wtx 7399b0bf14 Merge origin/master before analysis handoff push

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.codegraph

Initial commit: PlantAI-dev

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.local/meme-4.11.2-mpi

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.planning

Initial commit: PlantAI-dev

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.recovery

Initial commit: PlantAI-dev

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

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

.superpowers

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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

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

apps

Merge origin/master before analysis handoff push

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assets

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benchmarks/plantgenebench

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

codeMiaoshu

Initial commit: PlantAI-dev

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config

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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

fix: delegate analysis planning from main agent

2026-08-08 10:40:01 +08:00

enviroment

Initial commit: PlantAI-dev

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extension_code_data_staging/genome_shell_30

Initial commit: PlantAI-dev

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extension_stages

Initial commit: PlantAI-dev

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

gfa_core

Merge origin/master before analysis handoff push

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graphify-out

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

manuscript/plantai_aiia_zh

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memory

Add memory directory

2026-08-07 09:39:30 +08:00

models/bge-m3_from_web

Initial commit: PlantAI-dev

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prompts

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rollback_backups

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scripts

Initial commit: PlantAI-dev

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skills

Initial commit: PlantAI-dev

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test_integration

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

test-results/completed-stage-pruning

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

tests

Merge origin/master before analysis handoff push

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tools

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validation/rnaseq_design_20260719

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w/final

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.env.example

Initial commit: PlantAI-dev

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.gitignore

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.gitignore.opensource

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.revision_memory.json

Initial commit: PlantAI-dev

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.run_ident_enhance.py.swp

Initial commit: PlantAI-dev

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.tmp_meme_parallel_test.fa

Initial commit: PlantAI-dev

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=1.0.0,

Initial commit: PlantAI-dev

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AGENTS.md

Initial commit: PlantAI-dev

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ANALYSIS_FLOW_ANALYSIS.md

Initial commit: PlantAI-dev

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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

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check_cost.py

Initial commit: PlantAI-dev

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CLAUDE.md

Initial commit: PlantAI-dev

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cleanup_agents.sh

Initial commit: PlantAI-dev

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CONVERSATION_MANAGER_REPORT.md

Initial commit: PlantAI-dev

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data

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

download_prjna530826_rnaseq_aria2c.sh

Initial commit: PlantAI-dev

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download_prjna530826_rnaseq_aria2c.sh.bak

Initial commit: PlantAI-dev

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enable_persistent_memory.py

Initial commit: PlantAI-dev

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example_task_with_wechat.py

Initial commit: PlantAI-dev

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

Initial commit: PlantAI-dev

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Ft.SPL.expression.gene-cor.txt

Initial commit: PlantAI-dev

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

Initial commit: PlantAI-dev

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

Initial commit: PlantAI-dev

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Ft.SPL.expression.gene-exp.txt

Initial commit: PlantAI-dev

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get_wechat_id.py

Initial commit: PlantAI-dev

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

IDENTIFY_AGENT_FLOW.md

Initial commit: PlantAI-dev

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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

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

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

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Os.NAC_promoter_05_upset_data.csv

Initial commit: PlantAI-dev

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pipeline_backend_patch.py

Initial commit: PlantAI-dev

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

PLAN-REVIEW-LOG.md

Initial commit: PlantAI-dev

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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

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PRJNA530826.fastq.md5

Initial commit: PlantAI-dev

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PROJECT_PLAN.md

Initial commit: PlantAI-dev

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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

restart_with_prompts.sh

Initial commit: PlantAI-dev

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REVISION_2026-04-13.md

Initial commit: PlantAI-dev

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rnaseq.before_salmon_downgrade.txt

Initial commit: PlantAI-dev

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rnaseq.before_salmon_downgrade.yml

Initial commit: PlantAI-dev

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run_kaks_manual.sh

Initial commit: PlantAI-dev

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run_tests.sh

Initial commit: PlantAI-dev

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

SECRET_AUDIT.md

Initial commit: PlantAI-dev

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session_storage.py

Initial commit: PlantAI-dev

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

start_celery_7880.sh

Initial commit: PlantAI-dev

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

start_celery_9000.sh

1. main.py 指向了新extension_stage_lightweight.api接口

2026-08-05 20:15:29 +08:00

start_celery_port9000.sh

Initial commit: PlantAI-dev

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

start_celery.sh

Initial commit: PlantAI-dev

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

start_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

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

start-webui.sh

Initial commit: PlantAI-dev

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

tasks.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

test_agent_manual.sh

Initial commit: PlantAI-dev

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

test_annotation_skill.sh

Initial commit: PlantAI-dev

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test_full_integration.sh

Initial commit: PlantAI-dev

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test_langgraph_state.py

Initial commit: PlantAI-dev

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test_rnaseq_align.sh

Initial commit: PlantAI-dev

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test_router.py

Initial commit: PlantAI-dev

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test_tree_plot.sh

Initial commit: PlantAI-dev

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update_prompts.py

Initial commit: PlantAI-dev

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validate_js.py

Initial commit: PlantAI-dev

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

VUE3_CONVERSATION_SIDEBAR_REPORT.md

Initial commit: PlantAI-dev

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wechat_bot.py

Initial commit: PlantAI-dev

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

WECHAT_INTEGRATION.md

Initial commit: PlantAI-dev

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wechat_integration.py

Initial commit: PlantAI-dev

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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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