451: Avoid Unnecessary Re-Creation of Bins in scool to Prevent File Bloat

src/cooler/create/_create.py

@@ -1239,34 +1239,62 @@ def create_scool(
     n_chroms = len(chroms)
     n_bins = len(bins)
 
-    # Create root group
+    # Create root group (updated)
+    bins_identical = False
     with h5py.File(file_path, mode) as f:
         logger.info(f'Creating cooler at "{file_path}::{group_path}"')
-        if group_path == "/":
-            for name in ["chroms", "bins"]:
-                if name in f:
-                    del f[name]
+        if group_path in f:
+            grp = f[group_path]
+            # Check if a bins group already exists
+            if "bins" in grp:
+                # Read the existing bins datasets
+                existing_chrom = grp["bins/chrom"][()]
+                existing_start = grp["bins/start"][()]
+                existing_end = grp["bins/end"][()]
+                # If stored as bytes, decode to string
+                if existing_chrom.dtype.kind == "S":
+                    existing_chrom = np.char.decode(existing_chrom, "utf-8")
+                existing_bins = pd.DataFrame({
+                    "chrom": existing_chrom,
+                    "start": existing_start,
+                    "end": existing_end,
+                }).reset_index(drop=True)
+                new_bins = bins[["chrom", "start", "end"]].reset_index(drop=True)
+                if existing_bins.equals(new_bins):
+                    logger.info(
+                        "Existing bins are identical; skipping bins re-creation."
+                    )
+                    bins_identical = True
+                else:
+                    logger.info("Bins differ; re-creating bins group.")
+                    del grp["bins"]
+            # Always re-create chroms for consistency
+            # (or add a similar check if desired)
+            if "chroms" in grp:
+                del grp["chroms"]
         else:
             try:
                 f.create_group(group_path)
             except ValueError:
                 del f[group_path]
                 f.create_group(group_path)
 
+    # Write chroms and bins
     with h5py.File(file_path, "r+") as f:
         h5 = f[group_path]
-
         logger.info("Writing chroms")
         grp = h5.create_group("chroms")
         write_chroms(grp, chroms, h5opts)
+        if not bins_identical:
+            logger.info("Writing bins")
+            grp = h5.create_group("bins")
+            write_bins(grp, bins, chroms["name"], h5opts)
+        else:
+            logger.info("Skipping writing bins since they are identical.")
 
-        logger.info("Writing bins")
-        grp = h5.create_group("bins")
-        write_bins(grp, bins, chroms["name"], h5opts)
-
+    # Write info
     with h5py.File(file_path, "r+") as f:
         h5 = f[group_path]
-
         logger.info("Writing info")
         info = {}
         info["bin-type"] = "fixed" if binsize is not None else "variable"
@@ -1282,11 +1310,7 @@ def create_scool(
 
     # Append single cells
     for key in cell_names:
-        if "/" in key:
-            cell_name = key.split("/")[-1]
-        else:
-            cell_name = key
-
+        cell_name = key.split("/")[-1] if "/" in key else key
         create(
             cool_uri + "::/cells/" + cell_name,
             bins_dict[key],