can run add_files from anywhere

add_files.py

@@ -8,9 +8,10 @@ import pandas as pd
 
 def main(args):
     path = Path(args.path)
+    root = Path(__file__).parent
 
-    df_all = pd.read_csv("metadata_all.csv", index_col=0)
-    df = pd.read_csv("metadata.csv", index_col=0)
+    df_all = pd.read_csv(root / "metadata_all.csv", index_col=0)
+    df = pd.read_csv(root / "metadata.csv", index_col=0)
 
     missing_files = np.array(list(set(df_all.index) - set(df.index)))
     exists = np.array([(path / f"{f}.h5ad").exists() for f in missing_files])
@@ -20,13 +21,13 @@ def main(args):
     existing_files = missing_files[exists]
 
     if args.dry_run:
-        print(f"Files will be copied inside {Path(__file__).parent}/<species>/<tissue>")
+        print(f"Files will be copied inside {root}/<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_dir: Path = root / species / tissue
             dst = dst_dir / f"{name}.h5ad"
 
             dst_dir.mkdir(parents=True, exist_ok=True)
@@ -36,9 +37,7 @@ def main(args):
 
     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
-        )
+        df_all.loc[existing_files].to_csv(root / "metadata.csv", mode="a", header=False)
 
 
 if __name__ == "__main__":