From 480b7fb81e41af959106c823c4988f17ec1e932c Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Wed, 9 Oct 2024 01:44:20 +0200
Subject: [PATCH] Make `MSAFile` generic over the `MSA` type based on `digital`
flag
---
pyhmmer/easel.pyi | 28 ++++++++++++++++++++--------
1 file changed, 20 insertions(+), 8 deletions(-)
diff --git a/pyhmmer/easel.pyi b/pyhmmer/easel.pyi
index ed2bd60e..5be61693 100644
--- a/pyhmmer/easel.pyi
+++ b/pyhmmer/easel.pyi
@@ -442,27 +442,39 @@ class DigitalMSA(MSA):
# --- MSA File ---------------------------------------------------------------
-class MSAFile(typing.ContextManager[MSAFile], typing.Iterator[MSA]):
+M = typing.TypeVar("M", TextMSA, DigitalMSA)
+
+class MSAFile(typing.Generic[M], typing.ContextManager[MSAFile[M]], typing.Iterator[M]):
_FORMATS: typing.ClassVar[typing.Dict[str, int]]
alphabet: typing.Optional[Alphabet]
name: typing.Optional[str]
+ @typing.overload
def __init__(
- self,
+ self: MSAFile[DigitalMSA],
+ file: typing.Union[typing.AnyStr, os.PathLike[typing.AnyStr], typing.BinaryIO],
+ format: typing.Optional[str] = None,
+ *,
+ digital: Literal[True],
+ alphabet: typing.Optional[Alphabet] = None,
+ ) -> None: ...
+ @typing.overload
+ def __init__(
+ self: MSAFile[TextMSA],
file: typing.Union[typing.AnyStr, os.PathLike[typing.AnyStr], typing.BinaryIO],
format: typing.Optional[str] = None,
*,
- digital: bool = False,
+ digital: Literal[False] = False,
alphabet: typing.Optional[Alphabet] = None,
) -> None: ...
- def __enter__(self) -> MSAFile: ...
+ def __enter__(self) -> MSAFile[M]: ...
def __exit__(
self,
exc_type: typing.Optional[typing.Type[BaseException]],
exc_value: typing.Optional[BaseException],
traceback: typing.Optional[types.TracebackType],
) -> bool: ...
- def __iter__(self) -> MSAFile: ...
- def __next__(self) -> MSA: ...
+ def __iter__(self) -> MSAFile[M]: ...
+ def __next__(self) -> M: ...
def __repr__(self) -> str: ...
@property
def closed(self) -> bool: ...
@@ -470,7 +482,7 @@ class MSAFile(typing.ContextManager[MSAFile], typing.Iterator[MSA]):
def digital(self) -> bool: ...
@property
def format(self) -> str: ...
- def read(self) -> typing.Optional[MSA]: ...
+ def read(self) -> typing.Optional[M]: ...
def close(self) -> None: ...
# --- Randomness -------------------------------------------------------------
@@ -585,7 +597,7 @@ class DigitalSequence(Sequence):
S = typing.TypeVar("S", TextSequence, DigitalSequence)
B = typing.TypeVar("B", SequenceBlock[TextSequence], SequenceBlock[DigitalSequence])
-class SequenceBlock(typing.MutableSequence[S], typing.Generic[S]):
+class SequenceBlock(typing.Generic[S], typing.MutableSequence[S]):
def __len__(self) -> int: ...
@typing.overload
def __getitem__(self, index: int) -> S: ...
--
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