Replace placeholder demo images, add Python/Julia gallery sections, and improve skill generation

.github/scripts/generate_skills.py

@@ -270,8 +270,12 @@ def qmd_to_skill_offline(filepath: Path, base_url: str = DEFAULT_BASE_URL) -> Di
     tips = _generate_tips(content, language, category, headings, all_blocks)
     tips_text = "\n".join(f"- {t}" for t in tips)
 
+    # Build the skill title: strip any existing language tag from the QMD title to avoid
+    # duplication (e.g., QMD title "Scatter Plot (Python)" + "(Python)" = "Scatter Plot (Python) (Python)")
+    skill_title = re.sub(r'\s*\((R|Python|Julia)\)\s*$', '', title, flags=re.IGNORECASE).strip()
+
     skill_text = (
-        f"# Skill: {title} ({lang_display})\n\n"
+        f"# Skill: {skill_title} ({lang_display})\n\n"
         f"## Category\n{category}\n\n"
         f"## When to Use\n{use_when}\n\n"
         f"## Required {lang_display} Packages\n{pkg_list}\n\n"
@@ -327,6 +331,11 @@ def _build_combined_code(content: str, language: str, packages: List[str]) -> st
                 parts.append("# Load packages\n" + "\n".join(imp_lines))
     elif language == 'julia':
         using_lines = [f"using {p}" for p in packages[:6]]
+        # Also add `using Random` if the code references Random functions but Random is not in packages
+        # (Random is in JULIA_STDLIB so it's excluded from packages list)
+        all_code = "\n".join(code for _, code in blocks)
+        if 'Random.' in all_code and 'Random' not in packages:
+            using_lines.append("using Random")
         if using_lines:
             parts.append("# Load packages\n" + "\n".join(using_lines))
 
@@ -411,14 +420,21 @@ def _extract_key_parameters(content: str, language: str,
         jl_params = {
             'colormap': 'Color scheme for the plot (e.g., :viridis, :RdBu)',
             'markersize': 'Size of scatter plot markers',
-            'alpha': 'Transparency level (0–1)',
-            'color': 'Color of plot elements',
+            'color': 'Color of plot elements (e.g., :steelblue or (:red, 0.5) for alpha)',
             'linewidth': 'Width of lines in the plot',
             'colorrange': 'Range for color mapping as (min, max) tuple',
+            'alpha': 'Transparency level (0–1) via color tuple (color, alpha)',
+            'side': 'Side of violin to draw (:left, :right, or both)',
+            'width': 'Width of violin or box plot elements',
+            'bandwidth': 'Kernel bandwidth for density estimation in violin plots',
+            'size': 'Figure size as (width, height) in pixels',
         }
         for param, desc in jl_params.items():
             if param in combined_code and len(params) < 8:
                 params[param] = desc
+        # Detect color tuple usage (alpha via tuple syntax)
+        if re.search(r'\(\s*:\w+\s*,\s*[\d.]+\s*\)', combined_code) and 'alpha' not in params and len(params) < 8:
+            params['alpha'] = 'Transparency via color tuple syntax: color=(:steelblue, 0.7)'
 
     # Ensure at least 3 params
     if len(params) < 3:
@@ -430,9 +446,15 @@ def _extract_key_parameters(content: str, language: str,
         elif language == 'python':
             if 'figsize' not in params:
                 params['figsize'] = 'Figure dimensions as (width, height) in inches'
+            if 'alpha' not in params:
+                params['alpha'] = 'Transparency level (0–1)'
         elif language == 'julia':
             if 'color' not in params:
-                params['color'] = 'Color of plot elements'
+                params['color'] = 'Color of plot elements (e.g., :steelblue or (:red, 0.5) for alpha)'
+            if 'markersize' not in params:
+                params['markersize'] = 'Size of scatter plot markers'
+            if len(params) < 3 and 'size' not in params:
+                params['size'] = 'Figure size as (width, height) in pixels'
 
     return dict(list(params.items())[:8])
 
@@ -553,6 +575,10 @@ def generate_skill(self, filepath: Path,
         rel_html = str(filepath.with_suffix(".html")).lstrip("./")
         tutorial_url = base_url.rstrip("/") + "/" + rel_html
 
+        # Strip language tag from title for the skill header to avoid duplication
+        # (e.g., "Scatter Plot (Python)" becomes "Scatter Plot" before "(Python)" is appended)
+        skill_title = re.sub(r'\s*\((R|Python|Julia)\)\s*$', '', title, flags=re.IGNORECASE).strip()
+
         system_prompt = f"""You are an expert at creating AI skill documents for biomedical visualization tutorials.
 
 Follow this specification exactly:
@@ -572,7 +598,7 @@ def generate_skill(self, filepath: Path,
         user_prompt = f"""Convert this Bizard QMD tutorial into a skill document.
 
 **Tutorial metadata:**
-- Title: {title}
+- Title: {skill_title}
 - Language: {lang_display}
 - Category: {category}
 - Packages detected: {', '.join(packages) if packages else 'none detected'}

GraphGallery.qmd

@@ -356,6 +356,80 @@ div(
 )
 ```
 
+## 𝐏𝐘𝐓𝐇𝐎𝐍
+
+```{r}
+#| echo: false
+data_PYTHON <- data[data$Level1=="PYTHON",]
+
+tbl <- reactable(
+  data_PYTHON,
+  defaultColDef = colDef(vAlign = "center", headerClass = "header"),
+  columns = list(
+    Id = colDef(
+      name = "Id", align = "center", minWidth = 70, maxWidth = 90
+    ),
+    Name = colDef(
+      name = "Graph", cell = JS("renderGraph"), html = TRUE, minWidth = 250
+    ),
+    Image_url = colDef(show = FALSE),
+    Tutorial_url = colDef(show = FALSE),
+    Description =colDef(show = FALSE),
+    Type = colDef(name = "Type"),
+    Level1 =colDef(show = FALSE),
+    Level2 =colDef(show = FALSE)
+  ), 
+  searchable = TRUE,
+  defaultPageSize = 7
+)
+
+div(
+  class = "movies",
+  tbl,
+  div(id = "modal",  class="modal", onclick="hideModal()",
+      img(
+        id="modal-image", class="modal-image"
+      ))
+)
+```
+
+## 𝐉𝐔𝐋𝐈𝐀
+
+```{r}
+#| echo: false
+data_JULIA <- data[data$Level1=="JULIA",]
+
+tbl <- reactable(
+  data_JULIA,
+  defaultColDef = colDef(vAlign = "center", headerClass = "header"),
+  columns = list(
+    Id = colDef(
+      name = "Id", align = "center", minWidth = 70, maxWidth = 90
+    ),
+    Name = colDef(
+      name = "Graph", cell = JS("renderGraph"), html = TRUE, minWidth = 250
+    ),
+    Image_url = colDef(show = FALSE),
+    Tutorial_url = colDef(show = FALSE),
+    Description =colDef(show = FALSE),
+    Type = colDef(name = "Type"),
+    Level1 =colDef(show = FALSE),
+    Level2 =colDef(show = FALSE)
+  ), 
+  searchable = TRUE,
+  defaultPageSize = 7
+)
+
+div(
+  class = "movies",
+  tbl,
+  div(id = "modal",  class="modal", onclick="hideModal()",
+      img(
+        id="modal-image", class="modal-image"
+      ))
+)
+```
+
 ## 𝐇𝐈𝐏𝐋𝐎𝐓
 
 ### BASICS

GraphGallery.zh.qmd

@@ -356,6 +356,80 @@ div(
 )
 ```
 
+## 𝐏𝐘𝐓𝐇𝐎𝐍
+
+```{r}
+#| echo: false
+data_PYTHON <- data[data$Level1=="PYTHON",]
+
+tbl <- reactable(
+  data_PYTHON,
+  defaultColDef = colDef(vAlign = "center", headerClass = "header"),
+  columns = list(
+    Id = colDef(
+      name = "Id", align = "center", minWidth = 70, maxWidth = 90
+    ),
+    Name = colDef(
+      name = "Graph", cell = JS("renderGraph"), html = TRUE, minWidth = 250
+    ),
+    Image_url = colDef(show = FALSE),
+    Tutorial_url = colDef(show = FALSE),
+    Description =colDef(show = FALSE),
+    Type = colDef(name = "Type"),
+    Level1 =colDef(show = FALSE),
+    Level2 =colDef(show = FALSE)
+  ), 
+  searchable = TRUE,
+  defaultPageSize = 7
+)
+
+div(
+  class = "movies",
+  tbl,
+  div(id = "modal",  class="modal", onclick="hideModal()",
+      img(
+        id="modal-image", class="modal-image"
+      ))
+)
+```
+
+## 𝐉𝐔𝐋𝐈𝐀
+
+```{r}
+#| echo: false
+data_JULIA <- data[data$Level1=="JULIA",]
+
+tbl <- reactable(
+  data_JULIA,
+  defaultColDef = colDef(vAlign = "center", headerClass = "header"),
+  columns = list(
+    Id = colDef(
+      name = "Id", align = "center", minWidth = 70, maxWidth = 90
+    ),
+    Name = colDef(
+      name = "Graph", cell = JS("renderGraph"), html = TRUE, minWidth = 250
+    ),
+    Image_url = colDef(show = FALSE),
+    Tutorial_url = colDef(show = FALSE),
+    Description =colDef(show = FALSE),
+    Type = colDef(name = "Type"),
+    Level1 =colDef(show = FALSE),
+    Level2 =colDef(show = FALSE)
+  ), 
+  searchable = TRUE,
+  defaultPageSize = 7
+)
+
+div(
+  class = "movies",
+  tbl,
+  div(id = "modal",  class="modal", onclick="hideModal()",
+      img(
+        id="modal-image", class="modal-image"
+      ))
+)
+```
+
 ## 𝐇𝐈𝐏𝐋𝐎𝐓
 
 ### 基础

files/gallery_data.csv

@@ -785,3 +785,10 @@
 784,Dice Plot with custom theme,https://openbiox.github.io/Bizard/Proportion/DicePlot_files/figure-html/fig-3ThemedDice-1.png,https://openbiox.github.io/Bizard/Proportion/DicePlot.html#fig-3ThemedDice,The package includes theme_dice() for cleaner visualization,Dice Plot,BASICS,Proportion
 785,Basic Text Enrichment BarPlot,https://openbiox.github.io/Bizard/Omics/TextEnrichmentBarPlot_files/figure-html/fig1.SimpleRound-1.png,https://openbiox.github.io/Bizard/Omics/TextEnrichmentBarPlot.html#basic-plotting-simplified-version,Basic Enrichment Analysis Barplot,Text Enrichment BarPlot,OMICS,TextEnrichmentBarPlot
 786,Advanced Enrichment Analysis Barplot,https://openbiox.github.io/Bizard/Omics/TextEnrichmentBarPlot_files/figure-html/fig2.ComplexRound-1.png,https://openbiox.github.io/Bizard/Omics/TextEnrichmentBarPlot.html#advanced-plotting-detailed-version,Advanced Enrichment Analysis Barplot,Text Enrichment BarPlot,OMICS,TextEnrichmentBarPlot
+787,Scatter Plot (Python),https://openbiox.github.io/Bizard/images/Python/ScatterPlot_demo.png,https://openbiox.github.io/Bizard/Python/ScatterPlot.html,Scatter plot showing correlations using matplotlib and seaborn,Scatter Plot,PYTHON,Python
+788,Violin Plot (Python),https://openbiox.github.io/Bizard/images/Python/ViolinPlot_demo.png,https://openbiox.github.io/Bizard/Python/ViolinPlot.html,Violin plot combining box plot and kernel density estimation,Violin Plot,PYTHON,Python
+789,Heatmap (Python),https://openbiox.github.io/Bizard/images/Python/Heatmap_demo.png,https://openbiox.github.io/Bizard/Python/Heatmap.html,Heatmap for gene expression profiles and correlation matrices,Heatmap,PYTHON,Python
+790,Volcano Plot (Python),https://openbiox.github.io/Bizard/images/Python/VolcanoPlot_demo.png,https://openbiox.github.io/Bizard/Python/VolcanoPlot.html,Volcano plot for differential expression analysis,Volcano Plot,PYTHON,Python
+791,Scatter Plot (Julia),https://openbiox.github.io/Bizard/images/Julia/ScatterPlot_demo.png,https://openbiox.github.io/Bizard/Julia/ScatterPlot.html,High-performance scatter plot using CairoMakie,Scatter Plot,JULIA,Julia
+792,Violin Plot (Julia),https://openbiox.github.io/Bizard/images/Julia/ViolinPlot_demo.png,https://openbiox.github.io/Bizard/Julia/ViolinPlot.html,Violin plot for distribution comparison using CairoMakie,Violin Plot,JULIA,Julia
+793,Heatmap (Julia),https://openbiox.github.io/Bizard/images/Julia/Heatmap_demo.png,https://openbiox.github.io/Bizard/Julia/Heatmap.html,Heatmap for matrix visualization using CairoMakie,Heatmap,JULIA,Julia

files/gallery_data_zh.csv

@@ -785,3 +785,10 @@
 784,自定义骰子图主题,https://openbiox.github.io/Bizard/zh/Proportion/DicePlot_files/figure-html/fig-3ThemedDice-1.png,https://openbiox.github.io/Bizard/zh/Proportion/DicePlot.html#fig-3ThemedDice,该包包含 theme_dice() 以实现更清晰的可视化,骰子图,BASICS,Proportion
 785,基础富集分析柱状图,https://openbiox.github.io/Bizard/zh/Omics/TextEnrichmentBarPlot_files/figure-html/fig1.SimpleRound-1.png,https://openbiox.github.io/Bizard/zh/Omics/TextEnrichmentBarPlot.html#basic-plotting-simplified-version,基础富集分析柱状图,文字叠加的富集分析柱状图,OMICS,TextEnrichmentBarPlot
 786,进阶富集分析柱状图,https://openbiox.github.io/Bizard/zh/Omics/TextEnrichmentBarPlot_files/figure-html/fig2.ComplexRound-1.png,https://openbiox.github.io/Bizard/zh/Omics/TextEnrichmentBarPlot.html#advanced-plotting-detailed-version,进阶富集分析柱状图,文字叠加的富集分析柱状图,OMICS,TextEnrichmentBarPlot
+787,散点图 (Python),https://openbiox.github.io/Bizard/images/Python/ScatterPlot_demo.png,https://openbiox.github.io/Bizard/zh/Python/ScatterPlot.html,使用 matplotlib 和 seaborn 绘制散点图展示变量间相关性,散点图,PYTHON,Python
+788,小提琴图 (Python),https://openbiox.github.io/Bizard/images/Python/ViolinPlot_demo.png,https://openbiox.github.io/Bizard/zh/Python/ViolinPlot.html,小提琴图结合箱线图和核密度估计展示数据分布,小提琴图,PYTHON,Python
+789,热力图 (Python),https://openbiox.github.io/Bizard/images/Python/Heatmap_demo.png,https://openbiox.github.io/Bizard/zh/Python/Heatmap.html,热力图用于基因表达谱和相关性矩阵可视化,热力图,PYTHON,Python
+790,火山图 (Python),https://openbiox.github.io/Bizard/images/Python/VolcanoPlot_demo.png,https://openbiox.github.io/Bizard/zh/Python/VolcanoPlot.html,火山图用于差异表达分析结果可视化,火山图,PYTHON,Python
+791,散点图 (Julia),https://openbiox.github.io/Bizard/images/Julia/ScatterPlot_demo.png,https://openbiox.github.io/Bizard/zh/Julia/ScatterPlot.html,使用 CairoMakie 绘制高性能散点图,散点图,JULIA,Julia
+792,小提琴图 (Julia),https://openbiox.github.io/Bizard/images/Julia/ViolinPlot_demo.png,https://openbiox.github.io/Bizard/zh/Julia/ViolinPlot.html,使用 CairoMakie 绘制小提琴图展示数据分布,小提琴图,JULIA,Julia
+793,热力图 (Julia),https://openbiox.github.io/Bizard/images/Julia/Heatmap_demo.png,https://openbiox.github.io/Bizard/zh/Julia/Heatmap.html,使用 CairoMakie 绘制热力图进行矩阵可视化,热力图,JULIA,Julia