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112 Commits

Author SHA1 Message Date
Safi 762b85d7ca Merge pull request #622 from chronicgiardia/docs/colabfold-macos-install 
docs: add LocalColabFold macOS Apple Silicon install runbook
 2026-05-02 16:40:29 +01:00
Safi 6c82f81d13 Merge pull request #614 from robertmonka/codex/use-user-prompt-submit-hook 
Use UserPromptSubmit for Codex graph reminders
 2026-05-02 16:37:47 +01:00
Safi 0999822364 update README: add yaml/yml to file type table and feature description 2026-04-30 22:36:24 +01:00
Robert Mońka 18d697aac9 Preserve Codex user hooks 2026-04-30 21:25:20 +02:00
chronicgiardia 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
Safi 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
Safi a4ad901284 Update v0.5.5 release notes in README 2026-04-29 09:48:55 +01:00
Safi 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
Safi 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>
 2026-04-28 11:22:39 +01:00
Safi 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>
 2026-04-28 00:56:54 +01:00
Safi a566bfb566 Bump to v0.5.1 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-27 21:45:57 +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 2026-04-23 20:09:03 +01:00
Safi b326aa83c4 update README: add check-update command, Java inheritance note 2026-04-22 23:32:25 +01:00
Safi 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>
 2026-04-22 06:26:15 +01:00
Safi f938714df0 make logo link to graphifylabs.ai 2026-04-21 22:51:21 +01:00
Safi 39bf0a3f80 Move translations/ to docs/translations/ 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-21 22:36:20 +01:00
Safi 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
Safi 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
Safi 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
Safi 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
Safi 339d9783fb add multilingual READMEs: de, fr, es, hi, pt, ru, ar; fix .agents refs in README 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-21 21:47:46 +01:00
Safi f0ebd07fd5 Improve packaging: uv tool install support, fix interpreter detection on Mac/Linux 2026-04-21 21:11:27 +01:00
Safi 2fd15115d9 Center language links and badges 2026-04-21 11:37:13 +01:00
Safi 3bf096438f Add Graphify text logo to README 2026-04-21 11:33:35 +01:00
Safi 45643380d1 Add logo to README 2026-04-21 11:31:28 +01:00
Safi cc53e00bcc readme: revert to pepy.tech total downloads badge 2026-04-18 16:52:36 +01:00
Safi 3f5df2513b readme: show 200k+ total downloads badge 2026-04-18 16:51:36 +01:00
Safi 6892fd9309 readme: swap pepy badge for shields.io downloads 2026-04-18 16:50:15 +01:00
Safi d67436c065 v0.4.23: fix #178 stale version stamp, fix #260 add .html to DOC_EXTENSIONS 2026-04-18 10:47:37 +01:00
Safi f8a5328197 readme: add pipx as alternative install method 2026-04-18 09:51:38 +01:00
Safi 8171abf583 readme: add .mdx to docs extensions table 2026-04-18 09:50:14 +01:00
Safi 72d9779aaf readme: clarify graph.html opens in any browser 2026-04-17 15:50:05 +01:00
Safi 8a474eb1b3 v0.4.19: fix #390 #298 #410 #401 #385, team workflow docs, Windows/pipx tips 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-17 12:46:42 +01:00
Safi 429e46a665 v0.4.15: VS Code Copilot Chat, OpenCode/Gemini Windows fixes, .mjs/.ejs, macOS watch, god_nodes degree rename 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-15 23:08:43 +01:00
Safi dc41eceb9e Bump to 0.4.14, README: cross-file call-graph note 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-15 00:28:18 +01:00
Safi ac265ec495 docs: add Verilog/SystemVerilog to language count and list 2026-04-14 09:36:57 +01:00
Safi 2993cce8b2 v0.4.12: add Kiro IDE/CLI support, fix cache portability across machines 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-13 22:46:13 +01:00
Safi 521487aa2e Fix README: Codex does have PreToolUse hook support (#299) 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-13 22:33:33 +01:00
Safi b00813bcb2 v0.4.11: fix query crash on MultiGraph, NoneType in serve.py, MCP CWD path bug, .graphifyignore subfolder patterns; v0.4.10: Dart, Hermes, 6 CLI commands, PHP improvements 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-13 12:48:47 +01:00
Safi e737f5bf58 docs: add Hermes platform, Dart to language list, 22→23 languages 2026-04-13 08:46:20 +01:00
Safi 4210de270f Fix watch edge key, claw path, Blade support, WSL MCP docs (0.4.7) 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-12 20:49:24 +01:00
Safi f8c91a987f Add Google Antigravity platform support (0.4.6) 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-12 19:16:49 +01:00
Safi 8070909c04 update README: 22 languages, add .vue and .svelte to file types table 2026-04-12 13:02:45 +01:00
Safi b23e5de5a1 add LinkedIn badge to README 2026-04-11 21:15:32 +01:00
Safi 75c08a5b32 Remove YouTube URL references from README, use generic <video-url> placeholder 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-04-10 16:24:13 +01:00