From 0815f4865f1c8ae81027056db667ada0aee9c2e8 Mon Sep 17 00:00:00 2001
From: Cunliang Geng <c.geng@esciencecenter.nl>
Date: Mon, 30 Oct 2023 13:37:20 +0100
Subject: [PATCH 1/3] format `strain_collection.py`

---
 src/nplinker/strain_collection.py | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/nplinker/strain_collection.py b/src/nplinker/strain_collection.py
index f2f83c3c..a210d431 100644
--- a/src/nplinker/strain_collection.py
+++ b/src/nplinker/strain_collection.py
@@ -58,7 +58,10 @@ def add(self, strain: Strain) -> None:
         if strain in self._strains:
             # only one strain object per id
             strain_ref = self._strain_dict_name[strain.id][0]
-            new_aliases = [alias for alias in strain.aliases if alias not in strain_ref.aliases]
+            new_aliases = [
+                alias for alias in strain.aliases
+                if alias not in strain_ref.aliases
+            ]
             for alias in new_aliases:
                 strain_ref.add_alias(alias)
                 if alias not in self._strain_dict_name:
@@ -92,14 +95,16 @@ def remove(self, strain: Strain):
             for name in strain_ref.names:
                 if name in self._strain_dict_name:
                     new_strain_list = [
-                        s for s in self._strain_dict_name[name] if s.id != strain.id
+                        s for s in self._strain_dict_name[name]
+                        if s.id != strain.id
                     ]
                     if not new_strain_list:
                         del self._strain_dict_name[name]
                     else:
                         self._strain_dict_name[name] = new_strain_list
         else:
-            raise ValueError(f"Strain {strain} not found in strain collection.")
+            raise ValueError(
+                f"Strain {strain} not found in strain collection.")
 
     def filter(self, strain_set: set[Strain]):
         """

From e53ba6e0268cd44883b60c2ba8649d8867925f8f Mon Sep 17 00:00:00 2001
From: Cunliang Geng <c.geng@esciencecenter.nl>
Date: Mon, 30 Oct 2023 13:37:01 +0100
Subject: [PATCH 2/3] add `__add__` method to `StrainCollection` class

- add the `__add__` magic method
-  add unit tests for this magic method
---
 src/nplinker/strain_collection.py | 10 ++++++++++
 tests/test_strain_collection.py   | 28 ++++++++++++++++++++++++++++
 2 files changed, 38 insertions(+)

diff --git a/src/nplinker/strain_collection.py b/src/nplinker/strain_collection.py
index a210d431..1f430d4d 100644
--- a/src/nplinker/strain_collection.py
+++ b/src/nplinker/strain_collection.py
@@ -37,6 +37,16 @@ def __eq__(self, other) -> bool:
                     and self._strain_dict_name == other._strain_dict_name)
         return NotImplemented
 
+    def __add__(self, other) -> 'StrainCollection':
+        if isinstance(other, StrainCollection):
+            sc = StrainCollection()
+            for strain in self._strains:
+                sc.add(strain)
+            for strain in other._strains:
+                sc.add(strain)
+            return sc
+        return NotImplemented
+
     def __contains__(self, item: Strain) -> bool:
         """Check if the strain collection contains the given Strain object.
         """
diff --git a/tests/test_strain_collection.py b/tests/test_strain_collection.py
index 01d5134d..0a4ec786 100644
--- a/tests/test_strain_collection.py
+++ b/tests/test_strain_collection.py
@@ -29,6 +29,34 @@ def test_eq(collection: StrainCollection, strain: Strain):
     assert collection == other
 
 
+def test_magic_add(collection: StrainCollection, strain: Strain):
+    other = StrainCollection()
+    # same id, same alias
+    other.add(strain)
+    # same id, different alias
+    strain1 = Strain("strain_1")
+    strain1.add_alias("strain_1_b")
+    other.add(strain1)
+    # different id, same alias
+    strain2 = Strain("strain_2")
+    strain2.add_alias("strain_2_a")
+    other.add(strain2)
+
+    assert collection + other == other + collection
+
+    actual = collection + other
+    assert len(actual) == 2
+    assert strain in actual
+    assert strain1 in actual
+    assert strain2 in actual
+    assert len(actual._strain_dict_name) == 5
+    assert actual._strain_dict_name["strain_1"] == [strain]
+    assert actual._strain_dict_name["strain_1_a"] == [strain]
+    assert actual._strain_dict_name["strain_1_b"] == [strain]
+    assert actual._strain_dict_name["strain_2"] == [strain2]
+    assert actual._strain_dict_name["strain_2_a"] == [strain2]
+
+
 def test_contains(collection: StrainCollection, strain: Strain):
     assert strain in collection
     strain2 = Strain("strain_2")

From 62291ddf82acd13b1872f6894df27c1c2d7f8e0c Mon Sep 17 00:00:00 2001
From: Cunliang Geng <c.geng@esciencecenter.nl>
Date: Tue, 31 Oct 2023 15:38:44 +0100
Subject: [PATCH 3/3] update type hints for class itself

When using `from __future__ import annotations`, the class name can be directly used as type hint; Otherwise, use string like "ClassName" as type hint.
---
 src/nplinker/strain_collection.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/nplinker/strain_collection.py b/src/nplinker/strain_collection.py
index 1f430d4d..86993f6d 100644
--- a/src/nplinker/strain_collection.py
+++ b/src/nplinker/strain_collection.py
@@ -1,3 +1,4 @@
+from __future__ import annotations
 import json
 from os import PathLike
 from typing import Iterator
@@ -37,7 +38,7 @@ def __eq__(self, other) -> bool:
                     and self._strain_dict_name == other._strain_dict_name)
         return NotImplemented
 
-    def __add__(self, other) -> 'StrainCollection':
+    def __add__(self, other) -> StrainCollection:
         if isinstance(other, StrainCollection):
             sc = StrainCollection()
             for strain in self._strains: