Adds an opt-in --timing flag that prints per-stage wall-clock timings to stderr so
slow stages are visible on large corpora. extract reports detect / AST extract /
semantic extract / build / cluster / analyze / export (and write on --no-cluster);
cluster-only reports load / cluster / analyze / label / report / export; both end
with a total. A small _StageTimer helper uses monotonic perf_counter.
Off by default and stderr-only, so default output and machine-read stdout/graph.json
are byte-identical (the extract arg loop already swallows unknown flags). Added a
regression test asserting the lines appear with --timing and are absent without it.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
graphify extract <path> --out R is documented to send all output to
R/graphify-out/, but the AST and semantic extraction caches were still
anchored at the scanned project (cache_root=target / root=target). That
re-created a graphify-out/ directory inside the project the user
explicitly asked to keep clean.
Anchor both caches at out_root instead. With --out unset, out_root
equals target, so existing in-project behavior is unchanged.
Adds test_extract_out_keeps_project_root_clean: runs extract from a
project root with --out pointing elsewhere and asserts the artifacts
land under --out while the project directory stays byte-identical.
Backend resolution now defers until after file detection. A code-only
corpus (pure AST, zero LLM calls) runs without any API key.
Key validation only fires when needs_llm=True (semantic_files non-empty
or --dedup-llm passed). Error message now names why a key is needed and
notes that code-only corpora need none.
Applied from PR #1123 with one fix: _clear_backend_keys in tests now
also clears AWS_PROFILE/REGION, OLLAMA_BASE_URL to prevent CI flakes
on machines with ambient credentials.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
If `graphify extract --backend claude` runs without the `anthropic`
package installed (pip install graphifyy doesn't pull it in), every
semantic chunk fails inside extract_corpus_parallel. The per-chunk
errors print to stderr but the function returns the empty merged
accumulator anyway, so extract proceeds to write an AST-only graph.json
and exit 0. CI that checks exit status sees success even though the
requested semantic pass produced no nodes.
Track per-chunk success via the existing on_chunk_done callback, which
only fires after a chunk succeeds. If fresh extraction was requested
(uncached_paths non-empty) and zero chunks completed, abort before the
merge/cluster/write phase with exit 1 and a message naming the backend.
The same shape covers other backends with optional SDK deps (openai,
google-generativeai). Cached-only runs are unaffected: uncached_paths
is empty and the guard does not fire.
Tests in tests/test_extract_cli.py simulate the all-failed and
one-succeeded paths by patching extract_corpus_parallel directly.
tpateeq