potaser 81b0a7045d 修复：对话触发轻量拓展分析三缺陷（帮助意图误判、Phase A 弱命中抢占、LLM 空响应重试）

2026-08-27 11:22:08 +08:00

.codegraph

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

.local/meme-4.11.2-mpi

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

.planning

feat: deepseek summary agent + clean old memory logs + merge prep

2026-08-09 09:04:27 +08:00

.recovery

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

.revision-ppi-kaks-plan-pruning-v1

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

.superpowers

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

.tmp_meme_mpi

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

.tmp_meme_parallel_test_out

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

.worktrees/router-error-detail

chore: track worktree checkout, lightweight extension staging and wgs manifests

2026-08-21 11:49:48 +08:00

apps

修复：对话触发轻量拓展分析三缺陷（帮助意图误判、Phase A 弱命中抢占、LLM 空响应重试）

2026-08-27 11:22:08 +08:00

assets

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

benchmarks/plantgenebench

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

codeMiaoshu

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

config

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

contrib/methodology-rag-substage-progress

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

docs

测试：轻量拓展分析 NL 触发两轮测试交付（单测 79 + 集成 23 + 前端契约 20）

2026-08-27 00:34:19 +08:00

enviroment

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

extension_code_data_staging/genome_shell_30

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

extension_stages

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

extension_stages_lightweight

全量扩展分析样本验证测试

2026-08-24 20:52:42 +08:00

gfa_core

修复：对话触发轻量拓展分析三缺陷（帮助意图误判、Phase A 弱命中抢占、LLM 空响应重试）

2026-08-27 11:22:08 +08:00

graphify-out

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

manuscript/plantai_aiia_zh

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

memory

fix: restore memory logs and keep absolute data symlink

2026-08-21 11:06:49 +08:00

models/bge-m3_from_web

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

prompts

feat: deepseek summary agent + clean old memory logs + merge prep

2026-08-09 09:04:27 +08:00

rollback_backups

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

scripts

fix(runtime): standardize 9000 startup and isolate project services

2026-08-10 10:57:49 +08:00

skills

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

test_integration

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

test-results/completed-stage-pruning

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

tests

测试：轻量拓展分析 NL 触发两轮测试交付（单测 79 + 集成 23 + 前端契约 20）

2026-08-27 00:34:19 +08:00

tools

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

validation/rnaseq_design_20260719

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

w/final

chore: track worktree checkout, lightweight extension staging and wgs manifests

2026-08-21 11:49:48 +08:00

.env.example

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

.gitignore

feat: deepseek summary agent + clean old memory logs + merge prep

2026-08-09 09:04:27 +08:00

.gitignore.opensource

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

.revision_memory.json

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

.run_ident_enhance.py.swp

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

.tmp_meme_parallel_test.fa

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

=1.0.0,

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

AGENTS.md

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

ANALYSIS_FLOW_ANALYSIS.md

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

At.HD-ZIP.short_names.subfamily.locus.tsv

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

At.HD-ZIP.short_names.subfamily.tsv

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

celery_app.py

feat: 轻量拓展分析 + WGS2GWAS 阶段支持 + 结果区域重构 + 物种角色解析增强 + 会话 Job 隔离

2026-08-05 09:40:45 +08:00

CHANGELOG_2026-04-14.md

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

check_cost.py

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

CLAUDE.md

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

cleanup_agents.sh

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

CONVERSATION_MANAGER_REPORT.md

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

data

fix: restore memory logs and keep absolute data symlink

2026-08-21 11:06:49 +08:00

download_prjna530826_rnaseq_aria2c.sh

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

download_prjna530826_rnaseq_aria2c.sh.bak

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

enable_persistent_memory.py

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

example_task_with_wechat.py

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

Ft.SPL.expression.gene-cor.heatmap.pdf

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

Ft.SPL.expression.gene-cor.txt

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

Ft.SPL.expression.gene-exp.heatmap.pdf

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

Ft.SPL.expression.gene-exp.hist.pdf

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

Ft.SPL.expression.gene-exp.txt

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

get_wechat_id.py

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

IDENTIFY_AGENT_FLOW.md

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

input

chore: 清理旧 data 目录数据文件，新增 data/input/workspace 路径入口

2026-08-05 14:51:04 +08:00

input.shared_bbav5_7880_bak_link

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

interproscanpy311.yaml

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

manage_plantai.sh

feat:sync-report-workflows-and-migration-runtime

2026-08-10 11:40:20 +08:00

MEMORY.md

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

notify_integration.py

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

OPEN_SOURCE_EXCLUDE.md

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

Os.NAC_promoter_05_upset_data.csv

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

pipeline_backend_patch.py

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

PLAN-REVIEW-LOG.md

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

PLAN.md

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

PRJNA530826.aria2c.urls.txt

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

PRJNA530826.ena_fastq.tsv

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

PRJNA530826.fastq.md5

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

PROJECT_PLAN.md

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

pytest.ini

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

restart_plantai_9000.sh

增加了启动时可以指定web端口的功能；将主页运行结果按钮挪到了拓展分析title的后方

2026-08-06 19:34:11 +08:00

REVISION_2026-04-13.md

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

rnaseq.before_salmon_downgrade.txt

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

rnaseq.before_salmon_downgrade.yml

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

run_kaks_manual.sh

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

run_tests.sh

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

SECRET_AUDIT.md

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

session_storage.py

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

start_celery_9000.sh

feat:sync-report-workflows-and-migration-runtime

2026-08-10 11:40:20 +08:00

start_plantai_9000.sh

feat:sync-report-workflows-and-migration-runtime

2026-08-10 11:40:20 +08:00

start_wechat_bot.sh

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

start_wechat_service.sh

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

tasks.py

feat: add gene family result reports

2026-08-09 04:32:28 +08:00

test_agent_manual.sh

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

test_annotation_skill.sh

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

test_full_integration.sh

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

test_langgraph_state.py

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

test_rnaseq_align.sh

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

test_router.py

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

test_tree_plot.sh

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

update_prompts.py

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

validate_js.py

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

VUE3_CONVERSATION_SIDEBAR_REPORT.md

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

wechat_bot.py

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

WECHAT_INTEGRATION.md

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

wechat_integration.py

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

wechat_service.py

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

wechat_task_bridge.py

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

WORKLINE.md

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

workspace

chore: 清理旧 data 目录数据文件，新增 data/input/workspace 路径入口

2026-08-05 14:51:04 +08:00

workspace.shared_bbav5_7880_bak_link

Initial commit: PlantAI-dev

2026-08-03 18:42:47 +08:00

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