UPdate modality counts

Author: mikemartinez99

README.md

@@ -92,12 +92,10 @@ The **GDSC** aims to facilitate advanced bioinformatic, computational, and stati
 
 | Modality | Count |
 |----------|-------|
-| 1 | 9 |
 | Bulk-Transcriptomics | 3 |
 | 10x Multiome | 1 |
 | 10x Visium | 1 |
 | 10x Xenium | 1 |
-| Count | 1 |
 | Epigenetics | 1 |
 | Metagenomics | 1 |
 | ResolveOME | 1 |

scripts/tallyModalities.py

@@ -57,20 +57,35 @@ def normalize(modality: str) -> str:
 
 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:
+            in_counts_section = True
+            continue
+        if END in line:
+            in_counts_section = False
+            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, Date, trailing empty
+        # 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)