remove lookup_index method from StrainCollection (#90)

- remove method `lookup_index`
- remove attribute `_strain_dict_index`

src/nplinker/strain_collection.py

@@ -1,5 +1,4 @@
 import csv
-import os
 from os import PathLike
 from pathlib import Path
 from typing import Iterator
@@ -9,7 +8,6 @@
 from .utils import list_dirs
 from .utils import list_files
 
-
 logger = LogConfig.getLogger(__name__)
 
 
@@ -20,7 +18,6 @@ def __init__(self):
         self._strains: list[Strain] = []
         # dict of strain name (id and alias) to strain object
         self._strain_dict_name: dict[str, Strain] = {}
-        self._strain_dict_index: dict[int, Strain] = {}
 
     def __repr__(self) -> str:
         return str(self)
@@ -38,7 +35,7 @@ def __len__(self) -> int:
     def __eq__(self, other) -> bool:
         if isinstance(other, StrainCollection):
             return (self._strains == other._strains
-                    and self._strain_dict_index == other._strain_dict_index)
+                    and self._strain_dict_name == other._strain_dict_name)
         return NotImplemented
 
     def __contains__(self, item: str | Strain) -> bool:
@@ -74,7 +71,6 @@ def add(self, strain: Strain) -> None:
                 existing.add_alias(alias)
                 self._strain_dict_name[alias] = existing
         else:
-            self._strain_dict_index[len(self)] = strain
             self._strains.append(strain)
             self._strain_dict_name[strain.id] = strain
             for alias in strain.aliases:
@@ -88,7 +84,6 @@ def remove(self, strain: Strain):
         """
         if strain.id in self._strain_dict_name:
             self._strains.remove(strain)
-            # remove from dict id
             del self._strain_dict_name[strain.id]
             for alias in strain.aliases:
                 del self._strain_dict_name[alias]
@@ -102,17 +97,6 @@ def filter(self, strain_set: set[Strain]):
             if strain not in strain_set:
                 self.remove(strain)
 
-    def lookup_index(self, index: int) -> Strain:
-        """Return the strain from lookup by index.
-
-        Args:
-            index(int): Position index from which to retrieve the strain
-
-        Returns:
-            Strain: Strain identified by the given index.
-        """
-        return self._strain_dict_index[index]
-
     def lookup(self, name: str) -> Strain:
         """Lookup a strain by name (id or alias).
 

tests/test_strain_collection.py

@@ -41,13 +41,13 @@ def test_iter(collection: StrainCollection, strain: Strain):
     for actual in collection:
         assert actual == strain
 
+
 def test_add(strain: Strain):
     sut = StrainCollection()
     sut.add(strain)
     assert strain in sut
     for alias in strain.aliases:
         assert alias in sut
-    assert sut._strain_dict_index[0] == strain
 
 
 def test_remove(collection: StrainCollection, strain: Strain):
@@ -56,9 +56,6 @@ def test_remove(collection: StrainCollection, strain: Strain):
     with pytest.raises(KeyError):
         _ = collection._strain_dict_name[strain.id]
     assert strain not in collection
-    # TODO: issue #90
-    # with pytest.raises(KeyError):
-    #     collection.lookup_index(0)
 
 
 def test_filter(collection: StrainCollection, strain: Strain):
@@ -70,13 +67,6 @@ def test_filter(collection: StrainCollection, strain: Strain):
     assert len(collection) == 1
 
 
-def test_lookup_index(collection: StrainCollection, strain: Strain):
-    actual = collection.lookup_index(0)
-    assert actual == strain
-    with pytest.raises(KeyError):
-        collection.lookup_index(1)
-
-
 def test_lookup(collection: StrainCollection, strain: Strain):
     assert collection.lookup(strain.id) == strain
     for alias in strain.aliases:
@@ -89,7 +79,6 @@ def test_add_from_file():
     sut = StrainCollection()
     sut.add_from_file(DATA_DIR / "strain_mappings.csv")
     assert len(sut) == 27
-    assert len(sut.lookup_index(1).aliases) == 29
 
 
 def test_save_to_file(collection: StrainCollection, tmp_path):