Commit graph

17 commits

Author SHA1 Message Date
Research Assistant
fa51cf70ac fix(08-deep-helper-deployment): fix ld_deep.py importability and doctor checks
- Upgrade Agent script check from directory existence to actual importability
- Fix doctor env var check: prefer PADDLEOCR_API_TOKEN over old names
- Support per-domain JSON export validation (not just library.json)
- Remove blanket tests/ exclusion from .gitignore
2026-04-24 12:55:57 +08:00
Research Assistant
ff1251522f fix: initialize validated_status and validated_error before try block
Both variables were assigned inside the try block but used after it.
If the try block threw before assignment, validated_error would be unbound
when line 2909 referenced it with done_incomplete status.

Also initialized validated_status = None for consistency since it could
also be unset if the try block fails before assignment.
2026-04-24 00:59:01 +08:00
Research Assistant
d0ba1da715 fix(run_repair): case 2 repair updates all three + case 3 handles None; add test_fix_case4 2026-04-24 00:42:44 +08:00
Research Assistant
6052c823e6 Add run_repair() function for three-way OCR state divergence repair 2026-04-24 00:02:32 +08:00
Research Assistant
981f5fa8ba fix(run_deep_reading): call validate_ocr_meta() before using ocr_status
- Replace direct meta.get('ocr_status') read with validate_ocr_meta() call
  in run_deep_reading() to properly validate OCR completion status
- Fixes bug where meta.json with ocr_status=done but missing files
  incorrectly marked paper as ready for deep reading
- validate_ocr_meta() checks 7 conditions before returning 'done':
  file existence, sizes, page markers, etc.
- done_incomplete status is correctly treated as blocked (not ready)
  by existing blocked logic at line 2810
- Add regression test: test_smoke_deep_reading_done_incomplete_is_blocked
2026-04-23 23:42:09 +08:00
Research Assistant
b9f06ccad3 feat: complete PaperForge Lite v1.0 release hardening (5 phases, 28 reqs, 145 tests) 2026-04-23 20:15:20 +08:00
Research Assistant
1c1e6d7c0d feat(01-03): replace duplicated resolver logic with shared wrappers
- literature_pipeline: load_vault_config and pipeline_paths now
  delegate to paperforge_lite.config, preserving public names
- ld_deep: _load_vault_config and _paperforge_paths now delegate
  to shared resolver, preserving public names
- Both scripts require paperforge_lite package to be available
  (via pip install or copied install in deployed vaults)
- Existing load_simple_env preserved for .env loading before dispatch
2026-04-23 12:00:24 +08:00
Research Assistant
881457dd92 Fix configurable Lite setup paths 2026-04-23 01:44:13 +08:00
Research Assistant
6fcd1132fa feat: read system_dir/resources_dir from paperforge.json instead of hardcoding 99_System/03_Resources 2026-04-23 01:07:50 +08:00
Research Assistant
7517ead1a6 fix: deploy scripts and .env to 99_System/PaperForge/ instead of vault root 2026-04-23 01:05:44 +08:00
Research Assistant
89374cb35f remove: all 科研读图指南 and Template references from project 2026-04-22 23:20:49 +08:00
Research Assistant
c607dd0441 rename: LiteraturePipeline -> PaperForge in all paths and references 2026-04-22 22:10:16 +08:00
Research Assistant
eafbab7594 feat: add TUI setup wizard and setup guide
- Add setup_wizard.py: Textual TUI with checklist + guide
  - Detects: Python, Vault structure, Zotero, Better BibTeX, JSON exports
  - Blocked guide until all checks pass
  - Open local docs/setup-guide.md from TUI
- Add docs/setup-guide.md: Detailed text-based setup instructions
  - Menu path diagrams for Zotero/BBT configuration
  - JSON-to-Base relationship explanation
  - FAQ section
- Integrate 'wizard' command into literature_pipeline.py
2026-04-22 19:28:52 +08:00
Research Assistant
acec4a67eb feat: integrate update command into literature_pipeline.py
- Add 'update' subcommand to check and install updates from GitHub
- Support both git pull and zip download modes
- Auto-backup before update, auto-rollback on failure
- Protect user data (03_Resources/, 05_Bases/, .env, AGENTS.md)
- Add paperforge.json for version tracking
- Add standalone update.py as alternative entry point
- Fix 'all' worker to only run Lite workers
- Add missing imports (sys, tempfile, hashlib, subprocess, zipfile)
2026-04-22 19:03:49 +08:00
Research Assistant
f564fec664 sync: auto-update from Full version (prepare command, chart-reading guides, first_author/journal/impact_factor) 2026-04-22 18:41:26 +08:00
Research Assistant
aa084e7d94 feat: simplify to core 4-worker pipeline
- Remove candidate/search/harvest/writeback workers (7 deleted)
- Keep only: selection_sync, index_refresh, ocr, deep_reading
- Simplify setup.py: remove agent selection, remove non-core dirs
- Update AGENTS.md generation for lite architecture
- Reduce pipeline.py from ~4000 to ~3500 lines
2026-04-21 22:44:09 +08:00
Research Assistant
d916b13b50 refactor: restructure repo to generic names
- 99_System/ -> pipeline/ + templates/
- .opencode/skills/ -> skills/
- Chart guides moved to skills/chart-reading/
- Update setup.py deploy paths accordingly
2026-04-21 22:17:45 +08:00