tally edits

Refactor modality handling by removing color definitions and badge generation. Update the upsert_section function to only include the table of modality counts.

Author: mikemartinez99

scripts/tallyModalities.py

@@ -17,63 +17,51 @@
     "rnaseq": "Bulk-Transcriptomics",
     "rna seq": "Bulk-Transcriptomics",
     "rna seq.": "Bulk-Transcriptomics",
+
     # Single-cell gene expression
     "sc gex": "scRNA-Seq",
     "single cell rna-seq": "scRNA-Seq",
     "scrna-seq": "scRNA-Seq",
     "sc rna-seq": "scRNA-Seq",
+
     # ATAC-seq
     "bulk atacseq": "Bulk-Epigenetics",
     "bulk atac-seq": "Bulk-Epigenetics",
     "sc atac": "scATAC-Seq",
     "sc atac-seq": "scATAC-Seq",
+
     # Multiome and others
     "10x multiome": "10x Multiome",
     "resolveome": "ResolveOME",
+    
     # Spatial platforms
     "spatial": "Spatial",
     "visium": "10x Visium",
     "10x visium": "10x Visium",
     "xenium": "10x Xenium",
     "xeniums": "10x Xenium",
     "10x xenium": "10x Xenium",
+
     # Misc
     "mgx": "Metagenomics",
     "workflow dev": "Workflow development",
-    "workflow development": "Workflow development",
-    "workflows": "Workflow development",
-    "development": "Workflow development",
+    "workflow development" : "Workflow development",
+    "workflows" : "Workflow development",
+    "development" : "Workflow development",
     "other": "Other",
 }
 
-# Color palette for modalities (GitHub-style colors)
-COLORS: Dict[str, str] = {
-    "Bulk-Transcriptomics": "#e34c26",
-    "scRNA-Seq": "#3572A5",
-    "Bulk-Epigenetics": "#178600",
-    "scATAC-Seq": "#89e051",
-    "10x Multiome": "#f1e05a",
-    "ResolveOME": "#b07219",
-    "Spatial": "#555555",
-    "10x Visium": "#4F5D95",
-    "10x Xenium": "#DA5B0B",
-    "Metagenomics": "#701516",
-    "Workflow development": "#384d54",
-    "Other": "#cccccc",
-}
-
-
 def normalize(modality: str) -> str:
     m = modality.strip()
     if not m:
         return ""
     key = m.lower()
     return ALIASES.get(key, m)
 
-
 def extract_modalities_from_markdown(md_text: str) -> List[str]:
     modalities: List[str] = []
     in_counts_section = False
+
     for line in md_text.splitlines():
         # Skip the generated counts section entirely
         if START in line:
@@ -84,19 +72,23 @@ def extract_modalities_from_markdown(md_text: str) -> List[str]:
             continue
         if in_counts_section:
             continue
+
         if not line.startswith("|"):
             continue
         if re.match(r"^\|\s*Project\s*\|", line):
             continue
         if re.match(r"^\|\s*-+\s*\|", line):
             continue
+
         cells = [c.strip() for c in line.split("|")]
         # Expect at least 4 cells: leading empty, Project, Modality, Repo/Count, trailing empty
         if len(cells) < 4:
             continue
+
         modality_cell = cells[2]  # Modality is the second visible column
         if not modality_cell:
             continue
+
         parts = re.split(r"\s*,\s*", modality_cell)
         for p in parts:
             n = normalize(p)
@@ -105,84 +97,7 @@ def extract_modalities_from_markdown(md_text: str) -> List[str]:
     return modalities
 
 
-def get_color(modality: str) -> str:
-    """Get color for a modality, or generate a default one."""
-    return COLORS.get(modality, "#cccccc")
-
-
-def build_badge_svg(counts: Counter) -> str:
-    """Build an SVG badge similar to GitHub's language bar."""
-    if not counts:
-        return ""
-    
-    total = sum(counts.values())
-    rows: List[Tuple[str, int]] = sorted(
-        counts.items(), key=lambda x: (-x[1], x[0].lower())
-    )
-    
-    # SVG dimensions
-    width = 600
-    bar_height = 8
-    legend_item_height = 25
-    legend_height = len(rows) * legend_item_height
-    total_height = bar_height + 20 + legend_height
-    
-    # Build bar segments
-    x_pos = 0
-    bar_rects = []
-    for modality, count in rows:
-        percentage = (count / total) * 100
-        segment_width = (count / total) * width
-        color = get_color(modality)
-        bar_rects.append(
-            f'<rect x="{x_pos:.2f}" y="0" width="{segment_width:.2f}" height="{bar_height}" '
-            f'fill="{color}"><title>{modality}: {count} ({percentage:.1f}%)</title></rect>'
-        )
-        x_pos += segment_width
-    
-    # Build legend
-    legend_items = []
-    y_pos = bar_height + 20
-    for modality, count in rows:
-        percentage = (count / total) * 100
-        color = get_color(modality)
-        legend_items.append(
-            f'<circle cx="6" cy="{y_pos}" r="5" fill="{color}"/>'
-        )
-        legend_items.append(
-            f'<text x="18" y="{y_pos + 4}" class="legend-text">{modality}</text>'
-        )
-        legend_items.append(
-            f'<text x="{width - 10}" y="{y_pos + 4}" class="legend-percent" text-anchor="end">'
-            f'{percentage:.1f}% ({count})</text>'
-        )
-        y_pos += legend_item_height
-    
-    svg = f'''<svg width="{width}" height="{total_height}" xmlns="http://www.w3.org/2000/svg">
-  <style>
-    .legend-text {{ 
-      font: 12px -apple-system, BlinkMacSystemFont, "Segoe UI", Helvetica, Arial, sans-serif; 
-      fill: #24292f; 
-    }}
-    .legend-percent {{ 
-      font: 12px -apple-system, BlinkMacSystemFont, "Segoe UI", Helvetica, Arial, sans-serif; 
-      fill: #656d76; 
-      font-weight: 600;
-    }}
-  </style>
-  <g id="bar">
-    {chr(10).join(f"    {rect}" for rect in bar_rects)}
-  </g>
-  <g id="legend">
-    {chr(10).join(f"    {item}" for item in legend_items)}
-  </g>
-</svg>'''
-    
-    return f'<p align="center">\n{svg}\n</p>'
-
-
 def build_table(counts: Counter) -> str:
-    """Build a simple markdown table (fallback)."""
     rows: List[Tuple[str, int]] = sorted(
         counts.items(), key=lambda x: (-x[1], x[0].lower())
     )
@@ -194,18 +109,12 @@ def build_table(counts: Counter) -> str:
         lines.append(f"| {modality} | {cnt} |")
     return "\n".join(lines)
 
-
-def upsert_section(md_text: str, badge_svg: str, table_md: str) -> str:
-    """Insert both badge and table into README."""
+def upsert_section(md_text: str, table_md: str) -> str:
     section = (
         f"{START}\n"
         f"\n"
-        f"### Modality Distribution\n\n"
-        f"{badge_svg}\n\n"
-        f"<details>\n"
-        f"<summary>View as table</summary>\n\n"
-        f"{table_md}\n\n"
-        f"</details>\n"
+        f"### Modality counts\n\n"
+        f"{table_md}\n"
         f"\n"
         f"{END}"
     )
@@ -219,29 +128,21 @@ def upsert_section(md_text: str, badge_svg: str, table_md: str) -> str:
     sep = "\n\n" if not md_text.endswith("\n") else "\n"
     return md_text + sep + section + "\n"
 
-
 def main() -> int:
     if not README.exists():
         print("README.md not found at repo root.")
         return 1
-    
     md_text = README.read_text(encoding="utf-8")
     modalities = extract_modalities_from_markdown(md_text)
     counts = Counter(modalities)
-    
-    badge_svg = build_badge_svg(counts)
     table_md = build_table(counts)
-    
-    new_md = upsert_section(md_text, badge_svg, table_md)
-    
+    new_md = upsert_section(md_text, table_md)
     if new_md != md_text:
         README.write_text(new_md, encoding="utf-8")
         print("README.md updated with modality counts.")
     else:
         print("No changes to README.md.")
-    
     return 0
 
-
 if __name__ == "__main__":
     raise SystemExit(main())