Fix leiden hanging when insufficient shared memory is available.

CHANGELOG.md

@@ -50,6 +50,8 @@
 
 # BUG FIXES
 
+* `cluster/leiden`: Fix an issue where insufficient shared memory (size of `/dev/shm`) causes the processing to hang.  
+
 * `utils/subset_vars`: Convert .var column used for subsetting of dtype "boolean" to dtype "bool" when it doesn't contain NaN values (PR #959).
 
 * `resources_test_scripts/annotation_test_data.sh`: Add a layer to the annotation reference dataset with log normalized counts (PR #960).

src/cluster/leiden/script.py

@@ -45,7 +45,7 @@
     "uns_name": "leiden",
     "output_compression": "gzip",
 }
-meta = {"cpus": 8, "resources_dir": "."}
+meta = {"cpus": 8, "resources_dir": "src/utils"}
 ## VIASH END
 
 sys.path.append(meta["resources_dir"])
@@ -55,6 +55,13 @@
 _shared_logger_name = "leiden"
 
 
+# Function to check available space in /dev/shm
+def get_available_shared_memory():
+    shm_path = "/dev/shm"
+    shm_stats = os.statvfs(shm_path)
+    return shm_stats.f_bsize * shm_stats.f_bavail
+
+
 class SharedNumpyMatrix:
     def __init__(
         self,
@@ -70,6 +77,13 @@ def __init__(
     def from_numpy(
         cls, memory_manager: managers.SharedMemoryManager, array: npt.ArrayLike
     ):
+        available_shared_memory = get_available_shared_memory()
+        n_bytes_required = array.nbytes
+        if available_shared_memory < n_bytes_required:
+            raise ValueError(
+                "Not enough shared memory (/dev/shm) is available to load the data. "
+                f"Required amount: {n_bytes_required}, available: {available_shared_memory}."
+            )
         shm = memory_manager.SharedMemory(size=array.nbytes)
         array_in_shared_memory = np.ndarray(
             array.shape, dtype=array.dtype, buffer=shm.buf