hashing removed

Author: inecik

notebooks/notebook.ipynb

@@ -207,7 +207,7 @@
         "\n",
         "# Normalize counts to 1e4 per cell and log-transform for export\n",
         "sc.pp.normalize_total(adata_complete, target_sum=1e4)\n",
-        "sc.pp.log1p(adata_complete)\n"
+        "sc.pp.log1p(adata_complete)"
       ]
     },
     {
@@ -273,8 +273,7 @@
             "⚠ Skipping points.bin.gz: /Users/kemalinecik/git_nosync/_/cellucid/assets/exports/points.bin.gz already exists (use force=True to overwrite)\n",
             "⚠ Skipping obs manifest: /Users/kemalinecik/git_nosync/_/cellucid/assets/exports/obs_manifest.json already exists (use force=True to overwrite)\n",
             "⚠ Skipping var manifest: /Users/kemalinecik/git_nosync/_/cellucid/assets/exports/var_manifest.json already exists (use force=True to overwrite)\n",
-            "⚠ Skipping connectivity manifest: /Users/kemalinecik/git_nosync/_/cellucid/assets/exports/connectivity_manifest.json already exists (use force=True to overwrite)\n",
-            "✓ Wrote dataset signature (hash=abeda2e0656c...) to /Users/kemalinecik/git_nosync/_/cellucid/assets/exports/dataset_hash.json\n"
+            "⚠ Skipping connectivity manifest: /Users/kemalinecik/git_nosync/_/cellucid/assets/exports/connectivity_manifest.json already exists (use force=True to overwrite)\n"
           ]
         }
       ],
@@ -311,7 +310,7 @@
     },
     {
       "cell_type": "code",
-      "execution_count": 10,
+      "execution_count": 11,
       "id": "a19552d8",
       "metadata": {},
       "outputs": [
@@ -335,7 +334,7 @@
               "   'var_gene_id_column': 'converted_id'}}}"
             ]
           },
-          "execution_count": 10,
+          "execution_count": 11,
           "metadata": {},
           "output_type": "execute_result"
         }

src/cellucid/prepare_data.py

@@ -17,11 +17,9 @@
 - connectivities: sparse matrix with KNN connectivities
 """
 import gzip
-import hashlib
 import json
 import re
 import tqdm
-from datetime import datetime
 from pathlib import Path
 from typing import Optional, Sequence, Union, Literal
 
@@ -45,17 +43,6 @@ def _safe_filename_component(name: str) -> str:
     return safe or "field"
 
 
-def _sha256_json(obj: object) -> str:
-    """Stable sha256 over a JSON-serializable object."""
-    normalized = json.dumps(obj, sort_keys=True, separators=(",", ":"), ensure_ascii=True)
-    return hashlib.sha256(normalized.encode("utf-8")).hexdigest()
-
-
-def _sha256_list_str(items: Sequence[str]) -> str:
-    """Convenience hash for lists of strings."""
-    return _sha256_json([str(x) for x in items])
-
-
 def _to_dense(arr: Union[np.ndarray, sparse.spmatrix]) -> np.ndarray:
     """Convert sparse matrix to dense numpy array if necessary."""
     if sparse.issparse(arr):
@@ -561,7 +548,6 @@ def export_data_for_web(
                     "key": str(key),
                     "kind": "category",
                     "category_count": n_categories,
-                    "categories_hash": _sha256_list_str(categories),
                     "codes_dtype": dtype_str,
                     "outlier_quantized": obs_continuous_quantization is not None,
                     "outlier_quantization_bits": int(obs_continuous_quantization)
@@ -802,7 +788,6 @@ def export_data_for_web(
 
     # Process gene expression if provided
     genes_to_export: list[str] = []
-    gene_ids_hash: Optional[str] = None
     if gene_expression is not None:
         if var is None:
             raise ValueError("var DataFrame must be provided when gene_expression is given.")
@@ -846,8 +831,6 @@ def export_data_for_web(
                 print(f"⚠ Warning: {len(missing_genes)} gene identifiers not found in var: {missing_genes[:5]}...")
             genes_to_export = [g for g in genes_to_export if g in gene_id_to_idx]
 
-        gene_ids_hash = _sha256_list_str(genes_to_export)
-
         var_manifest_path = out_dir / var_manifest_filename
         if _file_exists_skip(var_manifest_path, "var manifest", force):
             pass
@@ -1110,58 +1093,3 @@ def export_data_for_web(
             )
     else:
         print("INFO: No connectivity data provided, skipping connectivity export.")
-
-    # --- Dataset signature for clash detection ---------------------------------
-    obs_fields_hash = _sha256_json(obs_field_summaries)
-    gene_count = len(genes_to_export) if genes_to_export else 0
-
-    hash_inputs = {
-        "version": 1,
-        "manifest_format": MANIFEST_FORMAT_VERSION,
-        "n_cells": int(n_cells),
-        "latent_dims": int(latent.shape[1]),
-        "obs_keys": [str(k) for k in obs_keys],
-        "obs_fields_hash": obs_fields_hash,
-        "obs_fields": obs_field_summaries,
-        "obs_continuous_quantization": obs_continuous_quantization,
-        "obs_categorical_dtype": obs_categorical_dtype,
-        "var_present": gene_expression is not None,
-        "gene_count": gene_count,
-        "gene_list_hash": gene_ids_hash,
-        "var_gene_id_column": var_gene_id_column if gene_expression is not None else None,
-        "var_quantization": var_quantization,
-        "connectivity": connectivity_meta,
-        "compression": compression if compression else None,
-        "points_filename": points_filename + (".gz" if compression else ""),
-        "obs_manifest": obs_manifest_filename,
-        "var_manifest": var_manifest_filename if gene_expression is not None else None,
-        "connectivity_manifest": connectivity_manifest_filename if connectivities is not None else None,
-        "centroid_outlier_quantile": centroid_outlier_quantile if centroid_outlier_quantile is not None else None,
-        "centroid_min_points": centroid_min_points,
-    }
-
-    signature = _sha256_json(hash_inputs)
-    dataset_hash_payload = {
-        "version": 1,
-        "created_at": datetime.utcnow().isoformat() + "Z",
-        "signature": signature,
-        "summary": {
-            "n_cells": int(n_cells),
-            "obs_field_count": len(obs_field_summaries),
-            "obs_keys": [str(k) for k in obs_keys],
-            "obs_fields_hash": obs_fields_hash,
-            "gene_count": gene_count,
-            "gene_list_hash": gene_ids_hash,
-            "compression": compression if compression else None,
-            "connectivity_edges": connectivity_meta.get("n_edges"),
-        },
-        "details": {
-            "hash_inputs": hash_inputs,
-            "gene_sample": genes_to_export[:10] if genes_to_export else [],
-            "notes": "signature is sha256 over hash_inputs; compare two dataset_hash.json files to diagnose clashes",
-        },
-    }
-
-    dataset_hash_path = out_dir / "dataset_hash.json"
-    dataset_hash_path.write_text(json.dumps(dataset_hash_payload, ensure_ascii=True, indent=2), encoding="utf-8")
-    print(f"✓ Wrote dataset signature (hash={signature[:12]}...) to {dataset_hash_path}")