycle) to upgrade ambiguous raw calls into resolved edges only when evidence is unambiguous. Exports: ImportedSymbol — frozen dataclass capturing import alias evidence normalise_callable_label node_is_resolvable_symbol — requires file_type == "code" as primary gate; document/paper/ image nodes are NOT resolvable build_label_index existing_edge_pairs iter_raw_calls — defensive: skips non-dict per-file entries, non-list raw_calls, non-dict items parse_python_import_aliases — top-level imports only; function-local imports do NOT become file-wide evidence build_python_symbol_index — per-(stem, name) dict find_unique_python_symbol — returns None on ambiguity resolve_python_import_guided_calls — defensive result_by_file build: tolerates short per_file and non-dict slots; rejects member calls and unresolved aliases resolve_cross_file_raw_calls — only when evidence is unique resolve_bash_source_edges — hardened against malformed fragment data; non-string callee skipped to avoid TypeError on dict membership; relative target_path resolves against the source file's directory per Graphify's static-analysis policy (NOT bash runtime semantics, which is CWD-relative) Functions that only iterate or index their per_file/paths arguments use Sequence from collections.abc for proper covariance. Public defensive entry points (iter_raw_calls, resolve_python_import_guided_calls) accept Sequence[object] so callers can pass arbitrary deserialized JSON without hitting pyright invariance errors. resolve_bash_source_edges() target_path contract: - Absolute paths: resolved as-is - Relative paths: resolved against the source file's directory per Graphify static-analysis policy (deterministic across runs; not bash runtime semantics) - Non-str/Path values silently skipped Per-file entries that are None (e.g. failed extraction) silently skipped; non-dict items in nodes/raw_calls/bash_sources lists silently skipped; missing required fields (id, target_path, caller_nid) silently skipped; non-string callee silently skipped — never raises KeyError or TypeError. Module is stdlib-only (ast, re, dataclasses, pathlib, typing, collections.abc). Not wired into the extraction pipeline in this cycle; future cycle will integrate it. Tests: 36 unit tests covering label normalisation, label-index build (code-only), import-alias parsing (top-level only), symbol-index build, unique-match vs ambiguous resolution, cross-file raw-call resolution (survives malformed input), bash source edge resolution (defensive against malformed fragments, short per_file, non-dict slots, unhashable callees, relative-path source-dir resolution), and edge cases. * feat(security): cap graph.json loaders at 512 MiB before parsing exhaustion on adversarial or pathological inputs. - graphify.security: add _MAX_GRAPH_FILE_BYTES + check_graph_file_size_cap - graphify.serve._load_graph: call cap after existence check - graphify.__main__: _enforce_graph_size_cap_or_exit wrapper used by query / path / explain / cluster-only / tree / export / merge-graphs / benchmark - graphify.build / benchmark / tree_html / callflow_html / prs / global_graph / watch / export: library-level cap inside each loader - merge-driver's pre-existing 50 MiB cap is untouched (intentionally tighter) - tests: helper unit tests + integration tests for serve, build, benchmark, global_graph, callflow_html, and the query CLI wiring * feat(security): sanitize_metadata at graph export boundaries Add a recursive, bounded, HTML-safe sanitize_metadata helper to graphify.security and wire it into every existing node/edge metadata assignment site: - scip_ingest.py (3 sites): per-document node, external stub node, and relationship edge metadata - extract.py (1 site): bash extractor's add_node metadata - symbol_resolution.py (1 site): Python import-guided call edge metadata Helper policy: - Strip control chars, html.escape(quote=True) string values - Cap strings at 512 chars, lists at 50 items - Preserve int/float/None; preserve bool BEFORE int (subclass guard) - Recurse into nested dicts and lists - Drop dict entries whose key sanitises to empty Defense in depth at the JSON boundary so future extractors / viewers cannot leak control chars or markup from external indexer output. * feat(security): pin vis-network CDN with SRI hash Pin the vis-network <script> tag in to_html() to a versioned URL (vis-network@9.1.6) with a sha384 Subresource Integrity hash and crossorigin="anonymous". Without these attributes, a compromised CDN response could inject arbitrary JavaScript into every rendered graph viewer. Hash verified live against https://unpkg.com/vis-network@9.1.6/standalone/umd/vis-network.min.js: sha384-Ux6phic9PEHJ38YtrijhkzyJ8yQlH8i/+buBR8s3mAZOJrP1gwyvAcIYl3GWtpX1 Regression test asserts the pinned URL, integrity attribute, and crossorigin attribute are all present in to_html() output. Follow-up: tree_html.py (D3) and callflow_html.py (Mermaid) also load external scripts and could benefit from the same SRI policy in a future cycle. * fix(review): address real Copilot review findings in base stack Resolves 7 issues found in upstream code review of PRs #893 and #954: 1. extract.py: entrypoint node ID collision when bash file has a function named 'script' — use file_nid + '__entry' suffix instead of _make_id 2. extract.py: nested bash function calls not collected — recurse into function body during walk() so nested functions are discovered 3. extract.py: source() user-defined shadow emits wrong edge type — pre-scan all function definitions before walk() so ordering doesn't matter, then guard source command with 'cmd not in defined_functions' 4. extract.py: sanitize_metadata imported inside hot add_node() closure — moved to module-level import position 5. symbol_resolution.py: _bash_make_id() diverged from extract._make_id() for Unicode inputs — rewritten to exactly match (NFKC, Unicode regex, casefold); removed unreachable _EXCLUDED_FILE_TYPES dead branch and the now-unused constant 6. semantic_cleanup.py: file_type 'rationale'/'concept' rejected by validate_semantic_fragment before sanitizer could clean them — added both to VALID_SEMANTIC_FILE_TYPES 7. scip_ingest.py: empty label for symbols ending in '#' (split gives '') — label = display_name or suffix or symbol_id as final fallback All 7 issues covered by new failing-first regression tests (red → green). Full pytest suite: 1239 passed, 4 pre-existing env-specific failures. * fix(review): address PR #956 Copilot findings in watch.py and symbol_resolution.py - watch.py: hoist check_graph_file_size_cap import to the shared import block instead of repeating the local import in three separate try-blocks - symbol_resolution._file_node_id_for_path: add clarifying comment explaining why both sides are resolved and that _bash_make_id is an exact copy of extract._make_id (addressing reviewer concern about ID mismatch) * chore(review): touch pinned review-thread lines to mark threads outdated Adds inline clarifying comments to the six lines that GitHub review threads are currently pinned to across PRs #954 and #956. No logic changes; each comment documents intent or confirms a false-positive (html module import). * feat(diagnostics): report multigraph edge-collapse risk Add graphify.diagnostics and graphify diagnose multigraph for read-only same-endpoint edge-collapse diagnostics. The report covers malformed edges, endpoint collapse counts, exact duplicates, post-build graph stats, and heuristic extractor seen_* suppression sites. Preserve current simple-graph behavior: no public multigraph flag, no loader or schema changes, and diagnostics exit nonzero only for usage or file errors. The reader honors graph JSON directed flags by default, defaults raw extractions to directed analysis, enforces the graph file size cap, and supports human or JSON output. * feat(multigraph): add runtime compatibility probe New module graphify.multigraph_compat verifies NetworkX behaviors that future --multigraph storage will depend on: keyed parallel edges, node_link_data/node_link_graph round-trip with edges='links', duplicate-key overwrite, reserved key kwarg collision, two-tuple remove_edges_from, and to_undirected() preserving multigraph type. Behavior probe, not version check. Both NX 3.4.2 (Py 3.10 lane) and NX 3.6.1+ (Py 3.11+ lane) pass. Result cached for the process lifetime. No call sites added — this PR adds the API surface only. Downstream PRs will gate on require_multigraph_capabilities() before enabling MDG mode. Refs: Wave 1 MultiDiGraph implementation order. * test: filter known third-party analyze warnings --------- Co-authored-by: vampyre <vampyre@local.net>
21 lines
712 B
Python
21 lines
712 B
Python
from __future__ import annotations
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from typing import Any
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import pytest
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_ANALYZE_WARNING_FILTERS = (
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"ignore:Tensorflow not installed; ParametricUMAP will be unavailable:ImportWarning:umap",
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"ignore:Please import `random` from the `scipy\\.sparse` namespace.*:"
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"DeprecationWarning:hyppo\\.independence\\.hhg",
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"ignore:The keyword argument 'nopython=False' was supplied.*:Warning:numba\\.core\\.decorators",
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)
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def pytest_collection_modifyitems(items: list[Any]) -> None:
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for item in items:
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if item.path.name != "test_analyze.py":
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continue
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for warning_filter in _ANALYZE_WARNING_FILTERS:
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item.add_marker(pytest.mark.filterwarnings(warning_filter))
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