add dry run mode

add_files.py

@@ -19,21 +19,26 @@ def main(args):
 
     existing_files = missing_files[exists]
 
-    for name in existing_files:
-        species, tissue = df_all.loc[name, ["species", "tissue"]].values
+    if args.dry_run:
+        print(f"Files will be copied inside {Path(__file__).parent}/<species>/<tissue>")
+    else:
+        for name in existing_files:
+            species, tissue = df_all.loc[name, ["species", "tissue"]].values
 
-        src = path / f"{name}.h5ad"
-        dst_dir: Path = Path(__file__).parent / species / tissue
-        dst = dst_dir / f"{name}.h5ad"
+            src = path / f"{name}.h5ad"
+            dst_dir: Path = Path(__file__).parent / species / tissue
+            dst = dst_dir / f"{name}.h5ad"
 
-        dst_dir.mkdir(parents=True, exist_ok=True)
+            dst_dir.mkdir(parents=True, exist_ok=True)
 
-        print(f"Copying {src} to {dst}")
-        shutil.copyfile(src, dst)
+            print(f"Copying {src} to {dst}")
+            shutil.copyfile(src, dst)
 
-    df_all.loc[existing_files].to_csv(
-        Path(__file__).parent / "metadata.csv", mode="a", header=False
-    )
+    if not args.dry_run:
+        print(f"Appending {len(existing_files)} files to metadata.csv")
+        df_all.loc[existing_files].to_csv(
+            Path(__file__).parent / "metadata.csv", mode="a", header=False
+        )
 
 
 if __name__ == "__main__":
@@ -46,4 +51,10 @@ if __name__ == "__main__":
         help="Path to the data directories containing h5ad files to add",
     )
 
+    parser.add_argument(
+        "--dry-run",
+        action="store_true",
+        help="Perform a dry run without copying files",
+    )
+
     main(parser.parse_args())