fix ruff check errors for refactored code

src/nplinker/metabolomics/abc.py

@@ -1,21 +1,31 @@
 from abc import ABC
 from abc import abstractmethod
-from collections.abc import Sequence
 from typing import TYPE_CHECKING
 
 
 if TYPE_CHECKING:
+    from typing import Mapping
+    from typing import Sequence
     from .molecular_family import MolecularFamily
     from .spectrum import Spectrum
 
 
 class SpectrumLoaderBase(ABC):
+    """Abstract base class for SpectrumLoader."""
+
     @property
     @abstractmethod
-    def spectra(self) -> Sequence["Spectrum"]: ...
+    def spectra(self) -> Sequence["Spectrum"]:
+        """Get Spectrum objects.
+
+        Returns:
+            A sequence of Spectrum objects.
+        """
 
 
 class MolecularFamilyLoaderBase(ABC):
+    """Abstract base class for MolecularFamilyLoader."""
+
     @abstractmethod
     def get_mfs(self, keep_singleton: bool) -> Sequence["MolecularFamily"]:
         """Get MolecularFamily objects.
@@ -26,17 +36,31 @@ def get_mfs(self, keep_singleton: bool) -> Sequence["MolecularFamily"]:
                 only one spectrum.
 
         Returns:
-            A list of MolecularFamily objects.
+            A sequence of MolecularFamily objects.
         """
 
 
 class FileMappingLoaderBase(ABC):
+    """Abstract base class for FileMappingLoader."""
+
     @property
     @abstractmethod
-    def mappings(self) -> dict[str, list[str]]: ...
+    def mappings(self) -> Mapping[str, Sequence[str]]:
+        """Get file mappings.
+
+        Returns:
+            A mapping from spectrum ID to the names of files where the spectrum occurs.
+        """
 
 
 class AnnotationLoaderBase(ABC):
+    """Abstract base class for AnnotationLoader."""
+
     @property
     @abstractmethod
-    def annotations(self) -> dict[str, dict]: ...
+    def annotations(self) -> Mapping[str, Mapping]:
+        """Get annotations.
+
+        Returns:
+            A mapping from spectrum ID to its annotations.
+        """

src/nplinker/schemas/utils.py

@@ -13,7 +13,7 @@ def validate_podp_json(json_data: dict) -> None:
     All validation error messages are collected and raised as a single
     ValueError.
 
-    Parameters:
+    Args:
         json_data: The JSON data to validate.
 
     Raises:

src/nplinker/utils.py

@@ -109,6 +109,15 @@ def is_file_format(file: str | PathLike, format: str = "tsv") -> bool:
 
 
 def calculate_md5(fpath: str | PathLike, chunk_size: int = 1024 * 1024) -> str:
+    """Calculate the MD5 checksum of a file.
+
+    Args:
+        fpath: Path to the file.
+        chunk_size: Chunk size for reading the file. Defaults to 1024*1024.
+
+    Returns:
+        MD5 checksum of the file.
+    """
     if sys.version_info >= (3, 9):
         md5 = hashlib.md5(usedforsecurity=False)
     else:
@@ -120,6 +129,15 @@ def calculate_md5(fpath: str | PathLike, chunk_size: int = 1024 * 1024) -> str:
 
 
 def check_md5(fpath: str | PathLike, md5: str) -> bool:
+    """Verify the MD5 checksum of a file.
+
+    Args:
+        fpath: Path to the file.
+        md5: MD5 checksum to verify.
+
+    Returns:
+        True if the MD5 checksum matches, False otherwise.
+    """
     return md5 == calculate_md5(fpath)