Bump mypy and pytest, fix simple mypy issues

fgpyo/io/tests/test_io.py

@@ -80,14 +80,14 @@ def test_assert_path_is_writeable_pass() -> None:
     """Should return the correct writeable path"""
     with NamedTemp(suffix=".txt", mode="w", delete=True) as read_file:
         path = Path(read_file.name)
-        assert fio.assert_path_is_writeable(path=path) is None
+        fio.assert_path_is_writeable(path=path)
 
 
 @pytest.mark.parametrize(
     "suffix, expected",
     [
-        (".gz", io._io.TextIOWrapper),
-        (".fa", io._io.TextIOWrapper),
+        (".gz", io.TextIOWrapper),
+        (".fa", io.TextIOWrapper),
     ],
 )
 def test_reader(
@@ -103,8 +103,8 @@ def test_reader(
 @pytest.mark.parametrize(
     "suffix, expected",
     [
-        (".gz", io._io.TextIOWrapper),
-        (".fa", io._io.TextIOWrapper),
+        (".gz", io.TextIOWrapper),
+        (".fa", io.TextIOWrapper),
     ],
 )
 def test_writer(

fgpyo/util/logging.py

@@ -34,11 +34,13 @@
 """
 
 import logging
+import sys
 
-try:  # py>=38
+if sys.version_info >= (3, 8):
     from typing import Literal
-except ImportError:  # py<38
+else:
     from typing_extensions import Literal
+
 import socket
 from contextlib import AbstractContextManager
 from logging import Logger

fgpyo/util/metric.py

@@ -137,7 +137,7 @@ def values(self) -> Iterator[Any]:
         """An iterator over attribute values in the same order as the header."""
         return iter(attr.astuple(self, recurse=False))
 
-    def formatted_values(self) -> Iterator[str]:
+    def formatted_values(self) -> List[str]:
         """An iterator over formatted attribute values in the same order as the header."""
         return [self.format_value(value) for value in self.values()]
 
@@ -226,7 +226,7 @@ def parse(cls, fields: List[str]) -> Any:
         return inspect.attr_from(cls=cls, kwargs=dict(zip(header, fields)), parsers=parsers)
 
     @classmethod
-    def write(cls, path: Path, *values: MetricType) -> None:
+    def write(cls, path: Path, *values: "Metric") -> None:
         """Writes zero or more metrics to the given path.
 
         The header will always be written.

fgpyo/util/types.py

@@ -1,5 +1,6 @@
 import collections
 import inspect
+import sys
 import typing
 from enum import Enum
 from functools import partial
@@ -9,20 +10,19 @@
 from typing import TypeVar
 from typing import Union
 
-try:
+# `get_origin_type` is a method that gets the outer type (ex list in a List[str])
+# `get_arg_types` is a method that gets the inner type (ex str in a List[str])
+if sys.version_info >= (3, 8):
     from typing import Literal
-except ImportError:
-    from typing_extensions import Literal
-
 
-# `get_origin_type` is a method that gets the outer type (ex list in a List[str])
-if hasattr(typing, "get_origin"):  # py>=38
     get_origin_type = typing.get_origin
-else:  # py<38
+    get_arg_types = typing.get_args
+else:
+    import typing_inspect
+    from typing_extensions import Literal
 
     def get_origin_type(tp: Type) -> Type:
         """Returns the outer type of a Typing object (ex list in a List[T])"""
-        import typing_inspect
 
         if type(tp) is type(Literal):  # Py<=3.6.
             return Literal
@@ -37,15 +37,8 @@ def get_origin_type(tp: Type) -> Type:
             typing.Dict: dict,
         }.get(origin, origin)
 
-
-# `get_origin_type` is a method that gets the inner type (ex str in a List[str])
-if hasattr(typing, "get_args"):  # py>=38
-    get_arg_types = typing.get_args
-else:  # py<38
-
     def get_arg_types(tp: Type) -> Type:
         """Gets the inner types of a Typing object (ex T in a List[T])"""
-        import typing_inspect
 
         if type(tp) is type(Literal):  # Py<=3.6.
             return tp.__values__
@@ -122,7 +115,7 @@ def _make_union_parser_worker(
     union: Type[UnionType],
     parsers: Iterable[Callable[[str], UnionType]],
     value: str,
-) -> T:
+) -> UnionType:
     """Worker function behind union parsing. Iterates through possible parsers for the union and
     returns the value produced by the first parser that works. Otherwise raises an error if none
     work"""

fgpyo/vcf/tests/test_builder.py

@@ -5,6 +5,7 @@
 from typing import Any
 from typing import Dict
 from typing import Iterable
+from typing import List
 from typing import Mapping
 from typing import Tuple
 
@@ -33,7 +34,7 @@ def sequence_dict() -> Dict[str, Dict[str, Any]]:
 
 def _get_random_contig(
     random_generator: random.Random, sequence_dict: Dict[str, Dict[str, Any]]
-) -> (str, int):
+) -> Tuple[str, int]:
     """Randomly select a contig from the sequence dictionary and return its name and length."""
     contig = random_generator.choice(list(sequence_dict.values()))
     return contig["ID"], contig["length"]
@@ -102,7 +103,7 @@ def _get_random_variant_inputs(
 @pytest.fixture(scope="function")
 def zero_sample_record_inputs(
     random_generator: random.Random, sequence_dict: Dict[str, Dict[str, Any]]
-) -> Tuple[Mapping[str, Any]]:
+) -> Tuple[Mapping[str, Any], ...]:
     """
     Fixture with inputs to create test Variant records for zero-sample VCFs (no genotypes).
     Make them MappingProxyType so that they are immutable.
@@ -174,7 +175,7 @@ def test_minimal_inputs() -> None:
 
 def test_sort_order(random_generator: random.Random) -> None:
     """Test if the VariantBuilder sorts the Variant records in the correct order."""
-    sorted_inputs = [
+    sorted_inputs: List[Dict[str, Any]] = [
         {"contig": "chr1", "pos": 100},
         {"contig": "chr1", "pos": 500},
         {"contig": "chr2", "pos": 1000},
@@ -183,7 +184,9 @@ def test_sort_order(random_generator: random.Random) -> None:
         {"contig": "chr10", "pos": 20},
         {"contig": "chr11", "pos": 5},
     ]
-    scrambled_inputs = random_generator.sample(sorted_inputs, k=len(sorted_inputs))
+    scrambled_inputs: List[Dict[str, Any]] = random_generator.sample(
+        sorted_inputs, k=len(sorted_inputs)
+    )
     assert scrambled_inputs != sorted_inputs  # there should be something to actually sort
     variant_builder = VariantBuilder()
     for record_input in scrambled_inputs:
@@ -223,7 +226,7 @@ def _get_is_compressed(input_file: Path) -> bool:
 @pytest.mark.parametrize("compress", (True, False))
 def test_zero_sample_vcf_round_trip(
     temp_path: Path,
-    zero_sample_record_inputs,
+    zero_sample_record_inputs: Tuple[Mapping[str, Any], ...],
     compress: bool,
 ) -> None:
     """

pyproject.toml

@@ -32,14 +32,18 @@ typing_inspect = { version = ">=0.3.1", python = "<3.8" }  # inspecting types
 sphinx = {version = "4.3.1", optional = true}
 sphinx_rtd_theme = {version = "^1.3.0", optional = true}
 pysam = ">=0.22.0"
+pytest = ">=7.4.0"
 
 [tool.poetry.extras]
 docs = ["sphinx", "sphinx_rtd_theme"]
 
 [tool.poetry.dev-dependencies]
 setuptools = ">=68.0.0"
 pytest = ">=5.4.2"
-mypy = ">=0.770"
+mypy = [
+	{ version = ">=0.770", python = "<3.8" },
+	{ version = ">=1.7.0", python = ">=3.8"}
+]
 flake8 = [
 	{ version = ">=3.8.1", python = "<3.12.0" },
 	{ version = ">=6.1.0", python = ">=3.12.0" },