build: update misc configs from software template (#60)

Author: jsstevenson

.github/workflows/checks.yaml

@@ -14,11 +14,16 @@ jobs:
         with:
           python-version:  ${{ matrix.python-version }}
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+
       - name: Install dependencies
-        run: python3 -m pip install ".[tests]"
+        run: uv sync --extra tests
 
       - name: Run tests
-        run: python3 -m pytest tests/
+        run: uv run pytest
   python-lint:
     runs-on: ubuntu-latest
     steps:
@@ -29,11 +34,16 @@ jobs:
         with:
           python-version: 3.11
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+
       - name: Install dependencies
-        run: python3 -m pip install ".[dev]"
+        run: uv sync --extra dev
 
       - name: Check style
-        run: python3 -m ruff check . && ruff format --check .
+        run: uv run ruff check && uv run ruff format --check
   rust-lint:
     runs-on: ubuntu-latest
     defaults:

pyproject.toml

@@ -17,11 +17,11 @@ classifiers = [
     "Programming Language :: Python :: 3.13",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: MIT License",
 ]
 requires-python = ">=3.11"
 description = "Another Genome Conversion Tool: Python frontend to Rust chainfile crate"
-license = {file = "LICENSE"}
+license = "MIT"
+license-files = ["LICENSE"]
 dependencies = ["wags-tails"]
 
 [project.optional-dependencies]
@@ -121,6 +121,7 @@ fixable = [
     "FURB",
     "RUF"
 ]
+# ANN003 - missing-type-args
 # ANN003 - missing-type-kwargs
 # ANN101 - missing-type-self
 # ANN102 - missing-type-cls
@@ -140,7 +141,7 @@ fixable = [
 # PLC0206 - dict-index-missing-items
 # *ignored for compatibility with formatter
 ignore = [
-    "ANN003",
+    "ANN002", "ANN003",
     "D203", "D205", "D206", "D213", "D300", "D400", "D415",
     "E111", "E114", "E117", "E501",
     "W191",

tests/test_converter.py

@@ -1,17 +1,17 @@
 """Module for testing Converter initialization"""
 
 import re
+from pathlib import Path
 
 import pytest
-from tests.conftest import DATA_DIR
 
 from agct import Converter, Genome
 
 
-def test_valid():
+def test_valid(data_dir: Path):
     """Test valid initialization"""
     assert Converter(
-        chainfile=str(DATA_DIR / "ucsc-chainfile" / "chainfile_hg19_to_hg38_.chain")
+        chainfile=str(data_dir / "ucsc-chainfile" / "chainfile_hg19_to_hg38_.chain")
     )
 
 
@@ -20,7 +20,9 @@ def test_invalid():
     with pytest.raises(ValueError, match="Must provide both `from_db` and `to_db`"):
         Converter()
 
-    with pytest.raises(ValueError, match="Liftover must be to/from different sources."):
+    with pytest.raises(
+        ValueError, match=re.escape("Liftover must be to/from different sources.")
+    ):
         Converter(Genome.HG19, Genome.HG19)
 
     with pytest.raises(