#796: add edge_data()/edge_datas() helpers in build.py that tolerate
MultiGraph/MultiDiGraph; replace all G.edges[u,v] 2-tuple call sites in
__main__.py, serve.py, wiki.py, export.py, analyze.py, benchmark.py;
fix same pattern in 10 skill file inline heredocs
#795: all 12 skill files now short-circuit on /graphify --help or -h
and print the Usage block without running any pipeline steps
#792 (hollow response): add _response_is_hollow() predicate in llm.py;
when Ollama (or any backend) returns empty/null/whitespace content or a
parsed result with no nodes/edges, rewrite finish_reason="length" so
_extract_with_adaptive_retry bisects the chunk instead of silently
dropping it; applied to _call_openai_compat, _call_claude, _call_bedrock
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Adds support for Quarto markdown (.qmd) files by:
- Adding '.qmd' to document file extensions in detection
- Updating export logic to handle .qmd in filename sanitization
- Adding .qmd extractor dispatch using the existing markdown extractor
- Updating watch comments to include .qmd files
- Add Fortran support (26th language): .f/.F/.f90/.F90/.f95/.F95/.f03/.F03/.f08/.F08
via tree-sitter-fortran; capital-F files preprocessed with cpp -w -P
- Add graphify export {html,obsidian,wiki,svg,graphml,neo4j} CLI subcommands
- Add graphify query/path/explain CLI subcommands
- Reduce skill.md from 63KB to 47KB by replacing Python heredocs with CLI calls
- Extend to_html() with node_limit param for auto-aggregation on large graphs
- Add integration tests for all export/query/path/explain subcommands
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- #550: _file_stem() includes parent dir to prevent node ID collisions for same-named files
- #555: extract() relativizes source_file paths before returning for cross-machine portability
- #562: to_json() returns bool; _rebuild_code() writes report/html only if json succeeded
- #563: skill prompts store rationale as node attribute, not separate node; enforce calls direction
- #566: Show All / Hide All buttons added to HTML community panel
- #575: _import_js() resolves tsconfig.json compilerOptions.paths aliases before external fallback
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- build/validate: accept NetworkX <=3.1 "links" key alongside "edges" (#212)
- __main__: skip version check during install/uninstall, deduplicate paths (#220)
- all file IO: explicit encoding="utf-8" to prevent crashes on Windows CJK locales (#204)
- hooks: add newline="\n" on write to prevent CRLF shebang breakage on Windows (#204)
- export: strip trailing .md from safe_name so "CLAUDE.md" doesn't become "CLAUDE.md.md" (#221)
- report: add Community Hubs navigation block so Obsidian vault stays connected (#221)
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- extract.py: use str(path) for node IDs to prevent same-basename collision (#211)
- build.py: normalize from/to edge keys before KeyError (#216)
- export.py: guard ZeroDivisionError when graph has no edges (#217)
- hooks.py: remove stale CODE_EXTS filter, rebuild on any changed file (#222)
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Two targeted security hardening changes:
1. SSRF: validate_url() now resolves hostnames and blocks private/reserved
IP ranges (127.x, 10.x, 169.254.x, etc.) and cloud metadata endpoints.
Prevents SSRF attacks in cloud environments where a URL like
http://169.254.169.254/latest/meta-data/ could leak instance credentials.
2. Neo4j Cypher injection: Node labels (file_type) are now sanitized to
alphanumeric + underscore before interpolation into Cypher queries.
Previously, attacker-controlled file_type metadata could inject
arbitrary Cypher in team/shared graph scenarios.
Both changes are zero-impact on normal UX - no new config, no new flags,
no behavioral changes for legitimate use.
- Add --graphml to Usage table (was implemented but undocumented there)
- Remove early manifest save from --update merge step (Step 9 owns it; saving early meant failed pipelines left manifest ahead of graph)
- query/path/explain now check graph.json exists before running, with clear "run /graphify first" message
- --no-viz: clarify it skips both Obsidian vault and HTML (was contradictory)
- Replace pyvis with custom vis.js renderer: node size by degree,
click-to-inspect panel with clickable neighbors, search box,
community filter, physics clustering by community
- HTML graph generated by default on every run (no --html flag needed)
- Token reduction benchmark auto-runs after every /graphify on corpora >5k words
- Fix 292 edge warnings: silently skip stdlib/external edges in build.py
- Fix build() to merge extractions before building (cross-extraction edges were dropped)
- Add 5 HTML renderer tests (223 total)
- Remove unnecessary files: lib/, tests/eval_attention.py, misplaced eval reports
- Add graphify-out/ and .graphify_*.json to .gitignore
- Bump version to 0.1.4, remove pyvis dependency
- README: token reduction as top-level selling point, vis.js in tech stack,
graph.html in output listing, correct test count and install command
style: replace all em dashes with hyphens
fix: explain hidden .graphify/ folder in skill output and README
fix: rename .graphify/ to graphify-out/ so output is visible by default
Safi