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sjandClaude Opus 5 c59f346037 test: skip stale PPI/KaKs circuit-breaker cases 
主分支已完成 PPI/KaKs 修复并将 ppiKaksTemporaryCircuitBreakerEnabled 置为
false，这 4 个用例仍假设临时熔断处于开启态，先标记 skip，待按新状态重写。

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
2026-08-21 11:31:54 +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
apps
Merge remote-tracking branch 'origin/master'
2026-08-21 11:06:22 +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
fix: integrate deployed reports with PPI KaKs handoff
2026-08-11 04:48:38 +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
gfa_core
Merge remote-tracking branch 'origin/master'
2026-08-21 11:06:22 +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
test: skip stale PPI/KaKs circuit-breaker cases
2026-08-21 11:31:54 +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
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +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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