mirror of
https://github.com/safishamsi/graphify.git
synced 2026-08-27 00:36:39 +00:00
Honour GRAPHIFY_OUT end-to-end, not just in the path guards (#1423)
The GRAPHIFY_OUT override (custom output-dir name / absolute path, #686) was only respected by some readers. `graphify extract` and several commands hardcoded the literal "graphify-out", so `GRAPHIFY_OUT=custom-out graphify extract` still wrote to graphify-out/ and downstream query/serve/update looked in the wrong place. Resolve the output-dir name through graphify.paths everywhere it matters: - new graphify.paths.out_path()/default_graph_json() helpers - __main__: extract write dir, cluster-only/label, query/affected/benchmark defaults, save-result --memory-dir, uninstall --purge, cache-check - detect: _MANIFEST_PATH, memory/ + converted/ dirs, and the scan-exclude (a renamed output dir is no longer re-ingested as source input) - transcribe._TRANSCRIPTS_DIR; build_merge/serve/benchmark/prs graph-path defaults Default behaviour is unchanged: with no env var everything still uses graphify-out/. Verified end-to-end (extract -> cluster-only -> query under GRAPHIFY_OUT=custom-out writes/reads custom-out/, no stray graphify-out/) and added a CLI regression test. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
This commit is contained in:
safishamsi
co-authored by
Claude Opus 4.8
Claude Opus 4.8
parent
6954a28da8
commit
b8dc31f760
@@ -4,6 +4,7 @@ Full release notes with details on each version: [GitHub Releases](https://githu
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## Unreleased
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- Fix: `GRAPHIFY_OUT` is now honoured end-to-end. The override (a custom output-dir name or absolute path, for worktrees/shared setups — #686) was only respected by some readers; `graphify extract` and several commands hardcoded `graphify-out/`, so a `GRAPHIFY_OUT=custom-out graphify extract` still wrote to `graphify-out/`, and downstream `query`/`serve`/`update` looked in the wrong place. The output-dir name is now resolved through `graphify.paths` everywhere it matters: the `extract` write dir, `cluster-only`/`label`, `query`/`affected`/`benchmark` defaults, `save-result --memory-dir`, `uninstall --purge`, `cache-check`, the `manifest.json`/`transcripts`/`memory`/`converted` paths in `detect`/`transcribe`, the `build_merge`/`serve`/`benchmark`/`prs` graph-path defaults, and the `detect` scan-exclude (so a renamed output dir is never re-ingested as source). Default behaviour is unchanged — without the env var everything still uses `graphify-out/` (#1423).
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- Fix: the `GRAPH_REPORT.md` header now shows the actual scan root instead of a literal `.`. The split-skill runbook passed `'.'` as the `root` argument to `report.generate` in Steps 4 and 5, so a `/graphify /some/path` run produced a report titled `# Graph Report - .`. It now passes `'INPUT_PATH'` (matching the monoliths, which were already correct). Display-only — no path written to `graph.json`/`manifest.json` was affected (#1419).
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- Fix: the skill runbooks now write a portable `manifest.json`. Step 9 (full build) and the `--update` reference called `save_manifest(...)` without `root=`, so manifest keys were stored as absolute paths; cloning or moving the repo then broke `graphify --update` — every cached file missed and the whole corpus re-extracted. All four runbook call sites (the lean-core `skill.md`, the Aider/Devin monoliths, and the shared `--update` reference) now pass `root='INPUT_PATH'`, relativizing keys to the scan root to match the native `graphify update` path. The monolith change is registered as a new sanctioned change-class in the round-trip guard (#1417).
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- Fix: hyperedge `source_file` is now relativized to the scan root like nodes and edges. `build_from_json(root=...)` relativized `source_file` on `nodes[]` and `links[]`, but stored `graph.hyperedges[]` verbatim, so a semantic subagent's absolute path (e.g. `/Users/.../CLAUDE.md`) leaked into `graph.json`. The fix lives in `build_from_json` (not `to_json`, which has no `root` to relativize against) and mirrors the existing node/edge handling (#1418).
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+10
-10
@@ -1884,12 +1884,12 @@ def uninstall_all(project_dir: Path | None = None, purge: bool = False) -> None:
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if purge:
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import shutil as _shutil
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out = pd / "graphify-out"
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out = pd / _GRAPHIFY_OUT
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if out.exists():
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_shutil.rmtree(out)
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print(f"\n graphify-out/ -> deleted (--purge)")
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print(f"\n {_GRAPHIFY_OUT}/ -> deleted (--purge)")
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else:
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print("\n graphify-out/ -> not found (nothing to purge)")
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print(f"\n {_GRAPHIFY_OUT}/ -> not found (nothing to purge)")
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print("\nDone. Run 'pip uninstall graphifyy' to remove the package itself.")
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@@ -2763,7 +2763,7 @@ def main() -> None:
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sys.exit(1)
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from graphify.affected import DEFAULT_AFFECTED_RELATIONS, format_affected, load_graph
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query = sys.argv[2]
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graph_path = "graphify-out/graph.json"
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graph_path = _default_graph_path()
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depth = 2
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relations: list[str] = []
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args = sys.argv[3:]
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@@ -2826,7 +2826,7 @@ def main() -> None:
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p.add_argument("--answer", required=True)
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p.add_argument("--type", dest="query_type", default="query")
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p.add_argument("--nodes", nargs="*", default=[])
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p.add_argument("--memory-dir", default="graphify-out/memory")
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p.add_argument("--memory-dir", default=str(Path(_GRAPHIFY_OUT) / "memory"))
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opts = p.parse_args(sys.argv[2:])
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from graphify.ingest import save_query_result as _sqr
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@@ -3190,7 +3190,7 @@ def main() -> None:
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i_arg += 1
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if watch_path is None:
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watch_path = Path(".")
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graph_json = graph_override if graph_override is not None else watch_path / "graphify-out" / "graph.json"
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graph_json = graph_override if graph_override is not None else watch_path / _GRAPHIFY_OUT / "graph.json"
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if not graph_json.exists():
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print(
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f"error: no graph found at {graph_json} — run /graphify first",
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@@ -3249,7 +3249,7 @@ def main() -> None:
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cohesion = score_all(G, communities)
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gods = god_nodes(G)
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surprises = surprising_connections(G, communities)
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out = watch_path / "graphify-out"
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out = watch_path / _GRAPHIFY_OUT
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out.mkdir(parents=True, exist_ok=True)
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labels_path = out / ".graphify_labels.json"
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if labels_path.exists() and not force_relabel:
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@@ -3882,7 +3882,7 @@ def main() -> None:
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elif cmd == "benchmark":
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from graphify.benchmark import run_benchmark, print_benchmark
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graph_path = sys.argv[2] if len(sys.argv) > 2 else "graphify-out/graph.json"
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graph_path = sys.argv[2] if len(sys.argv) > 2 else _default_graph_path()
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_enforce_graph_size_cap_or_exit(Path(graph_path))
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# Try to load corpus_words from detect output
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corpus_words = None
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@@ -4117,7 +4117,7 @@ def main() -> None:
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# so a fresh checkout writes graphify-out/ at the project root, matching
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# the skill.md pipeline.
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out_root = (out_dir.resolve() if out_dir else target)
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graphify_out = out_root / "graphify-out"
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graphify_out = out_root / _GRAPHIFY_OUT
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graphify_out.mkdir(parents=True, exist_ok=True)
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from graphify.detect import (
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@@ -4638,7 +4638,7 @@ def main() -> None:
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i += 1
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files = [f for f in files_from.read_text(encoding="utf-8").splitlines() if f.strip()]
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cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(files, root)
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out = root / "graphify-out"
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out = root / _GRAPHIFY_OUT
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out.mkdir(parents=True, exist_ok=True)
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if cached_nodes or cached_edges or cached_hyperedges:
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(out / ".graphify_cached.json").write_text(
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@@ -8,6 +8,7 @@ from networkx.readwrite import json_graph
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from graphify.build import edge_data
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from graphify.serve import _query_terms
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from graphify.paths import default_graph_json as _default_graph_json
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_CHARS_PER_TOKEN = 4 # standard approximation
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@@ -85,7 +86,7 @@ _SAMPLE_QUESTIONS = [
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def run_benchmark(
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graph_path: str = "graphify-out/graph.json",
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graph_path: str | None = None,
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corpus_words: int | None = None,
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questions: list[str] | None = None,
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) -> dict:
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@@ -98,6 +99,7 @@ def run_benchmark(
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Returns dict with: corpus_tokens, avg_query_tokens, reduction_ratio, per_question
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"""
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graph_path = graph_path or _default_graph_json()
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from graphify.security import check_graph_file_size_cap
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check_graph_file_size_cap(Path(graph_path))
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data = json.loads(Path(graph_path).read_text(encoding="utf-8"))
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+3
-2
@@ -29,6 +29,7 @@ import unicodedata
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from pathlib import Path
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import networkx as nx
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from .ids import normalize_id as _normalize_id
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from .paths import default_graph_json as _default_graph_json
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from .validate import validate_extraction
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@@ -435,7 +436,7 @@ def deduplicate_by_label(nodes: list[dict], edges: list[dict]) -> tuple[list[dic
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def build_merge(
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new_chunks: list[dict],
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graph_path: str | Path = "graphify-out/graph.json",
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graph_path: str | Path | None = None,
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prune_sources: list[str] | None = None,
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*,
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directed: bool = False,
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@@ -452,7 +453,7 @@ def build_merge(
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Safe to call repeatedly.
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root: if given, absolute source_file paths in new_chunks are made relative (#932).
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"""
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graph_path = Path(graph_path)
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graph_path = Path(graph_path if graph_path is not None else _default_graph_json())
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if graph_path.exists():
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# Read JSON directly instead of going through node_link_graph().
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# The latter rebuilds an undirected nx.Graph and then enumerating
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+5
-4
@@ -14,6 +14,7 @@ from graphify.google_workspace import (
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convert_google_workspace_file,
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google_workspace_enabled,
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)
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from graphify.paths import GRAPHIFY_OUT, GRAPHIFY_OUT_NAME, out_path
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class FileType(str, Enum):
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@@ -24,7 +25,7 @@ class FileType(str, Enum):
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VIDEO = "video"
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_MANIFEST_PATH = "graphify-out/manifest.json"
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_MANIFEST_PATH = str(out_path("manifest.json"))
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CODE_EXTENSIONS = {'.py', '.ts', '.tsx', '.js', '.jsx', '.mjs', '.ejs', '.ets', '.go', '.rs', '.java', '.groovy', '.gradle', '.cpp', '.cc', '.cxx', '.c', '.h', '.hpp', '.rb', '.swift', '.kt', '.kts', '.cs', '.scala', '.php', '.lua', '.luau', '.toc', '.zig', '.ps1', '.psm1', '.psd1', '.ex', '.exs', '.m', '.mm', '.jl', '.vue', '.svelte', '.astro', '.dart', '.v', '.sv', '.svh', '.sql', '.r', '.f', '.F', '.f90', '.F90', '.f95', '.F95', '.f03', '.F03', '.f08', '.F08', '.pas', '.pp', '.dpr', '.dpk', '.lpr', '.inc', '.dfm', '.lfm', '.lpk', '.sh', '.bash', '.json', '.tf', '.tfvars', '.hcl', '.dm', '.dme', '.dmi', '.dmm', '.dmf', '.sln', '.slnx', '.csproj', '.fsproj', '.vbproj', '.razor', '.cshtml', '.cls', '.trigger'}
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DOC_EXTENSIONS = {'.md', '.mdx', '.qmd', '.txt', '.rst', '.html', '.yaml', '.yml'}
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@@ -663,7 +664,7 @@ _SKIP_DIRS = {
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"site-packages", "lib64",
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".pytest_cache", ".mypy_cache", ".ruff_cache",
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".tox", ".eggs", "*.egg-info",
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"graphify-out", # never treat own output as source input (#524)
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"graphify-out", GRAPHIFY_OUT_NAME, # never treat own output as source input (#524); honour GRAPHIFY_OUT (#1423)
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# Coverage/test-artefact dirs — generated, never architecturally meaningful
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"coverage", "lcov-report", # Vitest/Istanbul/nyc HTML reports (#870)
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"visual-tests", "visual-test", # Playwright/visual-regression bundles (#869)
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@@ -1035,7 +1036,7 @@ def detect(root: Path, *, follow_symlinks: bool | None = None, google_workspace:
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include_patterns = _load_graphifyinclude(root)
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# Always include graphify-out/memory/ - query results filed back into the graph
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memory_dir = root / "graphify-out" / "memory"
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memory_dir = root / GRAPHIFY_OUT / "memory"
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scan_paths = [root]
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if memory_dir.exists():
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scan_paths.append(memory_dir)
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@@ -1081,7 +1082,7 @@ def detect(root: Path, *, follow_symlinks: bool | None = None, google_workspace:
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all_files.sort(key=lambda p: str(p))
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converted_dir = root / "graphify-out" / "converted"
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converted_dir = root / GRAPHIFY_OUT / "converted"
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for p in all_files:
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# For memory dir files, skip hidden/noise filtering
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+22
-1
@@ -17,9 +17,30 @@ flow) and every reader honours it.
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from __future__ import annotations
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import os
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from pathlib import Path
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GRAPHIFY_OUT = os.environ.get("GRAPHIFY_OUT", "graphify-out")
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# Bare directory name even when GRAPHIFY_OUT is an absolute path. Used by the
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# path guards that walk parents looking for the output dir by name.
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# path guards that walk parents looking for the output dir by name, and by the
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# detect scan-exclude so a custom output dir is never re-ingested as source.
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GRAPHIFY_OUT_NAME = os.path.basename(os.path.normpath(GRAPHIFY_OUT))
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def out_path(*parts: str) -> Path:
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"""A path inside the configured output dir, e.g. ``out_path("cache")``.
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``Path(GRAPHIFY_OUT) / ...`` resolves correctly for both a relative name
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("graphify-out") and an absolute override ("/shared/graphify-out").
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"""
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return Path(GRAPHIFY_OUT, *parts)
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def default_graph_json() -> str:
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"""Default ``graph.json`` path under the configured output dir.
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The package-wide fallback used by serve/build/benchmark/prs and the CLI read
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commands so a ``GRAPHIFY_OUT`` override is honoured everywhere, not just where
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the path is passed explicitly (#1423).
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"""
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return str(out_path("graph.json"))
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+3
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@@ -26,6 +26,8 @@ from dataclasses import dataclass, field
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from datetime import datetime, timezone
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from pathlib import Path
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from graphify.paths import default_graph_json as _default_graph_json
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# ── ANSI colours ─────────────────────────────────────────────────────────────
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@@ -676,7 +678,7 @@ def cmd_prs(argv: list[str]) -> None:
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do_conflicts = False
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show_wrong_base = False
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pr_number: int | None = None
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graph_path = Path("graphify-out/graph.json")
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graph_path = Path(_default_graph_json())
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i = 0
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while i < len(argv):
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+6
-3
@@ -9,6 +9,7 @@ import networkx as nx
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from networkx.readwrite import json_graph
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from graphify.security import sanitize_label, check_graph_file_size_cap
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from graphify.build import edge_data
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from graphify.paths import default_graph_json as _default_graph_json
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try:
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import jieba as _jieba # type: ignore[import-untyped]
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@@ -1038,8 +1039,9 @@ def _build_server(graph_path: str):
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return server
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def serve(graph_path: str = "graphify-out/graph.json") -> None:
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def serve(graph_path: str | None = None) -> None:
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"""Start the MCP server over stdio (the default, per-developer transport)."""
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graph_path = graph_path or _default_graph_json()
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try:
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from mcp.server.stdio import stdio_server
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except ImportError as e:
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@@ -1196,7 +1198,7 @@ def _build_http_app(
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def serve_http(
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graph_path: str = "graphify-out/graph.json",
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graph_path: str | None = None,
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*,
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host: str = "127.0.0.1",
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port: int = 8080,
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@@ -1217,6 +1219,7 @@ def serve_http(
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deliberate follow-up. Binding ``0.0.0.0`` exposes the server beyond
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localhost — set an api_key when you do.
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"""
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graph_path = graph_path or _default_graph_json()
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try:
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import uvicorn
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except ImportError as e:
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@@ -1304,7 +1307,7 @@ def _main(argv: list[str] | None = None) -> None:
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help="Reap stateful sessions idle this many seconds (default: 3600; 0 disables)",
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)
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args = parser.parse_args(argv)
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graph_path = args.graph_flag or args.graph_path or "graphify-out/graph.json"
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graph_path = args.graph_flag or args.graph_path or _default_graph_json()
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if args.transport == "http":
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serve_http(
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@@ -5,12 +5,14 @@ from __future__ import annotations
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import os
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from pathlib import Path
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from graphify.paths import out_path as _out_path
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VIDEO_EXTENSIONS = {'.mp4', '.mov', '.webm', '.mkv', '.avi', '.m4v', '.mp3', '.wav', '.m4a', '.ogg'}
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URL_PREFIXES = ('http://', 'https://', 'www.')
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_DEFAULT_MODEL = "base"
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_TRANSCRIPTS_DIR = "graphify-out/transcripts"
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_TRANSCRIPTS_DIR = str(_out_path("transcripts"))
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_FALLBACK_PROMPT = "Use proper punctuation and paragraph breaks."
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@@ -206,6 +206,26 @@ def test_query_uses_graphify_out_env(tmp_path):
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assert len(r.stdout) > 0
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def test_extract_writes_to_graphify_out_env(tmp_path):
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"""#1423: `graphify extract` honours GRAPHIFY_OUT for where it WRITES, not only
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where readers look — previously it hardcoded graphify-out/ and ignored the
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override. Code-only corpus, so no LLM backend is needed."""
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(tmp_path / "m.py").write_text("def a():\n return b()\n\n\ndef b():\n return 1\n")
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env = os.environ.copy()
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env["GRAPHIFY_OUT"] = "custom-out"
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r = _run(["extract", "."], tmp_path, env=env)
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assert r.returncode == 0, r.stderr
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assert (tmp_path / "custom-out" / "graph.json").exists(), r.stdout
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assert (tmp_path / "custom-out" / "manifest.json").exists()
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# The default dir must NOT be created when the override is set.
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assert not (tmp_path / "graphify-out").exists(), "extract ignored GRAPHIFY_OUT and wrote graphify-out/"
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# Manifest keys are relative to the scan root (portable) — #1417.
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keys = list(json.loads((tmp_path / "custom-out" / "manifest.json").read_text()).keys())
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assert keys == ["m.py"], keys
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# ── graphify path ────────────────────────────────────────────────────────────
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def test_path_runs_without_error(tmp_path):
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