add compare.py which contains functions for comparing.

.gitignore

@@ -234,8 +234,6 @@ docs/_build/
 .pybuilder/
 target/
 
-# Jupyter Notebook
-.ipynb_checkpoints
 
 # IPython
 profile_default/
@@ -302,3 +300,6 @@ gurobi.log
 /documentation_builder/test*\.*
 /.benchmarks
 /.testmondata
+
+# sonarlint
+.idea/sonarlint*

release-notes/next-release.md

@@ -6,6 +6,8 @@
 
 ## Other
 
+* Resolve `flake8` issues and add missing type annotations and docstrings in `src/cobra/io` and `tests/test_io` (#1212).
+
 ## Deprecated features
 
 ## Backwards incompatible changes

src/cobra/core/__init__.py

@@ -6,5 +6,5 @@
 from cobra.core.object import Object
 from cobra.core.reaction import Reaction
 from cobra.core.group import Group
-from cobra.core.solution import Solution, LegacySolution, get_solution
+from cobra.core.solution import Solution, get_solution
 from cobra.core.species import Species

src/cobra/core/object.py

@@ -2,6 +2,8 @@
 
 from typing import Optional
 
+from cobra.util import resettable
+
 
 class Object:
     """Defines common behavior of object in cobra.core."""
@@ -81,6 +83,7 @@ def annotation(self) -> dict:
         return self._annotation
 
     @annotation.setter
+    @resettable
     def annotation(self, annotation):
         """Set annotation.
 

src/cobra/core/singleton.py

@@ -1,9 +1,5 @@
-# -*- coding: utf-8 -*-
-
 """Define the singleton meta class."""
 
-from __future__ import absolute_import
-
 
 class Singleton(type):
     """Implementation of the singleton pattern as a meta class."""