sj 55338be930 merge: resolve .gitignore conflict, keep remote memory ignore pattern

2026-08-09 09:05:11 +08:00

..

agents

Initial commit: PlantAI-dev

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

skills

Initial commit: PlantAI-dev

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

test_admin_ops_contract.py

Initial commit: PlantAI-dev

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

test_agent_chat_actions.py

fix: preserve confirmed species roles in agent planning

2026-08-05 15:42:32 +08:00

test_autofill_entrypoints.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_celery_gwas_artifact_validation.py

Initial commit: PlantAI-dev

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

test_check_rnaseq_strandness.py

Initial commit: PlantAI-dev

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

test_combo_scoped_artifacts.py

Initial commit: PlantAI-dev

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

test_combo_upstream_failure.py

Initial commit: PlantAI-dev

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

test_deepseek_summary_report.py

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

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

test_effective_member_resolver.py

fix: allow reordered subfamily member records

2026-08-06 21:32:49 +08:00

test_extension_api_converter.py

Initial commit: PlantAI-dev

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

test_extension_stage_agent.py

Initial commit: PlantAI-dev

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

test_extension_stage_api_spec_sanitizer.py

Initial commit: PlantAI-dev

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

test_extension_stage_audit_and_fixtures.py

Initial commit: PlantAI-dev

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

test_extension_stage_code_artifacts.py

Initial commit: PlantAI-dev

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

test_extension_stage_diagnostics.py

Initial commit: PlantAI-dev

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

test_extension_stage_golden_comparators.py

Initial commit: PlantAI-dev

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

test_extension_stage_golden_runner_semantic.py

Initial commit: PlantAI-dev

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

test_extension_stage_input_binding.py

Initial commit: PlantAI-dev

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

test_extension_stage_intent.py

Initial commit: PlantAI-dev

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

test_extension_stage_lightweight_api.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_extension_stage_lightweight_command_model.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_extension_stage_lightweight_confirmation.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_extension_stage_lightweight_deepseek_semantics.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_extension_stage_lightweight_evidence.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_extension_stage_lightweight_fact_contract.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_extension_stage_lightweight_frontend_contract.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_extension_stage_lightweight_process_control.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_extension_stage_lightweight_raw_package_normalizer.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_extension_stage_lightweight_replay.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_extension_stage_lightweight_runtime_binding_resolver.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_extension_stage_lightweight_runtime_binding.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_extension_stage_lightweight_runtime_package.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_extension_stage_lightweight_semantic_model.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_extension_stage_lightweight_semantic_repair.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_extension_stage_lightweight_service.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_extension_stage_lightweight_shell_binding.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_extension_stage_lightweight_shell_pipeline.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_extension_stage_lightweight_target_launchers.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_extension_stage_publish_gate.py

Initial commit: PlantAI-dev

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

test_extension_stage_repair_candidates.py

Initial commit: PlantAI-dev

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

test_extension_stage_routing.py

Initial commit: PlantAI-dev

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

test_extension_stage_spec_v2.py

Initial commit: PlantAI-dev

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

test_extension_stage_template_cases.py

Initial commit: PlantAI-dev

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

test_extension_stage_template_gate.py

Initial commit: PlantAI-dev

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

test_extension_stage_template_validation.py

Initial commit: PlantAI-dev

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

test_extension_stage_tooling_audit.py

Initial commit: PlantAI-dev

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

test_extension_stage_wrapper_builder.py

Initial commit: PlantAI-dev

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

test_frontend_cpu_monitor_contract.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_frontend_execution_indicator_recovery.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_gene_family_report_intent.py

feat: add gene family result reports

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

test_gene_family_report_triggers.py

feat: add gene family result reports

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

test_gene_family_report_wiring.py

feat: add gene family result reports

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

test_gene_family_report.py

feat: add gene family result reports

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

test_gene_family_scope_reference_roots.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_gwas_chain_contracts.py

Initial commit: PlantAI-dev

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

test_gwas_chain_intent.py

Initial commit: PlantAI-dev

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

test_gwas_cov_stage21.py

Initial commit: PlantAI-dev

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

test_gwas_emmax_backend.py

Initial commit: PlantAI-dev

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

test_gwas_emmax_plot_backend.py

Initial commit: PlantAI-dev

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

test_gwas_emmax_plot_stage25.py

Initial commit: PlantAI-dev

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

test_gwas_emmax_stage24.py

Initial commit: PlantAI-dev

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

test_gwas_fmt_input_resolution.py

Initial commit: PlantAI-dev

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

test_gwas_fmt_manifest_v1.py

Initial commit: PlantAI-dev

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

test_gwas_fmt_postflight_ui.py

Initial commit: PlantAI-dev

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

test_gwas_fmt_results_display.py

Initial commit: PlantAI-dev

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

test_gwas_fmt_stage18.py

Initial commit: PlantAI-dev

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

test_gwas_kinship_backend.py

Initial commit: PlantAI-dev

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

test_gwas_kinship_results_display.py

Initial commit: PlantAI-dev

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

test_gwas_kinship_stage19.py

Initial commit: PlantAI-dev

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

test_gwas_legacy_lineage.py

Initial commit: PlantAI-dev

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

test_gwas_mlm_backend.py

Initial commit: PlantAI-dev

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

test_gwas_mlm_frontend_handoff.py

Initial commit: PlantAI-dev

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

test_gwas_mlm_planning_identity.py

Initial commit: PlantAI-dev

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

test_gwas_mlm_stage22.py

Initial commit: PlantAI-dev

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

test_gwas_natural_language_trigger.py

Initial commit: PlantAI-dev

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

test_gwas_plot_backend.py

Initial commit: PlantAI-dev

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

test_gwas_plot_stage23.py

Initial commit: PlantAI-dev

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

test_gwas_prefix_frontend_contract.py

Initial commit: PlantAI-dev

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

test_gwas_root_inputs.py

Initial commit: PlantAI-dev

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

test_gwas_scientific_identity.py

Initial commit: PlantAI-dev

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

test_gwas_scope_status_results.py

Initial commit: PlantAI-dev

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

test_gwas_tassel_glm_backend.py

Initial commit: PlantAI-dev

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

test_gwas_tassel_glm_stage26.py

Initial commit: PlantAI-dev

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

test_gwas_trait_cov_backend.py

Initial commit: PlantAI-dev

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

test_gwas_trait_stage20.py

Initial commit: PlantAI-dev

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

test_gwas_upstream_manifest.py

Initial commit: PlantAI-dev

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

test_gwas_wgs_path_configuration.py

Initial commit: PlantAI-dev

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

test_id_resolution.py

Initial commit: PlantAI-dev

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

test_identify_blast_direction.py

Initial commit: PlantAI-dev

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

test_identify_hmm_models.py

Initial commit: PlantAI-dev

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

test_intent_species_roles.py

fix: preserve species roles through confirmation

2026-08-07 08:57:22 +08:00

test_interpretation_claim_layers.py

Initial commit: PlantAI-dev

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

test_legacy_manifest_alias.py

Initial commit: PlantAI-dev

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

test_manifest_identity_postflight.py

Initial commit: PlantAI-dev

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

test_methodology_bridge.py

Initial commit: PlantAI-dev

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

test_msa_region_plot_scope.py

Initial commit: PlantAI-dev

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

test_ncbi_fetch_intent.py

Initial commit: PlantAI-dev

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

test_persistent_conversation_job_isolation.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_pipeline_backend_execution_env.py

Initial commit: PlantAI-dev

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

test_pipeline_backend_member_routing.py

Initial commit: PlantAI-dev

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

test_pop_ld_decay_stage.py

Initial commit: PlantAI-dev

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

test_pop_ld_plotter.py

Initial commit: PlantAI-dev

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

test_pop_pca_stage.py

Initial commit: PlantAI-dev

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

test_pop_phylogeny_stage.py

Initial commit: PlantAI-dev

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

test_pop_snp_density_stage.py

Initial commit: PlantAI-dev

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

test_pop_structure_stage.py

Initial commit: PlantAI-dev

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

test_population_chain_foundation.py

Initial commit: PlantAI-dev

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

test_population_chain_integration.py

Initial commit: PlantAI-dev

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

test_population_manifest.py

Initial commit: PlantAI-dev

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

test_population_stage_runtime.py

Initial commit: PlantAI-dev

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

test_ppi_batch_owner_isolation.py

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

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

test_ppi_frontend_display_contract.py

Initial commit: PlantAI-dev

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

test_ppi_id_resolution.py

Initial commit: PlantAI-dev

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

test_ppi_numeric_taxon_task4.py

Initial commit: PlantAI-dev

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

test_ppi_ortholog_owner_identity_task5b.py

Initial commit: PlantAI-dev

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

test_ppi_owner_scheduling_task5.py

Initial commit: PlantAI-dev

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

test_ppi_provenance_task6.py

Initial commit: PlantAI-dev

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

test_ppi_snapshot_preflight_task3.py

Initial commit: PlantAI-dev

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

test_ppi_string_policy.py

Initial commit: PlantAI-dev

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

test_ppi_target_identity.py

Initial commit: PlantAI-dev

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

test_pysam_bcftools_wrapper.py

Initial commit: PlantAI-dev

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

test_reference_bundle_download_progress.py

Initial commit: PlantAI-dev

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

test_reference_bundle_download_state.py

Initial commit: PlantAI-dev

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

test_reference_bundle_task_status.py

Initial commit: PlantAI-dev

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

test_resource_routing.py

Initial commit: PlantAI-dev

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

test_result_browser_persistence.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_rnaseq_context.py

Initial commit: PlantAI-dev

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

test_rnaseq_de_control_roles.py

Initial commit: PlantAI-dev

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

test_rnaseq_env_and_threads.py

Initial commit: PlantAI-dev

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

test_rnaseq_fastp_defaults.py

Initial commit: PlantAI-dev

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

test_rnaseq_m3_m4_priority.py

Initial commit: PlantAI-dev

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

test_rnaseq_m3_stratified_time.py

Initial commit: PlantAI-dev

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

test_rnaseq_quant_expression_policy.py

Initial commit: PlantAI-dev

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

test_rnaseq_report.py

feat: add evidence-bound RNA-seq result reports

2026-08-09 01:37:00 +08:00

test_rnaseq_stage_status.py

Initial commit: PlantAI-dev

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

test_router_analysis_handoff_boundary.py

fix: delegate analysis planning from main agent

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

test_run_domain_scope_protein_count.py

Initial commit: PlantAI-dev

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

test_stage_status_subfamily_routes.py

Initial commit: PlantAI-dev

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

test_stage_tool_tree_passthrough.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_start_plantai_9000_script.py

Initial commit: PlantAI-dev

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

test_string_ppi_production_wiring_red.py

Initial commit: PlantAI-dev

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

test_string_species_registry.py

Initial commit: PlantAI-dev

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

test_string_species_snapshot.py

Initial commit: PlantAI-dev

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

test_subfamily_confirm_member_promotion.py

fix: allow reordered subfamily member records

2026-08-06 21:32:49 +08:00

test_subfamily_confirm_source_scope.py

Initial commit: PlantAI-dev

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

test_subfamily_evidence_scope.py

Initial commit: PlantAI-dev

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

test_subfamily_prediction_plan.py

fix: preserve species roles through confirmation

2026-08-07 08:57:22 +08:00

test_subfamily_review_source_manifest.py

Initial commit: PlantAI-dev

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

test_task_status_attachment.py

Initial commit: PlantAI-dev

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

test_wgs_align_backend.py

Initial commit: PlantAI-dev

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

test_wgs_align_cli.py

Initial commit: PlantAI-dev

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

test_wgs_bam_qc_backend.py

Initial commit: PlantAI-dev

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

test_wgs_bam_qc_cli.py

Initial commit: PlantAI-dev

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

test_wgs_chain_contracts.py

Initial commit: PlantAI-dev

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

test_wgs_chain_intent.py

Initial commit: PlantAI-dev

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

test_wgs_frontend_contract.py

Initial commit: PlantAI-dev

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

test_wgs_gvcf_combine_backend.py

Initial commit: PlantAI-dev

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

test_wgs_gvcf_combine_cli.py

Initial commit: PlantAI-dev

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

test_wgs_haplotype_calling_backend.py

Initial commit: PlantAI-dev

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

test_wgs_haplotype_calling_cli.py

Initial commit: PlantAI-dev

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

test_wgs_identity_materialization.py

Initial commit: PlantAI-dev

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

test_wgs_impute_backend.py

Initial commit: PlantAI-dev

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

test_wgs_impute_cli.py

Initial commit: PlantAI-dev

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

test_wgs_index_backend.py

Initial commit: PlantAI-dev

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

test_wgs_index_cli.py

Initial commit: PlantAI-dev

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

test_wgs_joint_genotyping_backend.py

Initial commit: PlantAI-dev

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

test_wgs_joint_genotyping_cli.py

Initial commit: PlantAI-dev

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

test_wgs_maf_missing_filter_backend.py

Initial commit: PlantAI-dev

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

test_wgs_maf_missing_filter_cli.py

Initial commit: PlantAI-dev

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

test_wgs_markdup_backend.py

Initial commit: PlantAI-dev

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

test_wgs_markdup_cli.py

Initial commit: PlantAI-dev

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test_wgs_planning_input_resolution.py

Initial commit: PlantAI-dev

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test_wgs_qc_backend.py

Initial commit: PlantAI-dev

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

test_wgs_qc_cli.py

Initial commit: PlantAI-dev

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

test_wgs_samples.py

Initial commit: PlantAI-dev

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test_wgs_scientific_identity.py

Initial commit: PlantAI-dev

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test_wgs_scope_status_results.py

Initial commit: PlantAI-dev

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test_wgs_stage_tool_executor.py

Initial commit: PlantAI-dev

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test_wgs_upstream_manifest.py

Initial commit: PlantAI-dev

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test_wgs_variant_filter_backend.py

Initial commit: PlantAI-dev

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

test_wgs_variant_filter_cli.py

Initial commit: PlantAI-dev

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test_wgs_variant_select_backend.py

Initial commit: PlantAI-dev

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

test_wgs_variant_select_cli.py

Initial commit: PlantAI-dev

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