Merge pull request #305 from mayank-singh-sikarwar/cosmx_reader

Fixes #298: Repeatedly appending parent path to flatFiles

Author: LucaMarconato

src/spatialdata_io/readers/cosmx.py

@@ -105,10 +105,10 @@ def cosmx(
     if not labels_dir.exists():
         raise FileNotFoundError(f"Labels directory not found: {labels_dir}.")
 
-    counts = pd.read_csv(path / counts_file, header=0, index_col=CosmxKeys.INSTANCE_KEY)
+    counts = pd.read_csv(counts_file, header=0, index_col=CosmxKeys.INSTANCE_KEY)
     counts.index = counts.index.astype(str).str.cat(counts.pop(CosmxKeys.FOV).astype(str).values, sep="_")
 
-    obs = pd.read_csv(path / meta_file, header=0, index_col=CosmxKeys.INSTANCE_KEY)
+    obs = pd.read_csv(meta_file, header=0, index_col=CosmxKeys.INSTANCE_KEY)
     obs[CosmxKeys.FOV] = pd.Categorical(obs[CosmxKeys.FOV].astype(str))
     obs[CosmxKeys.REGION_KEY] = pd.Categorical(obs[CosmxKeys.FOV].astype(str).apply(lambda s: s + "_labels"))
     obs[CosmxKeys.INSTANCE_KEY] = obs.index.astype(np.int64)
@@ -254,9 +254,9 @@ def cosmx(
         import pyarrow.parquet as pq
 
         with tempfile.TemporaryDirectory() as tmpdir:
-            print("converting .csv to .parquet to improve the speed of the slicing operations... ", end="")
+            print("converting .csv to .parquet to improve the speed of the slicing operations... ", end="", flush=True)
             assert transcripts_file is not None
-            transcripts_data = pd.read_csv(path / transcripts_file, header=0)
+            transcripts_data = pd.read_csv(transcripts_file, header=0)
             transcripts_data.to_parquet(Path(tmpdir) / "transcripts.parquet")
             print("done")