Precommit found lint errors so here are the formatted files.

Signed-off-by: Eric T. Dawson <edawson@nvidia.com>

Author: Eric T. Dawson

sub-packages/bionemo-scdl/src/bionemo/scdl/io/single_cell_memmap_dataset.py

@@ -54,6 +54,7 @@ class FileNames(str, Enum):
     NEIGHBOR_INDICES = "neighbor_indices.npy"
     NEIGHBOR_INDICES_PTR = "neighbor_indptr.npy"
     NEIGHBOR_VALUES = "neighbor_values.npy"
+    HEADER = "header.sch"
 
 
 class Mode(str, Enum):
@@ -248,7 +249,6 @@ def __init__(
         """
         self._version: str = importlib.metadata.version("bionemo.scdl")
         self.data_path: str = data_path
-        self.header_file_name: str = "header.sch"
         self.header: SCDLHeader = None
         self.mode: Mode = mode
         self.paginated_load_cutoff = paginated_load_cutoff
@@ -309,6 +309,30 @@ def __init__(
                 case _:
                     raise ValueError("An np.memmap path, an h5ad path, or the number of elements and rows is required")
 
+    def _path_in_archive(self, filename: str | Path) -> str:
+        """Returns the full path to a file within the archive, joining self.data_path and the filename.
+
+        Args:
+            filename: The filename or Path object to resolve within the archive.
+
+        Returns:
+            The full path as a string.
+        """
+        if isinstance(filename, Path):
+            filename = str(filename)
+        return os.path.join(self.data_path, filename)
+
+    @property
+    def header_path(self) -> str:
+        """Returns the full path to the header file in the archive.
+
+        Example:
+            >>> ds = SingleCellMemMapDataset(data_path="my_data")
+            >>> ds.header_path
+            'my_data/scdl_header.json'
+        """
+        return self._path_in_archive(FileNames.HEADER.value)
+
     def _init_neighbor_args(self, neighbor_key, neighbor_sampling_strategy, fallback_to_identity):
         # Neighbor tracking
         self._has_neighbors = False  # Track if neighbor data was successfully loaded/found
@@ -686,7 +710,7 @@ def features(self) -> Optional[RowFeatureIndex]:
 
     def _load_mmap_file_if_exists(self, file_path, dtype):
         if os.path.exists(file_path):
-            return np.memmap(file_path, dtype=dtype, mode=self.mode)
+            return np.memmap(file_path, dtype=dtype, mode=self.mode.value)
         else:
             raise FileNotFoundError(f"The mmap file at {file_path} is missing")
 
@@ -708,15 +732,15 @@ def load(self, stored_path: str) -> None:
             )
         self.data_path = stored_path
         self.mode = Mode.READ_APPEND
-        # self.header_path = Path(stored_path) / self.header_file_name
         # Load header if present; keep None if missing or unreadable
-        if os.path.exists(self.data_path / self.header_file_name):
+        if os.path.exists(self.header_path):
             try:
-                self.header = SCDLHeader.load(str(self.data_path / self.header_file_name))
+                self.header = SCDLHeader.load(str(self.header_path))
             except Exception as e:
-                warnings.warn(f"Failed to load SCDL header at {Path(self.data_path) / self.header_file_name}: {e}")
+                warnings.warn(f"Failed to load SCDL header at {self.header_path}: {e}")
                 self.header = None
         else:
+            warnings.warn(f"SCDL header missing at {self.header_path}; continuing without header.")
             self.header = None
 
         # Metadata is required, so we must check if it exists and fail if not.
@@ -812,7 +836,12 @@ def regular_load_h5ad(
         self.row_index[0 : num_rows + 1] = count_data.indptr.astype(int)
 
         vars = adata.var
-        adata.file.close()
+        file_handle = getattr(adata, "file", None)
+        if file_handle is not None:
+            try:
+                file_handle.close()
+            except Exception:
+                pass
 
         return vars, num_rows
 
@@ -882,7 +911,12 @@ def paginated_load_h5ad(
             shape=(n_elements,),
         )
         vars = adata.var
-        adata.file.close()
+        file_handle = getattr(adata, "file", None)
+        if file_handle is not None:
+            try:
+                file_handle.close()
+            except Exception:
+                pass
 
         return vars, num_rows
 
@@ -1024,7 +1058,7 @@ def _write_header(self):
                 indexes,
             )
         )
-        header.save(Path(self.data_path) / self.header_file_name)
+        header.save(self.header_path)
 
     def save(self, output_path: Optional[str] = None) -> None:
         """Saves the class to a given output path.

sub-packages/bionemo-scdl/tests/bionemo/scdl/conftest.py

@@ -15,13 +15,36 @@
 
 
 import shutil
+import time
+from importlib.metadata import PackageNotFoundError, version
 from pathlib import Path
 
 import pytest
 
 from bionemo.core.data.load import load
 
 
+@pytest.fixture(scope="session", autouse=True)
+def verify_bionemo_core_installed() -> None:
+    """Ensure bionemo-core is installed, print its version, and pause briefly.
+
+    Runs once before any tests. If the distribution is not installed, aborts the
+    test session early with a clear message.
+    """
+    try:
+        core_version = version("bionemo-core")
+    except PackageNotFoundError:
+        pytest.exit(
+            "bionemo-core is not installed. Please install it (e.g., `pip install -e sub-packages/bionemo-core`) before running tests.",
+            returncode=1,
+        )
+
+    print("=" * 72)
+    print(f"BioNeMo Core (bionemo-core) version: {core_version}")
+    print("=" * 72, flush=True)
+    time.sleep(3)
+
+
 @pytest.fixture
 def test_directory() -> Path:
     """Gets the path to the directory with test data.