Update Python version support to 3.9-3.13

.github/workflows/build_wheels.yml

@@ -15,7 +15,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.8'
+          python-version: '3.13'
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
@@ -37,7 +37,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.8'
+          python-version: '3.13'
           architecture: ${{ matrix.target }}
       - name: Build wheels
         uses: PyO3/maturin-action@v1
@@ -59,7 +59,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.8'
+          python-version: '3.13'
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:

.github/workflows/tests_and_lint.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: [3.13]
         lint-flags:
           - "--run-only-fast-linters"
           - "--run-only-pylint"
@@ -38,7 +38,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -61,7 +61,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}

README.md

@@ -11,7 +11,7 @@ and other sequence alignment algorithms written in Rust with Python bindings via
 <p><img width="800px" src="https://raw.githubusercontent.com/kensho-technologies/sequence_align/main/docs/images/sequence_align.png"></p>
 
 ## Installation
-`sequence_align` is distributed via [PyPi](https://pypi.org/project/sequence_align) for Python 3.7+, making installation as simple as the following --
+`sequence_align` is distributed via [PyPi](https://pypi.org/project/sequence_align) for Python 3.9 - 3.13, making installation as simple as the following --
 no special setup required for cross-platform compatibility, Rust installation, etc.!
 
 ``` bash

pyproject.toml

@@ -4,26 +4,24 @@ build-backend = "maturin"
 
 [project]
 name = "sequence_align"
-version = "0.2.0"
+version = "0.3.0"
 description = "Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms in Rust with Python bindings."
 readme = "README.md"
-requires-python = ">=3.7"
+requires-python = ">=3.9,<3.14"
 authors = [
     {name = "Kensho Technologies LLC.", email = "sequence-align-maintainer@kensho.com"},
 ]
 maintainers = [
     {name = "Kensho Technologies LLC.", email = "sequence-align-maintainer@kensho.com"},
 ]
-license-files.paths = [
-    "LICENSE",  # Apache 2.0
-]
+license = {file = "LICENSE"}  # Apache 2.0
 classifiers = [
     "Operating System :: OS Independent",
-    "Programming Language :: Python :: 3.7",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Programming Language :: Rust",
     "Topic :: Scientific/Engineering :: Artificial Intelligence",
     "Topic :: Scientific/Engineering :: Bio-Informatics",

src/sequence_align/pairwise.py

@@ -1,5 +1,5 @@
 # Copyright 2023-present Kensho Technologies, LLC.
-from typing import Dict, List, Sequence, Tuple
+from typing import Sequence
 
 from sequence_align import _sequence_align  # type: ignore
 
@@ -12,13 +12,13 @@ def _entry2idx(
     seq_b: Sequence[str],
     gap: str,
     allow_gap: bool = False,
-) -> Tuple[Dict[int, str], List[int], List[int]]:
+) -> tuple[dict[int, str], list[int], list[int]]:
     symbols = set(seq_a).union(set(seq_b))
     if not allow_gap and gap in symbols:
         raise ValueError(f'Gap entry "{gap}" found in seq_a and/or seq_b; must not exist in either')
 
     symbols_without_gap = symbols - {gap}
-    idx2symbol: Dict[int, str] = {
+    idx2symbol: dict[int, str] = {
         _GAP_VAL: gap,
         **{idx: symbol for idx, symbol in enumerate(sorted(symbols_without_gap))},
     }
@@ -31,11 +31,11 @@ def _entry2idx(
 
 
 def _idx2entry(
-    idx2symbol: Dict[int, str],
-    seq_a_indices_aligned: List[int],
-    seq_b_indices_aligned: List[int],
+    idx2symbol: dict[int, str],
+    seq_a_indices_aligned: list[int],
+    seq_b_indices_aligned: list[int],
     gap: str,
-) -> Tuple[List[str], List[str]]:
+) -> tuple[list[str], list[str]]:
     seq_a_aligned = [gap if idx == _GAP_VAL else idx2symbol[idx] for idx in seq_a_indices_aligned]
     seq_b_aligned = [gap if idx == _GAP_VAL else idx2symbol[idx] for idx in seq_b_indices_aligned]
     return (seq_a_aligned, seq_b_aligned)
@@ -48,7 +48,7 @@ def needleman_wunsch(
     mismatch_score: float = -1.0,
     indel_score: float = -1.0,
     gap: str = "-",
-) -> Tuple[List[str], List[str]]:
+) -> tuple[list[str], list[str]]:
     """Compute an optimal global pairwise alignment using the Needleman-Wunsch algorithm.
 
     Args:
@@ -106,7 +106,7 @@ def hirschberg(
     mismatch_score: float = -1.0,
     indel_score: float = -1.0,
     gap: str = "-",
-) -> Tuple[List[str], List[str]]:
+) -> tuple[list[str], list[str]]:
     """Compute an optimal global pairwise alignment using the Hirschberg algorithm.
 
     Args:

tests/perf/test_hirschberg.py

@@ -1,6 +1,6 @@
 # Copyright 2023-present Kensho Technologies, LLC.
 import time
-from typing import Any, Dict
+from typing import Any
 import unittest
 
 from sequence_align.pairwise import hirschberg
@@ -23,7 +23,7 @@
 
 class TestHirschberg(unittest.TestCase):
     # Needed for mypy to not complain
-    expected_perf: Dict[str, Any] = dict()
+    expected_perf: dict[str, Any] = dict()
 
     @classmethod
     def setUpClass(cls) -> None:

tests/perf/test_needleman_wunsch.py

@@ -1,6 +1,6 @@
 # Copyright 2023-present Kensho Technologies, LLC.
 import time
-from typing import Any, Dict
+from typing import Any
 import unittest
 
 from sequence_align.pairwise import needleman_wunsch
@@ -23,7 +23,7 @@
 
 class TestNeedlemanWunsch(unittest.TestCase):
     # Needed for mypy to not complain
-    expected_perf: Dict[str, Any] = dict()
+    expected_perf: dict[str, Any] = dict()
 
     @classmethod
     def setUpClass(cls) -> None:

tests/perf/utils.py

@@ -2,7 +2,7 @@
 import multiprocessing as mp
 import os
 import random
-from typing import Any, Callable, Dict, List, Tuple
+from typing import Any, Callable
 
 import psutil
 import yaml
@@ -20,7 +20,7 @@
 MEM_CHECK_INTERVAL = 0.01  # seconds
 
 
-def _create_perturbed_seq(seq_a: List[str]) -> List[str]:
+def _create_perturbed_seq(seq_a: list[str]) -> list[str]:
     random.seed(1234)
 
     seq_b = list()
@@ -48,7 +48,7 @@ def _create_perturbed_seq(seq_a: List[str]) -> List[str]:
     return seq_b
 
 
-def create_seq_pair(seq_a_len: int) -> Tuple[List[str], List[str]]:
+def create_seq_pair(seq_a_len: int) -> tuple[list[str], list[str]]:
     """Create a pair of sequences, where the second is a perturbed version of the first."""
     seq_a = random.choices(CHARS, k=seq_a_len)
     seq_b = _create_perturbed_seq(seq_a)
@@ -63,7 +63,7 @@ def get_expected_perf(key: str) -> Any:
 
 
 def max_memory_usage(
-    func: Callable[..., Any], args: Tuple[Any, ...], kwargs: Dict[str, Any]
+    func: Callable[..., Any], args: tuple[Any, ...], kwargs: dict[str, Any]
 ) -> int:
     """Run the given function in a separate process and return the maximum memory usage in MiB."""
     max_mem = 0