remove: all 科研读图指南 and Template references from project

2026-07-22 06:50:53 +00:00 · 2026-04-22 23:20:49 +08:00 · 2026-04-22 23:20:49 +08:00 · 89374cb35f
commit 89374cb35f
parent 29949395ef
10 changed files with 5 additions and 122 deletions
--- a/AGENTS.md
+++ b/AGENTS.md
@ -92,8 +92,6 @@ Zotero 添加文献
 │   │   │       └── figure-map.json    ← 图表索引（自动创建）
 │   │   └── worker/scripts/
 │   │       └── literature_pipeline.py ← 核心脚本
-│   ├── Template/
-│   │   └── 科研读图指南.md            ← 图表阅读参考
 │   └── Zotero/                        ← Junction/Symlink 到 Zotero 数据目录
 │
 ├── .opencode/                         ← OpenCode Agent 配置（自动创建）
--- a/README.md
+++ b/README.md
@ -48,7 +48,6 @@ python setup.py

 - [安装指南](docs/INSTALLATION.md)
 - [使用指南](docs/USAGE.md)
- [读图指南](99_System/Template/科研读图指南.md)

 ## License

--- a/docs/INSTALLATION.md
+++ b/docs/INSTALLATION.md
@ -115,9 +115,6 @@ Copy the following files from the repository to your vault:
 # Copy scripts
 cp -r scripts/* "{vault_path}/99_System/PaperForge/worker/scripts/"

-# Copy templates
-cp -r templates/* "{vault_path}/99_System/Template/"
-
 # Copy AGENTS.md
 cp AGENTS.md "{vault_path}/AGENTS.md"
 ```
--- a/paperforge.json
+++ b/paperforge.json
@ -21,7 +21,6 @@
  "updateable_paths": [
    "skills/",
    "pipeline/",
-    "templates/",
    "command/",
    "scripts/"
  ],
--- a/pipeline/worker/scripts/literature_pipeline.py
+++ b/pipeline/worker/scripts/literature_pipeline.py
@ -2391,7 +2391,7 @@ PROTECTED_PATHS = {
    "99_System/PaperForge/candidates",
    ".env", "AGENTS.md",
 }
-UPDATEABLE_PATHS = ["skills", "pipeline", "templates", "command", "scripts"]
+UPDATEABLE_PATHS = ["skills", "pipeline", "command", "scripts"]


 def _color(text: str, c: str = "") -> str:
--- a/scripts/setup.py
+++ b/scripts/setup.py
@ -116,8 +116,7 @@ def configure_vault_paths(vault_path: Path) -> dict:
    
    # Build derived paths
    paths["pipeline_path"] = f"{paths['system_dir']}/PaperForge"
-    paths["template_path"] = f"{paths['system_dir']}/Template"
-    paths["literature_path"] = f"{paths['resources_dir']}/{paths['literature_dir']}"
+        paths["literature_path"] = f"{paths['resources_dir']}/{paths['literature_dir']}"
    
    return paths
    
@ -257,9 +256,6 @@ def create_directory_structure(vault_path: Path, paths: dict) -> None:
        f"{paths['pipeline_path']}/indexes",
        f"{paths['pipeline_path']}/exports",
        
-        # Template directories
-        f"{paths['template_path']}",
-        
        # Zotero junction point
        f"{paths['system_dir']}/Zotero",
        
@ -293,7 +289,7 @@ def create_env_file(vault_path: Path, config: dict, paths: dict) -> None:
        "# Path Configuration",
        f"PAPERFORGE_SYSTEM_DIR={paths['system_dir']}",
        f"PAPERFORGE_PIPELINE_PATH={paths['pipeline_path']}",
-        f"PAPERFORGE_TEMPLATE_PATH={paths['template_path']}",
+        f"PAPERFORGE_RESOURCES_PATH={paths['literature_path']}",
        f"PAPERFORGE_VAULT_PATH={vault_path}",
    ]
    
@ -412,8 +408,6 @@ Zotero 添加文献
 │   │   │       └── figure-map.json             ← 图表索引（自动创建）
 │   │   └── worker/scripts/
 │   │       └── literature_pipeline.py          ← 核心脚本
-│   ├── Template/
-│   │   └── 科研读图指南.md                     ← 图表阅读参考
 │   └── Zotero/                                 ← Junction/Symlink 到 Zotero 数据目录
 │
 ├── {agent_config['skill_dir']}/                ← {agent_config['name']} Skill 目录
@ -831,26 +825,6 @@ def deploy_workflow_scripts(vault_path: Path, agent_key: str, agent_config: dict
                    fail_count += 1
            print_success(f"Deployed {len(chart_files)} chart reading guides")
    
-    # Deploy template files
-    template_files = [
-        ("templates/科研读图指南.md",
-         f"{paths['template_path']}/科研读图指南.md"),
-    ]
-    
-    for src_rel, dst_rel in template_files:
-        src_path = repo_root / src_rel
-        dst_path = vault_path / dst_rel
-        
-        if src_path.exists():
-            if safe_copy(src_path, dst_path):
-                print_success(f"Deployed template: {src_rel}")
-                success_count += 1
-            else:
-                fail_count += 1
-        else:
-            print_warning(f"Template not found (skipping): {src_rel}")
-            fail_count += 1
-    
    # Deploy agent commands
    command_src = repo_root / "command"
    command_dst = vault_path / ".opencode/command"
--- a/scripts/validate_setup.py
+++ b/scripts/validate_setup.py
@ -125,9 +125,7 @@ def validate_ld_deep(vault_path: str) -> list[tuple[bool, str]]:
    results.append((ok, msg))
    
    # Check chart reading guides
-    chart_guide_dir = vault_dir / "99_System" / "Template" / "读图指南"
-    ok, msg = check_path("Chart reading guides directory", chart_guide_dir, "dir")
-    results.append((ok, msg))
+    
    
    if ok:
        # Count guide files
--- a/setup_wizard.py
+++ b/setup_wizard.py
@ -985,7 +985,6 @@ python pipeline/worker/scripts/literature_pipeline.py --vault . <command>
 ### 详细文档

 - 安装后指南：`AGENTS.md`
- 图表阅读指南：`99_System/Template/科研读图指南.md`
 - GitHub: https://github.com/LLLin000/PaperForge
        """)
        yield Horizontal(
--- a/templates/科研读图指南.md
+++ b/templates/科研读图指南.md
@ -1,81 +0,0 @@
-# 科研读图指南
-
-## 使用方式
-
-在精读 **Figure-by-Figure** 时，识别图表类型，然后加载对应子指南。
-
-**识别方法**：
-1. 看标题/caption中的关键词
-2. 看图像本身的视觉特征（坐标轴、颜色、几何图形）
-3. 如果不确定，参考下方的「图表类型索引」
-
---
-
-## 通用检查清单（适用于所有图表）
-
-在深入类型-specific分析前，先回答这6个问题：
-
- [ ] **类型匹配**：图表类型是否匹配作者声称的分析方法？（例如：说做差异分析却用散点图而非箱式图）
- [ ] **样本量**：n值是否标注？每个点/柱/箱代表多少样本？
- [ ] **统计方法**：p值、检验方法、置信区间是否明确？
- [ ] **颜色图例**：是否自解释？色盲友好吗？
- [ ] **坐标轴**：单位、刻度、截断是否合理？（警惕Y轴截断造成的视觉放大）
- [ ] **视觉误导**：是否存在不连续刻度、面积误导、三维透视扭曲等？
-
---
-
-## 图表类型索引
-
-| 图表类型 | 识别关键词 | 子指南文件 |
-|---------|-----------|-----------|
-| 箱式图 / 小提琴图 | boxplot, violin, quartile, median, IQR | 箱式图与小提琴图 |
-| 热图 / 聚类图 | heatmap, clustering, dendrogram, z-score | 热图与聚类图 |
-| PCA / t-SNE / UMAP | principal component, embedding, dimensionality reduction | 降维图(PCA-tSNE-UMAP) |
-| ROC / PR 曲线 | ROC, AUC, sensitivity, specificity, precision-recall | ROC与PR曲线 |
-| 生存曲线 | Kaplan-Meier, survival, hazard ratio, log-rank | 生存曲线 |
-| 火山图 / 曼哈顿图 | volcano plot, log2 fold change, -log10 p, GWAS | 火山图与曼哈顿图 |
-| 散点图 / 气泡图 | scatter plot, bubble, correlation, regression | 散点图与气泡图 |
-| 条形图 / 误差棒 | bar chart, SEM, SD, confidence interval | 条形图与误差棒 |
-| GSEA 富集图 | enrichment plot, ES, NES, leading edge | GSEA富集图 |
-| 森林图 / Meta 分析 | forest plot, meta-analysis, odds ratio, I2 | 森林图与Meta分析 |
-| 雷达图 / 漏斗图 | radar chart, funnel plot, publication bias | 雷达图与漏斗图 |
-| 网络图 / 通路图 | network, pathway, PPI, interaction | 网络图与通路图 |
-| 桑基图 / 弦图 | Sankey, chord, alluvial, flow | 桑基图与弦图 |
-| 蛋白质结构图 | protein structure, PDB, Cryo-EM, X-ray | 蛋白质结构图 |
-
---
-
-## 进阶：什么时候需要子指南？
-
-**所有 14 类图表均有子指南**。根据复杂度选择阅读深度：
-
-**复杂图表**（强烈建议读子指南）：
- 热图（聚类、标准化、注释层）
- PCA/t-SNE/UMAP（方差解释、批次效应）
- ROC/PR曲线（截断点、置信区间）
- 生存曲线（删失、比例风险假设）
- GSEA 富集图（ES曲线、Leading Edge、FDR阈值）
- 森林图（异质性、权重、发表偏倚）
- 蛋白质结构图（分辨率、界面、动态性）
-
-**中等复杂度**（建议读子指南）：
- 箱式图/小提琴图（统计检验选择、异常值处理）
- 火山图（多重检验校正、效应量阈值）
- 散点图/气泡图（过绘、假相关、气泡大小误导）
- 条形图/误差棒（SEM vs SD、Y轴截断、多重比较）
- 网络图/通路图（hairball、预测边、Hub偏倚）
-
-**相对简单但仍建议参考**：
- 雷达图/漏斗图（维度标准化、发表偏倚判断）
- 桑基图/弦图（流量守恒、路径追踪、方向性）
-
-**通用清单足够**（基础检查）：
- 简单的饼图、面积图、折线图
-
---
-
-## References
-
- Weissgerber et al. (2015). *Beyond bar and line graphs*. PLOS Biology. [DOI:10.1371/journal.pbio.1002128](https://doi.org/10.1371/journal.pbio.1002128)
- Weissgerber et al. (2019). *Reveal, don't conceal*. Circulation. [DOI:10.1161/CIRCULATIONAHA.118.037777](https://doi.org/10.1161/CIRCULATIONAHA.118.037777)
- Krzywinski & Altman (2013). *Visualizing samples with box plots*. Nature Methods. [DOI:10.1038/nmeth.2813](https://doi.org/10.1038/nmeth.2813)
--- a/update.py
+++ b/update.py
@ -58,7 +58,7 @@ PROTECTED_PATHS = {
 }

 # 可更新路径（代码文件）
-UPDATEABLE_PATHS = ["skills", "pipeline", "templates", "command", "scripts"]
+UPDATEABLE_PATHS = ["skills", "pipeline", "command", "scripts"]


 # =============================================================================