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  • f5a951f47a docs: add P5 PR report feature/p5-ppt-assistant potaser 2026-10-15 19:35:51 +08:00
  • 7ced30fa96 feat(review): P5 科研汇报助手 + 14 风格 + 真图嵌入 potaser 2026-10-15 18:05:29 +08:00
  • 69e3f35a43 Merge pull request 'feat(review): P3b+P4 论文重排版支持编译 PDF（含 zip 项目）' (#4) from wjq/PlantAI-rag-new:feature/p3b-compile-ui into main admin 2026-10-15 18:30:14 +08:00
  • de0b9f92be fix(review): EPS batch conversion in zip compile (v2) feature/p3b-compile-ui potaser 2026-10-14 09:47:49 +08:00
  • 2797145104 feat(review): P4 two-phase zip compile + XDV→PDF diagnostics + EPS fallback potaser 2026-10-13 18:42:04 +08:00
  • 4e19350115 docs: add P3b PR report potaser 2026-10-13 11:23:01 +08:00
  • e036301e1a feat(review): show format rules summary per target journal potaser 2026-10-13 11:22:52 +08:00
  • da84dff9bb fix(review): persist uploaded .tex file in reformat panel potaser 2026-10-13 11:20:33 +08:00
  • 3a72d3a861 feat(review): P3b enable compile PDF in reformat panel potaser 2026-10-13 10:24:55 +08:00
  • ac07cb2008 Merge pull request 'feat(review): AI 预审稿修复 + 审稿回复助手 Phase 1' (#3) from wjq/PlantAI-rag-new:feature/presubmit-explainable-engine into main admin 2026-10-13 09:34:41 +08:00
  • d077a5b930 test(docs): rebuttal + tracker tests + PR reports feature/presubmit-explainable-engine potaser 2026-10-12 16:38:28 +08:00
  • c4dc344a31 feat(edu): presubmit UI + rebuttal assistant + tracker removal potaser 2026-10-12 16:38:28 +08:00
  • cf5ccb3a37 feat(review): presubmit 4-bug fix + rebuttal Phase 1 backend potaser 2026-10-12 16:38:28 +08:00
  • d99d5ef74a fix(review): replace presubmit recommendation quota with explainable rule engine potaser 2026-10-12 09:55:07 +08:00
  • 4add9f176b Merge pull request 'feat(review): journal_directory 启动自动 seed（部署即运行）' (#2) from wjq/PlantAI-rag-new:feature/journal-seed-autoload into main admin 2026-10-11 21:12:56 +08:00
  • 1319328b85 feat(review): auto-seed journal_directory on startup when empty feature/journal-seed-autoload potaser 2026-10-11 20:41:05 +08:00
  • 2d0e3a4858 fix(build): compile_sdk 白名单加入 review_proxy.py（科研审稿反代断流高危点） admin 2026-10-11 16:40:24 +08:00
  • ea0f2b3fad Merge pull request 'feat(review): 教育科研工作台 + 论文自动重排版 + journals v4 数据集' (#1) from wjq/PlantAI-rag-new:feature/academic-review-assistant into main admin 2026-10-11 13:49:12 +08:00
  • 19fa12eb39 merge main: 解决 .gitignore 冲突（合并部署文档忽略规则） feature/academic-review-assistant admin 2026-10-11 13:47:47 +08:00
  • 11337a788f 更新 .gitignore admin 2026-10-11 13:29:35 +08:00
  • 55410b663a feat(review): journal format-rule fetch scripts (offline CLI) potaser 2026-10-11 12:19:18 +08:00
  • dddb70ff6f fix(review): directory partition source shown as constant note potaser 2026-10-11 12:19:18 +08:00
  • 649e66f41d feat(review): tectonic PDF compile API (P3a) + rename journals panel potaser 2026-10-11 12:19:18 +08:00
  • 42aeb8fa4c feat(review): paper auto-reformat P1 (.tex rule engine + diff panel) potaser 2026-10-11 12:19:17 +08:00
  • c747ebd77a feat(review): official format rules for 5 featured journals potaser 2026-10-11 12:19:17 +08:00
  • 60375b04d7 chore: .gitignore 忽略含凭据的部署方案文档 DEPLOY_PAPER_176.md main feature/paper-writer-mcp admin 2026-10-10 18:53:25 +08:00
  • 1bd4aea5fd fix(build): render_active_library_env 输出 GENE_FAMILY_ROOT 而非未定义的 QA_ROOT admin 2026-10-10 18:52:15 +08:00
  • 51532a30bc fix(ui): 工作台「提取任务」tab 与离线提示改为「上传文献」 admin 2026-10-10 18:27:06 +08:00
  • 5a71e29cf7 feat(edu): complete 7-panel academic assistant + journals v4 dataset potaser 2026-10-10 16:05:08 +08:00
  • d43d30ee3f feat: add review_service with plant genomics presubmit, journals endpoint, and BFF proxy potaser 2026-10-09 16:54:03 +08:00
  • d37e0d9c3a fix(paper): 确认大纲后即时 seed 进度卡并逐节刷新 admin 2026-10-08 17:10:50 +08:00
  • c923419d2d fix(paper): 大纲阶段修改意见路由回 sendPaper + 用原始 brief 重新生成大纲 admin 2026-10-08 16:23:28 +08:00
  • 43a7c6c132 feat(paper): UI 优化(卡片文字颜色/去模式按钮) + 模板下拉加论文选项并接线渲染 admin 2026-10-08 15:17:44 +08:00
  • 8b228923bd fix(paper): 取消路径(cancel_paper) + 引用元数据清洗(丢弃杜撰 DOI/PMID) admin 2026-10-08 14:59:16 +08:00
  • 2e5372cf90 fix(paper): 论文产物渲染为 HTML + 文末追加参考文献列表/disclaimer admin 2026-10-08 14:54:00 +08:00
  • 99bd86e535 feat(bioflow): 生信模块对话式改造 + MCP 外挂化 (S0-S6) feature/bioflow-conversation-orchestration admin 2026-09-30 22:56:06 +08:00
  • 91f6a1c242 feat: 新增论文撰写功能 paper-writer（独立 MCP 服务 + BFF 大脑 + 前端三卡） admin 2026-09-30 22:29:22 +08:00
  • 0282cfeeeb feat(bioflow): 阶段进度条+滚动日志+点击定位全链;图片注入三修;QA启动就绪等待 admin 2026-09-24 16:48:52 +08:00
  • 0f6e16ce79 fix(sdk): run.sh 读取 PORT/PYTHON/BIND 移到 source .env 之后 adminandClaude Fable 5 2026-09-17 14:47:38 +08:00
  • 964346dc77 fix(sdk): run.sh source .env + BIND host env 化(BFF_BIND_HOST) adminandClaude Fable 5 2026-09-17 14:45:01 +08:00
  • f10b86c088 feat(deploy): start_all 生信段尊重 BIOFLOW_ENABLED(默认 false=无生信版) adminandClaude Fable 5 2026-09-17 07:56:49 +08:00
  • d0e6c76ec1 feat(ui): 无生信启动时隐藏扩展按钮 adminandClaude Fable 5 2026-09-17 07:37:32 +08:00
  • 16bde32020 feat(ui): 右上角生信跳转按钮+四按钮文字标签 adminandClaude Fable 5 2026-09-16 20:44:23 +08:00
  • ba43ba90bf feat(bioflow): 样本配置 LLM 兜底——规则无法归纳时 DeepSeek 生成描述 adminandClaude Fable 5 2026-09-16 20:13:32 +08:00
  • 36d3d8d62a fix(bioflow): 描述文件候选择优+去除登记文件数上限 adminandClaude Fable 5 2026-09-16 20:03:49 +08:00
  • f2c101ec65 feat(bioflow): 样本配置智能分析——描述文件优先+实况分析+解压 adminandClaude Fable 5 2026-09-16 19:54:21 +08:00
  • 750e218541 fix(bioflow): 卡片防误操作+暂停立即生效+确认幂等 adminandClaude Fable 5 2026-09-16 18:01:24 +08:00
  • becf76ecd9 feat(bioflow): 分析路径规划中提示——planning 帧+前端思考中状态 adminandClaude Fable 5 2026-09-16 16:15:17 +08:00
  • dcb810a758 feat(bioflow): wgs/pop/gwas 26 阶段参数契约(与 rnaseq 同款机制) adminandClaude Fable 5 2026-09-16 15:33:43 +08:00
  • 3b512fffd0 fix(bioflow): rnaseq/wgs 阶段参数契约——CLI 参数注入+样本配置自动生成+产物路径对齐 adminandClaude Fable 5 2026-09-16 15:23:50 +08:00
  • 04fb306624 fix(bioflow): 内核树运行时挂载——非 gf 阶段镜像缺 cli 模块 adminandClaude Fable 5 2026-09-15 23:22:06 +08:00
  • 2ee9af4bd0 fix(bioflow): 路径登记目录展开+黑名单+自动挂载 adminandClaude Fable 5 2026-09-15 23:11:27 +08:00
  • 957f3cb062 feat(ui): 导航按钮迁移右上角+删除会话栏底部工具栏 adminandClaude Fable 5 2026-09-15 22:49:41 +08:00
  • e3870d19de fix(extension): run 方法守卫与 trial 统一——适配器 _real 非 None 即执行 admin 2026-09-15 12:35:48 +08:00
  • a008fbba2a fix(extension): 产物收割排除代码副本+删 work 目录——输出契约校验语义不变 adminandClaude Fable 5 2026-09-15 11:59:42 +08:00
  • 3989dd3c3a fix(extension): 容器入口可写工作目录——代码复制进 run_dir 执行+产物收割输出 adminandClaude Fable 5 2026-09-15 11:58:17 +08:00
  • 8a58703d61 fix(extension): converted_code 镜像保留嵌套结构(与 raw_code 落盘一致) admin 2026-09-15 11:51:27 +08:00
  • 4266a89872 fix(extension): 容器入口默认 cwd 改为代码目录(run.sh 相对脚本路径语义) admin 2026-09-15 11:43:16 +08:00
  • 1bce4bf587 fix(extension): context 接线改用 _default_exec_config(entry_script_dir 空串致 trial 入口缺失) admin 2026-09-15 11:37:39 +08:00
  • 9bbe2c83f6 fix(extension): 入口脚本目录解析——176 部署树路径深度不同致 trial 报入口缺失 adminandClaude Fable 5 2026-09-15 11:24:05 +08:00
  • 82b954b957 docs(deploy): BFF 手动重启 venv 绝对路径陷阱(2026-09-15 实测) adminandClaude Fable 5 2026-09-15 10:54:10 +08:00
  • d12071a4d7 feat(extension): 上传支持 zip/tar/目录三形态+结构自适应分类 adminandClaude Fable 5 2026-09-15 10:34:52 +08:00
  • 76529f78ab docs(deploy): 环境镜像全量同步原则固化 adminandClaude Fable 5 2026-09-14 22:15:47 +08:00
  • 835d55cb5b docs(images): bioflow-pan 镜像 panfamily 模块修复记录\n\n- 根因: conda activate.d 注入的 PYTHONPATH 指向宿主路径,容器内断链,\n 所有 from panfamily.io import 失败\n- 修复: panfamily 模块(68K)COPY 进 site-packages + 删断链脚本;\n 新镜像已 load 176,panfamily.io read_fasta 端到端通过(49432 序列)\n\nCo-Authored-By: Claude Fable 5 <noreply@anthropic.com> admin 2026-09-14 22:05:45 +08:00
  • 653d2211cf fix(extension): inject_executor 废弃——曾把生信 stage runner 函数塞进扩展 store adminandClaude Fable 5 2026-09-14 17:30:09 +08:00
  • 4128fbf3bf fix(extension): 执行器守卫与注入修复——active_store 不存在+占位误判已注入适配器 adminandClaude Fable 5 2026-09-14 17:27:49 +08:00
  • 68b45c60a0 fix(extension): 扩展意图检测提前到 route_intent 之前 adminandClaude Fable 5 2026-09-14 17:24:27 +08:00
  • c0b3026209 fix(extension): docker 镜像引用双后缀拼接——已含 tag 的自动镜像再补 suffix adminandClaude Fable 5 2026-09-14 16:01:28 +08:00
  • bb560d7bea fix(extension): 自动镜像生成两缺陷——Dockerfile FROM 顺序+timeout 参数名 adminandClaude Fable 5 2026-09-14 15:59:33 +08:00
  • 2a6315e615 docs(extension): 测试报告——TL 接管测试循环,B1-B4 缺陷修复,全量测试绿 adminandClaude Fable 5 2026-09-14 15:10:10 +08:00
  • 812decf310 fix(extension): 测试隔离+注入惰性适配+chat_stream 意图接线 adminandClaude Fable 5 2026-09-14 15:09:15 +08:00
  • 3b16397baf feat(extension): TL 接线——executor 适配/validate 帧/form_defaults/context 注入 adminandClaude Fable 5 2026-09-14 13:53:44 +08:00
  • 4fa758d602 Merge branch 'dev/extension-backend' into feature/bioflow-conversation-orchestration admin 2026-09-14 13:49:25 +08:00
  • d95c2b5761 Merge branch 'dev/extension-frontend' into feature/bioflow-conversation-orchestration admin 2026-09-14 13:49:18 +08:00
  • 4866b0408a feat(bioflow): extension lifecycle backend (P0) - spec whitelist, state machine, AI build, intent layers adminandClaude Fable 5 2026-09-14 13:48:37 +08:00
  • 03e6ff508a feat(extension-frontend): 扩展分析前端引导卡 + 事件分派(Dev-C) adminandClaude Fable 5 2026-09-14 13:43:20 +08:00
  • 79b4c7c52c feat(extension): docker 执行内核入口 + 176 本地自动镜像生成(并行链路) adminandClaude Fable 5 2026-09-14 13:36:18 +08:00
  • f0a1711ebc fix(aqua): batch_runner path sanitize, loader batch embed, alias expansion adminandClaude Fable 5 2026-09-13 01:06:38 +08:00
  • 688edba169 docs(aqua): backfill measured budget numbers from 530-paper pilot adminandClaude Fable 5 2026-09-12 22:20:06 +08:00
  • 730692a1f6 feat(aqua): KB build tooling, aqua configs, QA artifacts (P1) adminandClaude Fable 5 2026-09-12 22:19:40 +08:00
  • a9a0ece4b4 feat(aqua): aqua extraction chain v16_aqua_1_0 (copy of v16_1_2, aquatized) adminandClaude Fable 5 2026-09-12 22:19:32 +08:00
  • 00c77aa323 feat(aqua): figure chain dual-key generalization (PMCID/DOI) adminandClaude Fable 5 2026-09-12 22:19:25 +08:00
  • 6bcb88cf76 docs(deploy): 部署方法 Skill 化——含换机/无生信/自定义库路径变体与提示词示例 adminandClaude Fable 5 2026-09-12 20:05:57 +08:00
  • 037790c609 fix(aqua): DOI pairing decoder and MD extraction regexes adminandClaude Fable 5 2026-09-12 19:46:13 +08:00
  • afa7cce938 feat(aqua): unlock normalized KB identity via env with plant fallback - normalized_release EXPECTED_RELEASE defaults to NORMALIZED_RELEASE_ID (plant value) - from_env falls back to constant on empty env; backend_guard uses env-or-constant - start.sh sources env/active_library.env after prod.env (qa + legacy-rag) - build_all.sh --library <name|dir> renders library identity (no name whitelist) - add kb-libraries skeleton (plant/aqua identity cards) and tooling/aqua_kb Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> admin 2026-09-12 19:10:08 +08:00
  • 7444edf525 docs(acceptance): r4 六项缺陷验收用例与 TL 实测记录 adminandClaude Fable 5 2026-09-12 18:40:08 +08:00
  • 8d115f8f1c fix(ui): SourceRow 徽标宽度级联修正(特异性提升) adminandClaude Fable 5 2026-09-12 18:38:07 +08:00
  • 18e69046f1 fix(ui): 文献来源 SourceRow 徽标与标题重叠 adminandClaude Fable 5 2026-09-12 18:32:51 +08:00
  • 4b5b501463 fix(statusbar): loadSession 恢复时重建生信派生 pipeline 块 adminandClaude Fable 5 2026-09-12 18:25:44 +08:00
  • 7037a1d5d8 fix(deploy): restart 脚本 lsof 只取 LISTEN 态进程 adminandClaude Fable 5 2026-09-12 18:22:11 +08:00
  • 36fc2a7250 fix(statusbar): 生信任务活跃期回退消息列表点亮 4 点 adminandClaude Fable 5 2026-09-12 18:22:03 +08:00
  • 9d7ed1bdd3 feat(deploy): start_all.sh 编排生信服务(存在则启动/重启) adminandClaude Fable 5 2026-09-12 16:55:47 +08:00
  • f74b27daa1 fix(statusbar): 生信对话 4 个 agent 点不随相位点亮 adminandClaude Fable 5 2026-09-12 16:32:21 +08:00
  • 00fe6a379e docs(debug): r4 缺陷记录(六项缺陷+过程问题 P1-P7+环境部署问题 E1-E10,含根因/修复/验证/终态) admin 2026-09-12 09:32:59 +08:00
  • faa8686461 fix(figures): PMC 解析冷连接重试——176 实测首次 TLS 握手 10s+ 超时,重连秒回;失败重试一次走热路径 bugfix-r4-20260912 admin 2026-09-12 01:55:42 +08:00
  • 8e4fce062a fix(figures): PMC 外网超时 5s→15s——176 实测 EBI 2-8s 波动,5s 超时致已解析图片被整体吞掉 admin 2026-09-12 01:41:37 +08:00
  • 04bf099faf docs(deploy): DEPLOY_FLOW 增补 §5e figures 本地图片源/§5f BFF 重启陷阱/§5g r4 部署清单 admin 2026-09-12 00:10:45 +08:00
  • d54419f040 fix(r4-28v4): chat 候选腐烂根治——Qdrant 条目 paper_id 派生 DOI/PMCID 回填引用 adminandClaude Fable 5 2026-09-11 17:17:25 +08:00
  • 0252d52425 fix(r4-28v3): 检索模式关闭图证据检索(use_neo4j),arginine 150s->亚秒 adminandClaude Fable 5 2026-09-11 16:47:00 +08:00
  • 2895cd8497 Merge branch 'debug/backend1' into feature/bioflow-conversation-orchestration admin 2026-09-11 16:35:13 +08:00