corrected according to changes. Updated release notes.

Author: uri.akavia

.gitignore

@@ -87,11 +87,6 @@ ipython_config.py
 # Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
 
 # User-specific stuff
-.idea/**/workspace.xml
-.idea/**/tasks.xml
-.idea/**/usage.statistics.xml
-.idea/**/dictionaries
-.idea/**/shelf
 .idea/
 
 # Generated files
@@ -235,10 +230,6 @@ docs/_build/
 .pybuilder/
 target/
 
-# Jupyter Notebook
-
-# IPython
-
 # pyenv
 #   For a library or package, you might want to ignore these files since the code is
 #   intended to run in multiple environments; otherwise, check them in:

release-notes/next-release.md

@@ -13,7 +13,11 @@ of SBO:0000633 (see https://sourceforge.net/p/sbo/term-request/113/)
 ## Other
 
 * Resolve `flake8` issues and add missing type annotations and docstrings in `src/cobra/io` and `tests/test_io` (#1212).
+* Updated model.py and test_model.py to Python 3.6+, including type annotations and docstrings.
 
 ## Deprecated features
 
 ## Backwards incompatible changes
+* Removed `model.add_reaction()` and replaced remaining usages of it with `model.add_reactions()`
+* Removed the following tests: test_add_remove_reaction_benchmark, test_add_reaction, test_add_reaction_context, test_add_reaction_from_other_model, test_add_cobra_reaction
+* Removed `model.__add__` and `model.__iadd__` - use `model.merge` to replace them.

src/cobra/core/dictlist.py

@@ -12,12 +12,16 @@
     Pattern,
     Tuple,
     Type,
+    TypeVar,
     Union,
 )
 
 from numpy import bool_
 
-from cobra.core.object import Object
+from .object import Object
+
+
+Object_T = TypeVar("Object_T", bound=Object)
 
 
 class DictList(list):
@@ -50,12 +54,12 @@ def __init__(self, *args):
                 self.extend(other)
 
     # noinspection PyShadowingBuiltins
-    def has_id(self, id: Union[Object, str]) -> bool:
+    def has_id(self, id: Union[Object_T, str]) -> bool:
         """Check if id is in DictList."""
         return id in self._dict
 
     # noinspection PyShadowingBuiltins
-    def _check(self, id: Union[Object, str]) -> None:
+    def _check(self, id: Union[Object_T, str]) -> None:
         """Make sure duplicate id's are not added.
 
         This function is called before adding in elements.
@@ -69,15 +73,15 @@ def _generate_index(self) -> None:
         self._dict = {v.id: k for k, v in enumerate(self)}
 
     # noinspection PyShadowingBuiltins
-    def get_by_id(self, id: Union[Object, str]) -> Object:
+    def get_by_id(self, id: Union[Object_T, str]) -> Object_T:
         """Return the element with a matching id."""
         return list.__getitem__(self, self._dict[id])
 
     def list_attr(self, attribute: str) -> list:
         """Return a list of the given attribute for every object."""
         return [getattr(i, attribute) for i in self]
 
-    def get_by_any(self, iterable: List[Union[str, Object, int]]) -> list:
+    def get_by_any(self, iterable: List[Union[str, Object_T, int]]) -> list:
         """Get a list of members using several different ways of indexing.
 
         Parameters
@@ -168,29 +172,29 @@ def select_attribute(x: Optional[Any]) -> Any:
         results._extend_nocheck(matches)
         return results
 
-    def _replace_on_id(self, new_object: Object) -> None:
+    def _replace_on_id(self, new_object: Object_T) -> None:
         """Replace an object by another with the same id."""
         the_id = new_object.id
         the_index = self._dict[the_id]
         list.__setitem__(self, the_index, new_object)
 
     # overriding default list functions with new ones
-    def append(self, entity: Object) -> None:
+    def append(self, entity: Object_T) -> None:
         """Append object to end."""
         the_id = entity.id
         self._check(the_id)
         self._dict[the_id] = len(self)
         list.append(self, entity)
 
-    def union(self, iterable: Iterable[Object]) -> None:
+    def union(self, iterable: Iterable[Object_T]) -> None:
         """Add elements with id's not already in the model."""
         _dict = self._dict
         append = self.append
         for i in iterable:
             if i.id not in _dict:
                 append(i)
 
-    def extend(self, iterable: Iterable[Object]) -> None:
+    def extend(self, iterable: Iterable[Object_T]) -> None:
         """Extend list by appending elements from the iterable.
 
         Sometimes during initialization from an older pickle, _dict
@@ -223,7 +227,7 @@ def extend(self, iterable: Iterable[Object]) -> None:
                     f"Is it present twice?"
                 )
 
-    def _extend_nocheck(self, iterable: Iterable[Object]) -> None:
+    def _extend_nocheck(self, iterable: Iterable[Object_T]) -> None:
         """Extend without checking for uniqueness.
 
         This function should only be used internally by DictList when it
@@ -245,7 +249,7 @@ def _extend_nocheck(self, iterable: Iterable[Object]) -> None:
         for i, obj in enumerate(islice(self, current_length, None), current_length):
             _dict[obj.id] = i
 
-    def __sub__(self, other: Iterable[Object]) -> "DictList":
+    def __sub__(self, other: Iterable[Object_T]) -> "DictList":
         """Remove a value or values, and returns the new DictList.
 
         x.__sub__(y) <==> x - y
@@ -265,7 +269,7 @@ def __sub__(self, other: Iterable[Object]) -> "DictList":
             total.remove(item)
         return total
 
-    def __isub__(self, other: Iterable[Object]) -> "DictList":
+    def __isub__(self, other: Iterable[Object_T]) -> "DictList":
         """Remove a value or values in place.
 
         x.__sub__(y) <==> x -= y
@@ -279,7 +283,7 @@ def __isub__(self, other: Iterable[Object]) -> "DictList":
             self.remove(item)
         return self
 
-    def __add__(self, other: Iterable[Object]) -> "DictList":
+    def __add__(self, other: Iterable[Object_T]) -> "DictList":
         """Add item while returning a new DictList.
 
         x.__add__(y) <==> x + y
@@ -295,7 +299,7 @@ def __add__(self, other: Iterable[Object]) -> "DictList":
         total.extend(other)
         return total
 
-    def __iadd__(self, other: Iterable[Object]) -> "DictList":
+    def __iadd__(self, other: Iterable[Object_T]) -> "DictList":
         """Add item while returning the same DictList.
 
         x.__iadd__(y) <==> x += y
@@ -337,7 +341,7 @@ def __setstate__(self, state: dict) -> None:
         self._generate_index()
 
     # noinspection PyShadowingBuiltins
-    def index(self, id: Union[str, Object], *args) -> int:
+    def index(self, id: Union[str, Object_T], *args) -> int:
         """Determine the position in the list.
 
         Parameters
@@ -361,7 +365,7 @@ def index(self, id: Union[str, Object], *args) -> int:
         except KeyError:
             raise ValueError(f"{str(id)} not found")
 
-    def __contains__(self, entity: Union[str, Object]) -> bool:
+    def __contains__(self, entity: Union[str, Object_T]) -> bool:
         """Ask if the DictList contain an entity.
 
         DictList.__contains__(entity) <==> entity in DictList
@@ -385,7 +389,7 @@ def __copy__(self) -> "DictList":
         the_copy._dict = self._dict.copy()
         return the_copy
 
-    def insert(self, index: int, entity: Object) -> None:
+    def insert(self, index: int, entity: Object_T) -> None:
         """Insert entity before index."""
         self._check(entity.id)
         list.insert(self, index, entity)
@@ -396,7 +400,7 @@ def insert(self, index: int, entity: Object) -> None:
                 _dict[i] = j + 1
         _dict[entity.id] = index
 
-    def pop(self, *args) -> Object:
+    def pop(self, *args) -> Object_T:
         """Remove and return item at index (default last)."""
         value = list.pop(self, *args)
         index = self._dict.pop(value.id)
@@ -410,11 +414,11 @@ def pop(self, *args) -> Object:
                 _dict[i] = j - 1
         return value
 
-    def add(self, x: Object) -> None:
+    def add(self, x: Object_T) -> None:
         """Opposite of `remove`. Mirrors set.add."""
         self.extend([x])
 
-    def remove(self, x: Union[str, Object]) -> None:
+    def remove(self, x: Union[str, Object_T]) -> None:
         """.. warning :: Internal use only.
 
         Each item is unique in the list which allows this
@@ -446,8 +450,8 @@ def key(i):
         self._generate_index()
 
     def __getitem__(
-        self, i: Union[int, slice, Iterable, Object, "DictList"]
-    ) -> Union["DictList", Object]:
+        self, i: Union[int, slice, Iterable, Object_T, "DictList"]
+    ) -> Union["DictList", Object_T]:
         """Get item from DictList."""
         if isinstance(i, int):
             return list.__getitem__(self, i)
@@ -466,7 +470,7 @@ def __getitem__(
         else:
             return list.__getitem__(self, i)
 
-    def __setitem__(self, i: Union[slice, int], y: Union[list, Object]) -> None:
+    def __setitem__(self, i: Union[slice, int], y: Union[list, Object_T]) -> None:
         """Set an item via index or slice.
 
         Parameters
@@ -512,7 +516,7 @@ def __getslice__(self, i: int, j: int) -> "DictList":
         """Get a slice from it to j of DictList."""
         return self.__getitem__(slice(i, j))
 
-    def __setslice__(self, i: int, j: int, y: Union[list, Object]) -> None:
+    def __setslice__(self, i: int, j: int, y: Union[list, Object_T]) -> None:
         """Set slice, where y is an iterable."""
         self.__setitem__(slice(i, j), y)