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chronicgiardiaandOz e97379e551 docs: add LocalColabFold macOS Apple Silicon install runbook 
Adds docs/colabfold-macos-install.md, a reproducible recipe for
installing LocalColabFold (ColabFold + AlphaFold2 weights) on Apple
Silicon Macs, so users can predict protein structures locally and feed
the resulting PDBs / confidence scores into a graphify corpus.

Notes upstream LocalColabFold's current top-level installer hardcodes
Linux x86_64 Miniforge and jax[cuda12], which fail on Apple Silicon (no
macOS CUDA wheels, no NVIDIA GPU). Recommends the bundled v1.5.5 M1
installer as the working Apple Silicon path. ColabFold 1.6.1 with
JAX 0.4.23 CPU build, verified by 60s smoke test on a 62-residue FASTA.

Linked from README.md under the existing 'Optional integrations' section
(also added by this PR if not already present from #620).

Co-Authored-By: Oz <oz-agent@warp.dev>
 2026-04-30 03:23:00 -07:00
Safi 3755fdc885 swap downloads badge back to pepy.tech 2026-04-30 09:48:37 +01:00
Safi 4e871ad36c swap downloads badge to shields.io for cache refresh 2026-04-30 09:47:55 +01:00
SafiandClaude Sonnet 4.6 97099edc38 bump to v0.5.6 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
v0.5.6 		2026-04-30 09:01:35 +01:00
SafiandClaude Sonnet 4.6 4360f9644b move changelog out of README into CHANGELOG.md, add yt-dlp legal notice 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-29 22:44:12 +01:00
SafiandClaude Sonnet 4.6 f755aca58f fix kimi temperature 400 error and community label deletion on cleanup (fixes #610, #608) 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-29 17:03:44 +01:00
SafiandClaude Sonnet 4.6 28b17d37f1 remove Python upper bound to support 3.14+ (fixes #607) 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-29 13:33:41 +01:00
SafiandClaude Sonnet 4.6 326c03e132 remove product-site from graphify repo 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-29 12:28:30 +01:00
SafiandClaude Sonnet 4.6 44fc32e3e2 add product-site as part of graphify repo (was separate submodule) 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-29 12:27:56 +01:00
SafiandClaude Sonnet 4.6 744827166e update product site: fix pip install package name to graphifyy, update stats to 38k stars / 400k+ downloads / 1900+ waitlist 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-29 12:26:00 +01:00
SafiandClaude Sonnet 4.6 c750582db4 fix SyntaxWarning: use raw string for shell glob pattern with backslash escapes 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-29 10:02:56 +01:00
SafiandClaude Sonnet 4.6 71d1b394e9 fix NameError in Kimi tip: use module-level os import instead of _os 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-29 09:58:54 +01:00
Safi a4ad901284 Update v0.5.5 release notes in README v0.5.5 2026-04-29 09:48:55 +01:00
SafiandClaude Sonnet 4.6 f9c344b546 Remember scan root so graphify update works without a path arg 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-29 09:43:51 +01:00
SafiandClaude Sonnet 4.6 59cbad3937 Fix Go package-call false-negative and llm.py robustness 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-29 08:57:16 +01:00
SafiandClaude Sonnet 4.6 5904081d7a Add Kimi K2.6 backend, fix phantom god nodes (#598), fix concept file_type (#601) 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-29 08:51:53 +01:00
Safi eceaaad61e Add v0.5.4 release notes to README 2026-04-28 15:06:26 +01:00
SafiandClaude Sonnet 4.6 dd86271312 Fix SSRF DNS rebinding TOCTOU and yt-dlp URL bypass (#591, #592) 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
v0.5.4 		2026-04-28 15:04:52 +01:00
SafiandClaude Sonnet 4.6 7359cdace9 Fix AST/semantic cache namespace collision breaking graphify update (#582) 
AST and semantic entries now write to cache/ast/ and cache/semantic/
respectively. Previously both used the flat cache/ dir causing semantic
results to overwrite AST entries for code files on mixed corpora, making
the shrink guard fire on every subsequent update run.

Migration: load_cached falls back to legacy flat cache/ for AST reads
so existing cache entries are not lost on upgrade.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
v0.5.3 		2026-04-28 11:22:39 +01:00
SafiandClaude Sonnet 4.6 ee1df22b25 Fix PreToolUse hook for Claude Code v2.1.117+ (Glob|Grep → Bash matcher) 
Grep and Glob tools removed in CC v2.1.117; searches now go through Bash.
Hook now reads stdin tool_input and pattern-matches on search commands.
Uninstall/reinstall handles both old and new matcher for clean upgrades.

Closes #578

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
v0.5.2 		2026-04-28 00:56:54 +01:00
SafiandClaude Sonnet 4.6 a566bfb566 Bump to v0.5.1 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
v0.5.1 		2026-04-27 21:45:57 +01:00
SafiandClaude Sonnet 4.6 4563b043f2 Fix 6 bugs: ID collisions, path portability, alias resolution, HTML controls, desync guard, rationale prompt 
- #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>
 2026-04-27 21:44:22 +01:00
Safi 6175e0a8ea fix #547 #559 #570: expand ~ in hooksPath, fix gitignore inline comments, nosec on write sinks 2026-04-27 21:27:26 +01:00
Safi 770d7f54c4 Add The Memory Layer book badge to README 2026-04-25 15:56:59 +01:00
Safi 8bed332ff4 release: bump to v0.5.0 — clone, merge-graphs, shrink guard, dedup, bug fixes v0.5.0 2026-04-23 20:09:03 +01:00
Safi df9b7ec54f fix #479 #451: build_merge(), pre-write shrink guard, label dedup, chunk-suffix prompt block 2026-04-23 20:04:43 +01:00
Safi 2faeed99a2 feat: cross-repo merge-graphs; fix #527 CLAUDE_CONFIG_DIR; fix #524 graphify-out excluded from source scan 2026-04-23 19:59:14 +01:00
Safi 2c49da24f0 feat: graphify clone <github-url> — clone any repo and run full pipeline on it 2026-04-23 19:49:56 +01:00
Safi 5843ffc277 gitignore: exclude local benchmark scripts from repo 2026-04-23 19:38:54 +01:00
Safi b326aa83c4 update README: add check-update command, Java inheritance note 2026-04-22 23:32:25 +01:00
Safi e915a877e2 bump to v0.4.31 2026-04-22 23:28:22 +01:00
Safi 64f38acf3e implement #488 #482 #472 #490: legacy schema canonicalization, Java inheritance, aggregated HTML viz, check-update subcommand 2026-04-22 23:28:09 +01:00
Safi e4bdcc2487 add tests for canvas vault-relative paths and hook .exe skip 2026-04-22 23:04:40 +01:00
Safi 8981f7c8ef bump to v0.4.30 2026-04-22 23:02:41 +01:00
Safi 4bc20527c3 fix #513 #514: skip head -1 on .exe hook binary, fix to_canvas() hardcoded obsidian path 2026-04-22 23:01:53 +01:00
Safi 85e713644e bump to v0.4.29 2026-04-22 09:28:41 +01:00
Safi 52ad45bd27 fix #504: export PYTHONUTF8=1 in Step 1 to prevent garbled CJK output on Windows 2026-04-22 09:28:26 +01:00
Safi 86d6d9317f fix #498: opencode config to .opencode/opencode.json, fix skill temp file paths, add --wiki step 2026-04-22 09:19:53 +01:00
SafiandClaude Sonnet 4.6 d9b2928da1 fix: deterministic GRAPH_REPORT on large graphs, stable edge node IDs, correct common-root inference 
- analyze.py: add seed=42 to betweenness_centrality() — eliminates non-deterministic GRAPH_REPORT.md diffs on graphs >1000 nodes (#499)
- extract.py: fix common-root inference to stop at first diverging segment not sum of all matches (#502)
- extract.py: resolve root to absolute path; post-process file node IDs to project-relative after extraction so graph.json edge endpoints are stable across machines (#502)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
v0.4.27 		2026-04-22 09:04:38 +01:00
SafiandClaude Sonnet 4.6 f8fd8f8479 fix: wiki encoding+collisions, hook rebase guard, detect path resolve, readme gitignore docs 
- wiki.py: add encoding="utf-8" to all write_text() calls (fixes Windows cp1252 crash #496)
- wiki.py: deduplicate filenames with _unique_slug() to prevent silent article overwrites (#497)
- hooks.py: skip post-commit/post-checkout during rebase/merge/cherry-pick (#485)
- detect.py: resolve root path at detect() entry so .graphifyignore patterns match consistently (#495)
- README.md: document manifest.json, cost.json gitignore and .graphifyignore platform file examples (#369)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
v0.4.26 		2026-04-22 06:26:15 +01:00
Safi f938714df0 make logo link to graphifylabs.ai 2026-04-21 22:51:21 +01:00
SafiandClaude Sonnet 4.6 7cb639ae5d fix(report): complete empty-community fix — hubs, summary count, thin-community gaps; add graph-query CLI rules to install sections 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
v0.4.25 		2026-04-21 22:42:53 +01:00
SafiandClaude Sonnet 4.6 39bf0a3f80 Move translations/ to docs/translations/ 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-21 22:36:20 +01:00
SafiandClaude Sonnet 4.6 e241ce96cf Bump version to 0.4.24 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
v0.4.24 		2026-04-21 22:30:44 +01:00
SafiandClaude Sonnet 4.6 dbde78ca03 Fix four bugs from community PRs 
- cache: skip directory source_file in save_cached to prevent IsADirectoryError (#444)
- report: skip structural-only communities with no real nodes (#443)
- hooks: allow @ in python path allowlist for Homebrew paths (#474)
- watch: keep source_file paths project-relative after rebuild (#434)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-21 22:26:17 +01:00
SafiandClaude Sonnet 4.6 9c3d0fa517 Fix chunk temp files not cleaned up after graph build 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-21 22:21:37 +01:00
SafiandClaude Sonnet 4.6 69d4d7e9c3 Move 27 translation READMEs to translations/ subdirectory 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-21 22:14:53 +01:00
SafiandClaude Sonnet 4.6 2a35d7fd38 Add 17 language translations and expand language bar to 28 languages 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-21 22:12:55 +01:00
SafiandClaude Sonnet 4.6 ed4f12ab82 add country flags to language links, remove Trendshift badge 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-21 21:53:36 +01:00
SafiandClaude Sonnet 4.6 de136676ef add Trendshift badge and move star history to top of README 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-21 21:51:22 +01:00