diff --git a/.github/workflows/checks.yaml b/.github/workflows/checks.yaml index a282e24..a56ce47 100644 --- a/.github/workflows/checks.yaml +++ b/.github/workflows/checks.yaml @@ -7,15 +7,15 @@ jobs: matrix: python-version: ['3.11', '3.12', '3.13'] steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v6 - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v6 with: python-version: ${{ matrix.python-version }} - name: Install uv - uses: astral-sh/setup-uv@v6 + uses: astral-sh/setup-uv@v7 with: enable-cache: true @@ -24,18 +24,19 @@ jobs: - name: Run tests run: uv run pytest + python-lint: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: Setup 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@v6 + uses: astral-sh/setup-uv@v7 with: enable-cache: true @@ -44,13 +45,14 @@ jobs: - name: Check style run: uv run ruff check && uv run ruff format --check + rust-lint: runs-on: ubuntu-latest defaults: run: working-directory: ./rust steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: Update Rust run: rustup update stable && rustup default stable @@ -62,20 +64,9 @@ jobs: 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: actions/checkout@v6 - - uses: pre-commit/action@v3.0.1 + - uses: j178/prek-action@v1 with: - extra_args: ${{ matrix.cmd }} --all-files + extra_args: '--all-files --skip "ruff-format" --skip "ruff-check" --skip "fmt"' diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0ef674b..8b54957 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,21 +1,29 @@ 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 # ruff version + rev: v0.14.10 # ruff version hooks: - id: ruff-format - - id: ruff + - id: ruff-check args: [ --fix, --exit-non-zero-on-fix ] - repo: https://github.com/doublify/pre-commit-rust rev: v1.0 @@ -23,5 +31,4 @@ repos: - id: fmt entry: bash -c 'cd rust && cargo fmt' args: ['--verbose', '--'] - -minimum_pre_commit_version: 4.2.0 +minimum_prek_version: 0.2.23 diff --git a/pyproject.toml b/pyproject.toml index 2b46a58..a6a428f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,8 +31,8 @@ tests = [ ] dev = [ "maturin", - "ruff==0.12.1", - "pre-commit>=4.2.0", + "ruff==0.14.10", + "prek>=0.2.23", ] [project.urls] @@ -62,111 +62,72 @@ branch = true src = ["src"] [tool.ruff.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 - "INP", # https://docs.astral.sh/ruff/rules/#flake8-no-pep420-inp - "G", # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g - "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 -] -fixable = [ - "I", - "F401", - "D", - "UP", - "ANN", - "B", - "C4", - "LOG", - "G", - "PIE", - "PT", - "RSE", - "SIM", - "PLC", - "PLE", - "TRY", - "PERF", - "FURB", - "RUF" -] -# ANN003 - missing-type-args -# ANN003 - missing-type-kwargs -# ANN101 - missing-type-self -# ANN102 - missing-type-cls -# 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 +select = ["ALL"] ignore = [ - "ANN002", "ANN003", - "D203", "D205", "D206", "D213", "D300", "D400", "D415", - "E111", "E114", "E117", "E501", + # 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 # S101 - assert # B011 - assert-false # INP001 - implicit-namespace-package +# PLR2004 - magic-value-comparison "tests/*" = [ "ANN001", "ANN2", - "D100", - "D102", - "D103", + "D", "S101", "B011", - "INP001" + "INP001", + "PLR2004", ] [tool.ruff.lint.flake8-annotations] diff --git a/src/agct/converter.py b/src/agct/converter.py index 1f7cc81..14c6709 100644 --- a/src/agct/converter.py +++ b/src/agct/converter.py @@ -11,7 +11,7 @@ from wags_tails.utils.downloads import download_http, handle_gzip from wags_tails.utils.storage import get_data_dir -import agct._core as _core +from agct import _core from agct.seqref_registry import Assembly _logger = logging.getLogger(__name__) diff --git a/tests/test_rust_api.py b/tests/test_rust_api.py index 4f2d894..ecf64a4 100644 --- a/tests/test_rust_api.py +++ b/tests/test_rust_api.py @@ -1,7 +1,6 @@ """Test some non-public aspects of the Rust layer.""" import pytest - from agct._core import ChainfileError, Converter