support python 3.11 and 3.12, update black, flake8, and poetry versions

Author: jdidion

.github/workflows/pythonpackage.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        PYTHON_VERSION: ["3.8", "3.9", "3.10"]
+        PYTHON_VERSION: ["3.8", "3.9", "3.10", "3.11", "3.12"]
     steps:
     - uses: actions/checkout@v2
 

fgpyo/fasta/builder.py

@@ -32,6 +32,7 @@
     'AAAAAAAAAANNN'
 
 """
+
 import textwrap
 from pathlib import Path
 from typing import TYPE_CHECKING
@@ -48,7 +49,6 @@ def samtools_dict(*args: Any) -> None:
     def samtools_faidx(*args: Any) -> None:
         pass
 
-
 else:
     from pysam import dict as samtools_dict
     from pysam import faidx as samtools_faidx

fgpyo/fastx/__init__.py

@@ -24,6 +24,7 @@
    seq2: GGGG, seq2: TTTT
 
 """
+
 from contextlib import AbstractContextManager
 from pathlib import Path
 from types import TracebackType

fgpyo/io/__init__.py

@@ -42,6 +42,7 @@
     "10"
 
 """
+
 import gzip
 import io
 import os

fgpyo/read_structure.py

@@ -61,6 +61,7 @@
       correspond to the given read segment
 
 """
+
 import enum
 from typing import Iterable
 from typing import Iterator

fgpyo/sam/builder.py

@@ -10,6 +10,7 @@
     - :class:`~fgpyo.sam.builder.SamBuilder` -- A builder class that allows the accumulation
         of alignment records and access as a list and writing to file.
 """
+
 from array import array
 from pathlib import Path
 from random import Random

fgpyo/vcf/__init__.py

@@ -48,6 +48,7 @@
 order via the :func:`~fgpyo.vcf.builder.VariantBuilder.to_sorted_list()` method.
 
 """
+
 from contextlib import contextmanager
 from pathlib import Path
 from typing import Generator

poetry.lock

@@ -35,9 +35,9 @@ typing_extensions = { version = ">=3.7.4", python = "<3.12" }
 docs = ["sphinx", "sphinx_rtd_theme"]
 
 [tool.poetry.dev-dependencies]
-black = ">=19.10b0"
+black = ">=24.2.0"
 flake8 = [
-	{ version = ">=3.8.1", python = "<3.12.0" },
+	{ version = ">=5.0.0", python = "<3.12.0" },
 	{ version = ">=6.1.0", python = ">=3.12.0" },
 ]
 isort = ">=5.10.1"