Address linting errors.

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

Author: Eric T. Dawson

sub-packages/bionemo-scdl/README.md

@@ -265,7 +265,7 @@ BioNeMo-SCDL has an Apache 2.0 license, as found in the LICENSE file.
 
 Please follow the guidelines for contributions to the BioNeMo Framework.
 
-To contribute to SCDL, we recommend installing additional dependencies for development and 
+To contribute to SCDL, we recommend installing additional dependencies for development and
 installing the SCDL package from source.
 
 ```bash
@@ -286,4 +286,4 @@ To run a specific test:
 
 ```bash
 python -m pytest tests/test_<test name>.py
-```
+```

sub-packages/bionemo-scdl/docs/header_api_reference.md

@@ -10,29 +10,29 @@ Main header class for SCDL archives.
 
 ```python
 class SCDLHeader:
-    def __init__(self, version=None, backend=Backend.MEMMAP_V0, 
+    def __init__(self, version=None, backend=Backend.MEMMAP_V0,
                  arrays=None, feature_indices=None)
-    
+
     # Array management
     def add_array(self, array_info: ArrayInfo) -> None
     def get_array(self, name: str) -> Optional[ArrayInfo]
     def remove_array(self, name: str) -> bool
-    
-    # Feature index management  
+
+    # Feature index management
     def add_feature_index(self, feature_index: FeatureIndexInfo) -> None
     def get_feature_index(self, name: str) -> Optional[FeatureIndexInfo]
     def remove_feature_index(self, name: str) -> bool
-    
+
     # Serialization
     def serialize(self) -> bytes
     @classmethod
     def deserialize(cls, data: bytes) -> 'SCDLHeader'
-    
+
     # File I/O
     def save(self, file_path: str) -> None
     @classmethod
     def load(cls, file_path: str) -> 'SCDLHeader'
-    
+
     # Validation and utilities
     def validate(self) -> None
     def calculate_total_size(self) -> int
@@ -46,21 +46,21 @@ Information about arrays in the archive.
 
 ```python
 class ArrayInfo:
-    def __init__(self, name: str, length: int, dtype: ArrayDType, 
+    def __init__(self, name: str, length: int, dtype: ArrayDType,
                  shape: Optional[Tuple[int, ...]] = None)
-    
+
     # Properties
     name: str                           # Array filename
     length: int                        # Number of elements
     dtype: ArrayDType                  # Data type
     shape: Optional[Tuple[int, ...]]   # Optional shape
-    
+
     # Serialization
     def serialize(self, codec: BinaryHeaderCodec) -> bytes
     @classmethod
-    def deserialize(cls, codec: BinaryHeaderCodec, data: bytes, 
+    def deserialize(cls, codec: BinaryHeaderCodec, data: bytes,
                    offset: int = 0) -> Tuple['ArrayInfo', int]
-    
+
     # Utilities
     def calculate_size(self) -> int
 ```
@@ -74,20 +74,20 @@ class FeatureIndexInfo:
     def __init__(self, name: str, length: int, dtype: ArrayDType,
                  index_files: Optional[List[str]] = None,
                  shape: Optional[Tuple[int, ...]] = None)
-    
+
     # Properties
     name: str                           # Index name
     length: int                        # Number of entries
     dtype: ArrayDType                  # Data type
     index_files: List[str]             # Associated index files
     shape: Optional[Tuple[int, ...]]   # Optional shape
-    
+
     # Serialization
     def serialize(self, codec: BinaryHeaderCodec) -> bytes
     @classmethod
     def deserialize(cls, codec: BinaryHeaderCodec, data: bytes,
                    offset: int = 0) -> Tuple['FeatureIndexInfo', int]
-    
+
     # Utilities
     def calculate_size(self) -> int
 ```
@@ -101,18 +101,18 @@ Data types for arrays.
 ```python
 class ArrayDType(IntEnum):
     UINT8_ARRAY = 1          # 8-bit unsigned integers
-    UINT16_ARRAY = 2         # 16-bit unsigned integers  
+    UINT16_ARRAY = 2         # 16-bit unsigned integers
     UINT32_ARRAY = 3         # 32-bit unsigned integers
     UINT64_ARRAY = 4         # 64-bit unsigned integers
     FLOAT16_ARRAY = 5        # 16-bit floating point
     FLOAT32_ARRAY = 6        # 32-bit floating point
     FLOAT64_ARRAY = 7        # 64-bit floating point
     STRING_ARRAY = 8         # Variable-length strings
     FIXED_STRING_ARRAY = 9   # Fixed-length strings
-    
+
     @property
     def numpy_dtype_string(self) -> str  # Get NumPy dtype string
-    
+
     @classmethod
     def from_numpy_dtype(cls, dtype) -> 'ArrayDType'  # Convert from NumPy dtype
 ```
@@ -131,12 +131,12 @@ class Backend(IntEnum):
 ### Header Operations
 
 ```python
-def create_header_from_arrays(array_files: List[str], 
+def create_header_from_arrays(array_files: List[str],
                              backend: Backend = Backend.MEMMAP_V0,
                              version: Optional[SCDLVersion] = None) -> SCDLHeader
     """Create header by scanning array files."""
 
-def validate_header_compatibility(header1: SCDLHeader, 
+def validate_header_compatibility(header1: SCDLHeader,
                                 header2: SCDLHeader) -> bool
     """Check if two headers are compatible for merging."""
 
@@ -149,10 +149,10 @@ def merge_headers(header1: SCDLHeader, header2: SCDLHeader) -> SCDLHeader
 ```python
 class HeaderReader:
     def __init__(self, file_path: str)
-    
+
     def validate_magic(self) -> bool              # Quick magic number check
     def get_version(self) -> SCDLVersion         # Get version info
-    def get_backend(self) -> Backend             # Get backend info  
+    def get_backend(self) -> Backend             # Get backend info
     def get_array_count(self) -> int             # Get array count
     def get_full_header(self) -> SCDLHeader      # Get complete header
 ```
@@ -162,9 +162,9 @@ class HeaderReader:
 ```python
 class SCDLVersion:
     major: int = 0
-    minor: int = 0  
+    minor: int = 0
     point: int = 0
-    
+
     def __str__(self) -> str         # "major.minor.point"
     def __eq__(self, other) -> bool
     def __ne__(self, other) -> bool
@@ -181,8 +181,8 @@ class CurrentSCDLVersion(SCDLVersion):
 from bionemo.scdl.schema.magic import SCDL_MAGIC_NUMBER
 from bionemo.scdl.schema.headerutil import Endianness
 
-SCDL_MAGIC_NUMBER: bytes = b'SCDL'   # Archive magic number
-Endianness.NETWORK                    # Network byte order (required)
+SCDL_MAGIC_NUMBER: bytes = b"SCDL"  # Archive magic number
+Endianness.NETWORK  # Network byte order (required)
 ```
 
 ## Exceptions
@@ -245,7 +245,7 @@ reader = HeaderReader("large_header.bin")
 if reader.validate_magic():
     print(f"Version: {reader.get_version()}")
     print(f"Arrays: {reader.get_array_count()}")
-    
+
     # Only load full header when needed
     if reader.get_array_count() > 0:
         full_header = reader.get_full_header()
@@ -258,10 +258,10 @@ import numpy as np
 from bionemo.scdl.schema.header import ArrayDType
 
 # Convert various numpy dtypes to ArrayDType enums
-array_dtype1 = ArrayDType.from_numpy_dtype(np.float32)        # Type class
-array_dtype2 = ArrayDType.from_numpy_dtype('float32')         # String
-array_dtype3 = ArrayDType.from_numpy_dtype(np.dtype('f4'))    # Dtype object
+array_dtype1 = ArrayDType.from_numpy_dtype(np.float32)  # Type class
+array_dtype2 = ArrayDType.from_numpy_dtype("float32")  # String
+array_dtype3 = ArrayDType.from_numpy_dtype(np.dtype("f4"))  # Dtype object
 
 # Use in ArrayInfo creation
 array = ArrayInfo("data.dat", 1000, array_dtype1)
-```
+```