Merge pull request #105 from HuttleyLab/main

DEV: support python 3.13

.github/workflows/ci.yml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
       - uses: "actions/checkout@v4"
@@ -24,14 +24,19 @@ jobs:
         with:
             python-version: "${{ matrix.python-version }}"
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+
       - name: "Installs for ${{ matrix.python-version }}"
         run: |
-          python --version
-          pip install --upgrade pip wheel setuptools flit
-          pip install --upgrade nox
+          uv venv venv -p python${{ matrix.python-version }}
+          uv tool install -p venv nox
 
       - name: "Run nox for ${{ matrix.python-version }}"
-        run: "nox -s test_coveralls-${{ matrix.python-version }} -- --cov-report lcov:lcov-${{matrix.os}}-${{matrix.python-version}}.lcov --cov-report term --cov-append --cov diverse_seq"
+        run: "nox -db uv -s test_coveralls-${{ matrix.python-version }} -- --cov-report lcov:lcov-${{matrix.os}}-${{matrix.python-version}}.lcov --cov-report term --cov-append --cov diverse_seq"
 
       - name: Coveralls Parallel
         uses: coverallsapp/github-action@v2

noxfile.py

@@ -1,6 +1,6 @@
 import nox
 
-_py_versions = range(10, 13)
+_py_versions = range(10, 14)
 
 nox.options.sessions = ["test", "testcov"]
 
@@ -16,7 +16,7 @@ def test(session):
     )
 
 
-@nox.session(python=["3.12"])
+@nox.session(python=["3.13"])
 def testcov(session):
     session.install(".[test]")
     session.chdir("tests")

pyproject.toml

@@ -10,7 +10,7 @@ authors = [
 keywords = ["biology", "genomics", "statistics", "phylogeny", "evolution", "bioinformatics"]
 readme = "README.md"
 license = { file = "LICENSE" }
-requires-python = ">=3.10,<3.13"
+requires-python = ">=3.10,<3.14"
 dependencies = [
     "attrs",
     "click",
@@ -32,6 +32,8 @@ classifiers = [
         "Operating System :: OS Independent",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
+        "Programming Language :: Python :: 3.13",
     ]
 # the following are inferred from the source code
 dynamic = ["version", "description"]
@@ -50,7 +52,7 @@ test = [
     "pytest",
     "pytest-cov",
     "pytest-xdist",
-    "ruff==0.9.1",
+    "ruff==0.9.3",
 ]
 dev = [
     "cogapp",
@@ -60,7 +62,7 @@ dev = [
     "pytest",
     "pytest-cov",
     "pytest-xdist",
-    "ruff==0.9.1",
+    "ruff==0.9.3",
 ]
 doc  = ["click",
         "ipykernel",
@@ -136,7 +138,11 @@ target-version = "py310"
 # Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
 # McCabe complexity (`C901`) by default.
 select = ["ALL"]
-ignore = ["EXE002", "FA100", "E501", "D"]
+# turn of warnings for:
+# - import numpy as np, we pefer explicit and 3 extra characters is no burden
+# - strict camel case class names, we name classes with a __call__ method like
+#   functions since their instance behaves like a function
+ignore = ["EXE002", "FA100", "E501", "D", "ICN001", "N801"]
 
 # Allow fix for all enabled rules (when `--fix`) is provided.
 fixable = ["ALL"]

src/diverse_seq/__init__.py

@@ -4,4 +4,4 @@
 # found by h5py
 import hdf5plugin  # noqa
 
-__version__ = "2024.12.26a1"
+__version__ = "2024.12.26a2"