a few other things

Author: jsstevenson

.github/workflows/checks.yaml

@@ -7,72 +7,72 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: {{ "${{ matrix.python-version }}" }}
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
         with:
-          python-version: ${{ matrix.python-version }}
+          enable-cache: true
 
       - name: Install dependencies
-        run: |
-          python3 -m pip install pipenv
-          pipenv install --dev
+        run: uv sync
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
-          python-version: 3.11
+          python-version: 3.13
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        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 . && python3 -m ruff format --check .
+        run: uv run ruff check && uv run ruff format --check
+
+  precommit_hooks:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: j178/prek-action@v1
+        with:
+          extra_args: '--all-files --skip "ruff-format" --skip "ruff-check"'
 
   docs:
     runs-on: ubuntu-latest
     env:
       SPHINX_GITHUB_CHANGELOG_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
-          python-version: 3.11
+          python-version: 3.12  # broken on 3.13
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
 
       - name: Install dependencies
-        run: |
-          python3 -m pip install --upgrade pip
-          python3 -m pip install '.[docs]'
+        run: uv sync --extra docs
 
       - name: Attempt docs build
         working-directory: ./docs
-        run: make html
-
-  precommit_hooks:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        cmd:
-          - "end-of-file-fixer"
-          - "trailing-whitespace"
-          - "mixed-line-ending"
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Set up Python 3.12
-        uses: actions/setup-python@v5
-        with:
-          python-version: 3.12
-
-      - uses: pre-commit/[email protected]
-        with:
-          extra_args: ${{ matrix.cmd }} --all-files
+        run: source ../.venv/bin/activate && make html

.pre-commit-config.yaml

@@ -1,20 +1,28 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0  # pre-commit-hooks version
+    rev: v6.0.0  # pre-commit-hooks version
     hooks:
-      - id: check-added-large-files
-      - id: detect-private-key
-      - id: trailing-whitespace
-      - id: end-of-file-fixer
-      - id: check-merge-conflict
       - id: detect-aws-credentials
         args: [ --allow-missing-credentials ]
+  - repo: builtin
+    hooks:
+      - id: trailing-whitespace
+      - id: check-added-large-files
+        args: ['--maxkb=1500']
+      - id: check-case-conflict
+      - id: end-of-file-fixer
+      - id: fix-byte-order-marker
+      - id: check-json
+      - id: check-toml
+      - id: check-yaml
       - id: mixed-line-ending
         args: [ --fix=lf ]
+      - id: check-merge-conflict
+      - id: detect-private-key
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.10
+    rev: v0.14.10  # ruff version
     hooks:
+      - id: ruff-format
       - id: ruff-check
         args: [ --fix, --exit-non-zero-on-fix ]
-      - id: ruff-format
-minimum_pre_commit_version: 4.2.0
+minimum_prek_version: 0.2.23

pyproject.toml

@@ -14,15 +14,15 @@ classifiers = [
     "Intended Audience :: Science/Research",
     "Intended Audience :: Developers",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
-    "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
 ]
 requires-python = ">=3.11"
 description = "Common Operation on Lots of Sequences Tool"
-license = {file = "LICENSE"}
+license = "MIT"
+license-files = ["LICENSE"]
 dependencies = [
     "asyncpg",
     "boto3",
@@ -38,7 +38,7 @@ dynamic = ["version"]
 
 [project.optional-dependencies]
 dev = [
-    "pre-commit>=4.2.0",
+    "prek>=0.2.23",
     "ipython",
     "ipykernel",
     "psycopg2-binary",
@@ -68,13 +68,6 @@ build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
 
-# Scanning for namespace packages in the ``src`` directory is true by
-# default in pyproject.toml, so you do NOT need to include the
-# `tool.setuptools.packages.find` if it looks like the following:
-# [tool.setuptools.packages.find]
-# namespaces = true
-# where = ["src"]
-
 [tool.setuptools.package-data]
 "cool_seq_tool.resources" = ["transcript_mapping.tsv"]