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Merge pull request #404 from nipreps/maint/tox
MAINT: Automate testing with tox
2 parents 9e4438a + 2c039c9 commit 915fb6f

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‎.github/workflows/pytest.yml‎

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Original file line numberDiff line numberDiff line change
@@ -2,15 +2,18 @@ name: Pytest
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on:
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push:
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branches: [ '*' ]
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tags: [ '*' ]
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branches: ['*']
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tags: ['*']
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pull_request:
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branches: [ master, 'maint/*' ]
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branches: [master, 'maint/*']
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defaults:
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run:
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shell: bash
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env:
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FORCE_COLOR: true
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
@@ -19,32 +22,50 @@ permissions:
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contents: read
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jobs:
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build:
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if: "!contains(github.event.head_commit.message, '[skip ci]')"
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runs-on: ubuntu-latest
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test:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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python-version: ['3.10', '3.11']
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os: ['ubuntu-latest']
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python-version: ['3.10', '3.11', '3.12']
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dependencies: ['latest', 'pre']
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include:
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- os: ubuntu-latest
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python-version: '3.10'
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dependencies: 'min'
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env:
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DEPENDS: ${{ matrix.dependencies }}
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steps:
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- uses: actions/checkout@v4
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with:
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submodules: recursive
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fetch-depth: 0
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- name: Install nibabies
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- uses: actions/cache@v4
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with:
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path: ~/.cache/templateflow
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key: templateflow-v1
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- name: Install dependencies
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run: |
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python -m venv /tmp/venv
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source /tmp/venv/bin/activate
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python -m pip install -U pip
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python -m pip install ".[test]"
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- name: Run Pytest
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sudo apt update
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sudo apt install -y --no-install-recommends graphviz
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Install tox
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run: |
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source /tmp/venv/bin/activate
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pytest -sv --doctest-modules --cov nibabies --cov-report xml nibabies
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- name: Submit coverage
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uses: codecov/codecov-action@v3
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python -m pip install --upgrade pip
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python -m pip install tox tox-gh-actions
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- name: Show tox config
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run: tox c
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- name: Run tox
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run: tox -v --exit-and-dump-after 1200
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- uses: codecov/codecov-action@v4
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with:
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files: coverage.xml
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file: coverage.xml
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token: ${{ secrets.CODECOV_TOKEN }}
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if: ${{ always() }}

‎pyproject.toml‎

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Original file line numberDiff line numberDiff line change
@@ -37,6 +37,7 @@ dependencies = [
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"tedana >= 23.0.2",
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"templateflow >= 24.2.0",
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"toml",
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"typing_extensions; python_version<'3.11'",
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]
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dynamic = ["version"]
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@@ -71,10 +72,11 @@ maint = [
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"python-Levenshtein",
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]
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test = [
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"coverage",
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"coverage[toml]",
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"pytest",
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"pytest-cov",
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"pytest-env",
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"pytest-xdist",
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]
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telemetry = ["migas >= 0.4.0"]
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# Aliases
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]
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[tool.pytest.ini_options]
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minversion = "6"
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testpaths = ["nibabies"]
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log_cli_level = "INFO"
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xfail_strict = true
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norecursedirs = [".git"]
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addopts = "-svx --doctest-modules"
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addopts = [
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"-svx",
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"-ra",
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"--strict-config",
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"--strict-markers",
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"--doctest-modules",
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# Config pytest-cov
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"--cov=nibabies",
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"--cov-report=xml",
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"--cov-config=pyproject.toml",
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]
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doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS"
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env = "PYTHONHASHSEED=0"
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filterwarnings = ["ignore::DeprecationWarning"]
@@ -177,3 +193,15 @@ inline-quotes = "single"
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[tool.ruff.format]
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quote-style = "single"
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[tool.coverage.run]
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branch = true
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omit = [
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"*/_version.py"
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]
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[tool.coverage.paths]
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source = [
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"nibabies",
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"**/site-packages/nibabies"
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]

‎tox.ini‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,113 @@
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[tox]
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requires =
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tox>=4
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envlist =
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py3{10,11,12}-latest
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py310-min
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py3{10,11,12}-pre
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skip_missing_interpreters = true
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# Configuration that allows us to split tests across GitHub runners effectively
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[gh-actions]
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python =
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3.10: py310
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3.11: py311
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3.12: py312
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[gh-actions:env]
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DEPENDS =
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min: min
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latest: latest
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pre: pre
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[testenv]
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description = Pytest with coverage
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labels = test
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pip_pre =
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pre: true
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pass_env =
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# getpass.getuser() sources for Windows:
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LOGNAME
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USER
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LNAME
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USERNAME
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# Pass user color preferences through
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PY_COLORS
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FORCE_COLOR
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NO_COLOR
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CLICOLOR
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CLICOLOR_FORCE
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PYTHON_GIL
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extras = test
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setenv =
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pre: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
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deps =
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min: nibabel == 4.0.1
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min: nipype == 1.8.5
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min: nitransforms == 21.0.0
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min: numpy == 1.22
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min: psutil == 5.4
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min: pybids == 0.15.2
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min: tedana == 23.0.2
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min: templateflow == 24.1.0
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commands_pre =
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python scripts/fetch_templates.py
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commands =
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pytest --cov-report term-missing --durations=20 --durations-min=1.0 {posargs:-n auto}
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[testenv:style]
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description = Check our style guide
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labels = check
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deps =
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ruff
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skip_install = true
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commands =
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ruff check --diff
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ruff format --diff
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[testenv:style-fix]
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description = Auto-apply style guide to the extent possible
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labels = pre-release
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deps =
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ruff
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skip_install = true
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commands =
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ruff check --fix
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ruff format
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ruff check --select ISC001
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[testenv:spellcheck]
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description = Check spelling
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labels = check
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deps =
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codespell[toml]
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skip_install = true
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commands =
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codespell . {posargs}
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[testenv:build{,-strict}]
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labels =
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check
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pre-release
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deps =
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build
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twine
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skip_install = true
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set_env =
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# Ignore specific known warnings:
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# https://github.com/pypa/pip/issues/11684
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# https://github.com/pypa/pip/issues/12243
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strict: PYTHONWARNINGS=error,once:pkg_resources is deprecated as an API.:DeprecationWarning:pip._internal.metadata.importlib._envs,once:Unimplemented abstract methods {'locate_file'}:DeprecationWarning:pip._internal.metadata.importlib._dists
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commands =
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python -m build
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python -m twine check dist/*
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[testenv:publish]
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depends = build
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labels = release
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deps =
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twine
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skip_install = true
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commands =
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python -m twine upload dist/*

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