Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

type hint changes in dictlist.py #1256

Open
wants to merge 2 commits into
base: devel
Choose a base branch
from
Open

type hint changes in dictlist.py #1256

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
9c413c7
type hint changes in dictlist.py
Jul 26, 2022
b33ad79
Merge branch 'devel' into dictlist_typeupdate
akaviaLab Aug 15, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions release-notes/next-release.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@ 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).
* Change type hints in dictlist.py to include Object and derivate classes, which reduces type mismatch warnings.
* Updated model.py and test_model.py to Python 3.6+, including type annotations and docstrings.

## Deprecated features
Expand Down
54 changes: 29 additions & 25 deletions src/cobra/core/dictlist.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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):
Expand Down Expand Up @@ -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.
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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)
Expand All @@ -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)
Expand All @@ -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
Expand Down Expand Up @@ -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)
Expand All @@ -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
Expand Down Expand Up @@ -495,7 +499,7 @@ def __setitem__(self, i: Union[slice, int], y: Union[list, Object]) -> None:
list.__setitem__(self, i, y)
self._dict[the_id] = i

def __delitem__(self, index: int) -> None:
def __delitem__(self, index: Union[int, slice]) -> None:
"""Remove item from DictList."""
removed = self[index]
list.__delitem__(self, index)
Expand All @@ -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)

Expand Down