From 621635a978c6650fca31850bcd2f2b97005e8ff2 Mon Sep 17 00:00:00 2001
From: Cunliang Geng <c.geng@esciencecenter.nl>
Date: Fri, 14 Jun 2024 13:20:06 +0200
Subject: [PATCH] use specific types for return of abstract method when
 possible

use more general type when necessary
---
 src/nplinker/genomics/abc.py     | 10 ++++------
 src/nplinker/metabolomics/abc.py | 10 ++++------
 2 files changed, 8 insertions(+), 12 deletions(-)

diff --git a/src/nplinker/genomics/abc.py b/src/nplinker/genomics/abc.py
index da0dff44..daeb3bef 100644
--- a/src/nplinker/genomics/abc.py
+++ b/src/nplinker/genomics/abc.py
@@ -1,7 +1,5 @@
 from abc import ABC
 from abc import abstractmethod
-from typing import Mapping
-from typing import Sequence
 from .bgc import BGC
 from .gcf import GCF
 
@@ -9,7 +7,7 @@
 class BGCLoaderBase(ABC):
     """Abstract base class for BGC loader."""
 
-    def __init__(self, data_dir: str):
+    def __init__(self, data_dir: str) -> None:
         """Initialize the BGC loader.
 
         Args:
@@ -19,7 +17,7 @@ def __init__(self, data_dir: str):
         self.data_dir = data_dir
 
     @abstractmethod
-    def get_files(self) -> Mapping[str, str]:
+    def get_files(self) -> dict[str, str]:
         """Get path to BGC files.
 
         Returns:
@@ -27,7 +25,7 @@ def get_files(self) -> Mapping[str, str]:
         """
 
     @abstractmethod
-    def get_bgcs(self) -> Sequence[BGC]:
+    def get_bgcs(self) -> list[BGC]:
         """Get BGC objects.
 
         Returns:
@@ -39,7 +37,7 @@ class GCFLoaderBase(ABC):
     """Abstract base class for GCF loader."""
 
     @abstractmethod
-    def get_gcfs(self, keep_mibig_only: bool, keep_singleton: bool) -> Sequence[GCF]:
+    def get_gcfs(self, keep_mibig_only: bool, keep_singleton: bool) -> list[GCF]:
         """Get GCF objects.
 
         Args:
diff --git a/src/nplinker/metabolomics/abc.py b/src/nplinker/metabolomics/abc.py
index 4665c5b8..6af3052e 100644
--- a/src/nplinker/metabolomics/abc.py
+++ b/src/nplinker/metabolomics/abc.py
@@ -1,7 +1,5 @@
 from abc import ABC
 from abc import abstractmethod
-from typing import Mapping
-from typing import Sequence
 from .molecular_family import MolecularFamily
 from .spectrum import Spectrum
 
@@ -11,7 +9,7 @@ class SpectrumLoaderBase(ABC):
 
     @property
     @abstractmethod
-    def spectra(self) -> Sequence["Spectrum"]:
+    def spectra(self) -> list["Spectrum"]:
         """Get Spectrum objects.
 
         Returns:
@@ -23,7 +21,7 @@ class MolecularFamilyLoaderBase(ABC):
     """Abstract base class for MolecularFamilyLoader."""
 
     @abstractmethod
-    def get_mfs(self, keep_singleton: bool) -> Sequence["MolecularFamily"]:
+    def get_mfs(self, keep_singleton: bool) -> list["MolecularFamily"]:
         """Get MolecularFamily objects.
 
         Args:
@@ -41,7 +39,7 @@ class FileMappingLoaderBase(ABC):
 
     @property
     @abstractmethod
-    def mappings(self) -> Mapping[str, Sequence[str]]:
+    def mappings(self) -> dict[str, list[str]]:
         """Get file mappings.
 
         Returns:
@@ -54,7 +52,7 @@ class AnnotationLoaderBase(ABC):
 
     @property
     @abstractmethod
-    def annotations(self) -> Mapping[str, Mapping]:
+    def annotations(self) -> dict[str, dict]:
         """Get annotations.
 
         Returns: