cicd: update linting, git hooks, etc

.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:
+          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/action@v3.0.1
-        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: v0.12.1
+    rev: v0.14.10  # ruff version
     hooks:
       - id: ruff-format
-      - id: ruff
+      - id: ruff-check
         args: [ --fix, --exit-non-zero-on-fix ]
-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",
@@ -38,11 +38,11 @@ dynamic = ["version"]
 
 [project.optional-dependencies]
 dev = [
-    "pre-commit>=4.2.0",
+    "prek>=0.2.23",
     "ipython",
     "ipykernel",
     "psycopg2-binary",
-    "ruff==0.12.1",
+    "ruff==0.14.10",
 ]
 tests = ["pytest", "pytest-cov", "pytest-asyncio", "mock"]
 docs = [
@@ -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"]
 
@@ -91,113 +84,78 @@ branch = true
 [tool.ruff]
 src = ["src"]
 exclude = ["docs/source/conf.py"]
-lint.select = [
-    "F",  # https://docs.astral.sh/ruff/rules/#pyflakes-f
-    "E", "W",  # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
-    "I",  # https://docs.astral.sh/ruff/rules/#isort-i
-    "N",  # https://docs.astral.sh/ruff/rules/#pep8-naming-n
-    "D",  # https://docs.astral.sh/ruff/rules/#pydocstyle-d
-    "UP",  # https://docs.astral.sh/ruff/rules/#pyupgrade-up
-    "ANN",  # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
-    "ASYNC",  # https://docs.astral.sh/ruff/rules/#flake8-async-async
-    "S",  # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
-    "B",  # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
-    "A",  # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
-    "C4",  # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
-    "DTZ",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
-    "T10",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
-    "EM",  # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
-    "LOG",  # https://docs.astral.sh/ruff/rules/#flake8-logging-log
-    "G",  # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
-    "INP",  # https://docs.astral.sh/ruff/rules/#flake8-no-pep420-inp
-    "PIE",  # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
-    "T20",  # https://docs.astral.sh/ruff/rules/#flake8-print-t20
-    "PT",  # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
-    "Q",  # https://docs.astral.sh/ruff/rules/#flake8-quotes-q
-    "RSE",  # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
-    "RET",  # https://docs.astral.sh/ruff/rules/#flake8-return-ret
-    "SLF",  # https://docs.astral.sh/ruff/rules/#flake8-self-slf
-    "SLOT",  # https://docs.astral.sh/ruff/rules/#flake8-slots-slot
-    "SIM",  # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
-    "ARG",  # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
-    "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
-    "PGH",  # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
-    "PLC",  # https://docs.astral.sh/ruff/rules/#convention-c
-    "PLE",  # https://docs.astral.sh/ruff/rules/#error-e_1
-    "TRY",  # https://docs.astral.sh/ruff/rules/#tryceratops-try
-    "PERF",  # https://docs.astral.sh/ruff/rules/#perflint-perf
-    "FURB",  # https://docs.astral.sh/ruff/rules/#refurb-furb
-    "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
-]
-lint.fixable = [
-    "I",
-    "F401",
-    "D",
-    "UP",
-    "ANN",
-    "B",
-    "C4",
-    "LOG",
-    "G",
-    "PIE",
-    "PT",
-    "RSE",
-    "SIM",
-    "PLC",
-    "PLE",
-    "TRY",
-    "PERF",
-    "FURB",
-    "RUF"
-]
 
-# ANN003 - missing-type-kwargs
-# D203 - one-blank-line-before-class
-# D205 - blank-line-after-summary
-# D206 - indent-with-spaces*
-# D213 - multi-line-summary-second-line
-# D300 - triple-single-quotes*
-# D400 - ends-in-period
-# D415 - ends-in-punctuation
-# E111 - indentation-with-invalid-multiple*
-# E114 - indentation-with-invalid-multiple-comment*
-# E117 - over-indented*
-# E501 - line-too-long*
-# W191 - tab-indentation*
-# S321 - suspicious-ftp-lib-usage
-# PLC0206 - dict-index-missing-items
-# *ignored for compatibility with formatter
-lint.ignore = [
-    "ANN003",
-    "D203", "D205", "D206", "D213", "D300", "D400", "D415",
-    "E111", "E114", "E117", "E501",
+[tool.ruff.lint]
+select = ["ALL"]
+ignore = [
+    # unused
+    "AIR",
+    "ERA",
+    "YTT",
+    "BLE",
+    "FBT",
+    "CPY",
+    "DJ",
+    "EXE",
+    "FIX",
+    "FA",
+    "PYI",
+    "TD",
+    "C90",
+    "NPY",
+    "PD",
+    # ignore for compatibility with formatter
+    "D206",
+    "D300",
+    "W191",
+    "E111",
+    "E114",
+    "E117",
+    "E501",
     "W191",
     "S321",
+    "COM812",
+    "COM819",
+    "Q000",
+    "Q001",
+    "Q002",
+    "Q003",
+    # don't require types on *args, **kwargs
+    "ANN002",
+    "ANN003",
+    # subjective pylint thresholds
+    "PLR0904",
+    "PLR091",
+    "PLR1702",
     "PLC0206",
+    # misc unnecessary stuff
+    "S321",
+    "D203",
+    "D205",
+    "D213",
+    "D400",
+    "D415",
 ]
 
 [tool.ruff.lint.per-file-ignores]
 # ANN001 - missing-type-function-argument
 # ANN2 - missing-return-type
-# D100 - undocumented-public-module
-# D102 - undocumented-public-class
-# D103 - undocumented-public-function
 # N805 - invalid-first-argument-name-for-method
 # F821 - undefined-name
 # F401 - unused-import
 # INP001 - implicit-namespace-package
 # SLF001 - private-member-access
 # ARG001 - unused-function-argument
+# PLR2004 - magic-value-comparison
 "tests/*" = [
     "ANN001",
     "ANN2",
-    "D100",
-    "D102",
-    "D103",
+    "D",
     "S101",
     "INP001",
     "SLF001",
-    "ARG001"
+    "ARG001",
+    "PLR2004",
 ]
 "*__init__.py" = ["F401"]
 "src/cool_seq_tool/schemas.py" = ["ANN201", "N805", "ANN001"]

src/cool_seq_tool/handlers/seqrepo_access.py

@@ -58,9 +58,8 @@ def get_reference_sequence(
             start, end = get_inter_residue_pos(start, end, coordinate_type)
             if start == end:
                 end += 1
-        else:
-            if start is not None and coordinate_type == CoordinateType.RESIDUE:
-                start -= 1
+        elif start is not None and coordinate_type == CoordinateType.RESIDUE:
+            start -= 1
 
         try:
             sequence = self.sr.fetch(ac, start=start, end=end)

src/cool_seq_tool/mappers/alignment.py

@@ -68,11 +68,10 @@ async def p_to_c(
         # codon. We want to return inter-residue (0-based), so we subtract 1 from this.
         if coordinate_type == CoordinateType.RESIDUE:
             c_pos = (p_start_pos * 3) - 3, p_end_pos * 3
+        elif p_start_pos == p_end_pos:
+            c_pos = ((p_start_pos + 1) * 3) - 3, (p_end_pos + 1) * 3
         else:
-            if p_start_pos == p_end_pos:
-                c_pos = ((p_start_pos + 1) * 3) - 3, (p_end_pos + 1) * 3
-            else:
-                c_pos = ((p_start_pos + 1) * 3) - 3, p_end_pos * 3
+            c_pos = ((p_start_pos + 1) * 3) - 3, p_end_pos * 3
 
         return {
             "c_ac": c_ac,