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‎.github/workflows/docs.yml‎

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@@ -24,23 +24,34 @@ jobs:
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Setup Pages
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id: pages
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uses: actions/configure-pages@v3
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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- name: Set up Python
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run: uv python install 3.11
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install ".[doc]"
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uv sync --group doc
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# temporary fix for sphinx-polyversion
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uv pip install --force-reinstall git+https://github.com/ziw-liu/sphinx-polyversion.git@iohub-staging
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- name: Set environment
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run: |
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REPO_OWNER="${GITHUB_REPOSITORY%%/*}"
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REPO_NAME="${GITHUB_REPOSITORY#*/}"
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echo "GITHUB_PAGES_URL=https://$REPO_OWNER.github.io/$REPO_NAME" >> $GITHUB_ENV
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- name: Build the docs
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run: |
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echo $GITHUB_PAGES_URL
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make build -C docs
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uv run make build -C docs
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touch docs/build/.nojekyll
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- name: Upload build artifacts
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uses: actions/upload-pages-artifact@v3
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with:

‎.github/workflows/pr.yml‎

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# This workflow will install Python dependencies, run tests and lint with a single version of Python
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# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
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name: lint, style, and tests
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name: PR checks
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on:
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pull_request:
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branches:
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- "*"
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jobs:
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style:
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name: Style Check
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.11"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install black
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- name: Check code styling with Black
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run: |
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black --diff -S -t py310 iohub
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black --check -S -t py310 iohub
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lint:
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name: Lint Check
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.11"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install flake8
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- name: Check code with Flake8
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# E203 conflicts with black
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run: |
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flake8 iohub --extend-ignore=E203
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isort:
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name: isort Check
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name: Lint
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.11"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v4
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- uses: j178/prek-action@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install isort
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- name: Check code with isort
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run: |
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isort --check iohub
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extra-args: ''
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tests:
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needs: [style, lint, isort]
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runs-on: ubuntu-latest
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strategy:
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matrix:
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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- name: Set up Python ${{ matrix.python-version }}
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run: uv python install ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install ".[dev,acquire-zarr]"
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run: uv sync --group test
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- name: Test with pytest
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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run: |
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pytest -v --cov=./ --cov-report=xml
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run: uv run pytest -v --cov=./ --cov-report=xml
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# this checks that docs build and examples run
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# but does not deploy to GH Pages
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docs:
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needs: [style, lint, isort]
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v4
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with:
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python-version: "3.11"
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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- name: Set up Python
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run: uv python install 3.11
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install ".[doc]"
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uv sync --group doc
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# temporary fix for sphinx-polyversion
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pip install --force-reinstall git+https://github.com/ziw-liu/sphinx-polyversion.git@iohub-staging
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uv pip install --force-reinstall git+https://github.com/ziw-liu/sphinx-polyversion.git@iohub-staging
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- name: Test docs build
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run: |
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sphinx-polyversion docs/poly.py -vvv --local
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run: uv run sphinx-polyversion docs/poly.py -vvv --local

‎.github/workflows/test.yml‎

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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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- name: Set up Python ${{ matrix.python-version }}
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run: uv python install ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install ".[dev,acquire-zarr]"
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run: uv sync --group test
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- name: Test with pytest
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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run: |
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pytest -v --cov=./iohub --cov-report=xml
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run: uv run pytest -v --cov=./iohub --cov-report=xml

‎.pre-commit-config.yaml‎

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repos:
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# basic pre-commit
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.4.0
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rev: v6.0.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-added-large-files
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args: ['--maxkb=1000']
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- id: check-yaml
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- id: check-toml
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- id: detect-private-key
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# sorting imports
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- repo: https://github.com/pycqa/isort
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rev: 5.12.0
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# linting and formatting
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.14.14
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hooks:
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- id: isort
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# syntax linting and formatting
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- repo: https://github.com/myint/autoflake
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rev: v2.1.1
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hooks:
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- id: autoflake
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args: [--in-place, --remove-all-unused-imports,
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--ignore-init-module-imports]
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- repo: https://github.com/PyCQA/flake8
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rev: 6.0.0
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hooks:
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- id: flake8
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args: [--ignore, "E203,W503", --min-python-version, '3.11']
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additional_dependencies: [flake8-typing-imports==1.16.0]
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- repo: https://github.com/psf/black
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rev: 23.3.0
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hooks:
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- id: black
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- id: ruff-check
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args: [--fix]
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- id: ruff-format

‎CONTRIBUTING.md‎

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### Setting up development environment
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For local development, first install [Git](https://git-scm.com/)
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and Python with an environment management tool
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(e.g. [miniforge](https://github.com/conda-forge/miniforge), a minimal community distribution of Conda).
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This project uses [uv](https://docs.astral.sh/uv/) for dependency management.
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If you use Conda, set up an environment with:
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#### Install uv
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```sh
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conda create -n iohub-dev python=3.11
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conda activate iohub-dev
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```
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See [uv installation docs](https://docs.astral.sh/uv/getting-started/installation/).
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#### Clone the repository
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If you have push permission to the repository,
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clone the repository (the code blocks below are shell commands):
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If you have push permission to the repository:
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```sh
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cd # to the directory you want to work in
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Otherwise, you can follow [these instructions](https://docs.github.com/en/get-started/quickstart/fork-a-repo)
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to [fork](https://github.com/czbiohub-sf/iohub/fork) the repository.
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Then install the package in editable mode with the development dependencies.
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Remove acquire-zarr if you do not have glibc version 2.35 or later,
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for example on the Bruno cluster (Rocky Linux 8).
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#### Install dependencies
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First, create a virtual environment with a supported Python version (3.11-3.13):
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```sh
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cd iohub/
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uv venv -p 3.13 # or 3.11, 3.12
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```
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This makes a virtual environment in the `.venv` where the dependencies for `iohub` will be installed.
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Then sync dependencies:
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```sh
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cd iohub/ # or the renamed project root directory
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pip install -e ".[dev,acquire-zarr]"
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uv sync
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```
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> **Note**: `uv sync` installs the [`dev` group by default](https://docs.astral.sh/uv/concepts/projects/sync/#syncing-development-dependencies), which includes all development dependencies. iohub currently supports Python 3.11-3.13—if `uv sync` fails to resolve dependencies, ensure you've created a venv with a supported version as shown above. See [dependency groups](https://docs.astral.sh/uv/concepts/projects/dependencies/#dependency-groups) for more details.
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#### Dependency groups
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The project uses [dependency groups](https://docs.astral.sh/uv/concepts/projects/dependencies/#dependency-groups) for development tools and [optional dependencies](https://docs.astral.sh/uv/concepts/projects/dependencies/#optional-dependencies) for user-facing extras.
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| Group | Purpose |
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|-------|---------|
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| `test` | Testing tools (pytest, hypothesis, etc.) |
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| `acquire-zarr` | Acquire-zarr reader (requires glibc 2.35+) |
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| `doc` | Documentation (sphinx, etc.) |
118+
| `pre-commit` | Pre-commit hooks |
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| `dev` | Includes test, acquire-zarr, doc, pre-commit (installed by default via `uv sync`) |
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> **Note**: On older glibc systems (e.g., Rocky Linux 8), `acquire-zarr` won't work. Use `uv sync --no-group acquire-zarr` instead.
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Then make the changes and [track them with Git](https://docs.github.com/en/get-started/using-git/about-git#example-contribute-to-an-existing-repository).
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### Developing documentation
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107127
#### Prerequisites
108128

109-
Install a forked version of `sphinx-polyversion` due to an incompatibility with `setuptools_scm`.
129+
Install the [forked version of `sphinx-polyversion`](https://github.com/ziw-liu/sphinx-polyversion/tree/iohub-staging) (temporary fix for compatibility):
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```shell
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pip install --force-reinstall git+https://github.com/ziw-liu/sphinx-polyversion.git@iohub-staging
132+
uv pip install --force-reinstall git+https://github.com/ziw-liu/sphinx-polyversion.git@iohub-staging
113133
```
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#### Building the HTML version locally
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117-
Inside `/docs` folder
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Inside the `docs/` folder:
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```shell
120-
pip install "/PATH/TO/iohub[doc]"
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make clean
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sphinx-polyversion poly.py -vvv --local
141+
uv run sphinx-polyversion poly.py -vvv --local
123142
```
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Generated HTML documentation can be found in
126-
the ``build/html`` directory. Open ``build/html/index.html`` to view the home
127-
page for the documentation.
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Generated HTML documentation can be found in the `build/` directory.
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#### Writing examples
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They can also be executed as plain Python scripts
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or interactive code blocks in some IDEs (VS Code, PyCharm, Spyder etc.).
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See the syntax documentation
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[here](https://sphinx-gallery.github.io/stable/syntax.html).
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See the [syntax documentation](https://sphinx-gallery.github.io/stable/syntax.html).
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### Testing
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```sh
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uv run pytest --cov=iohub tests/
152168
```
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`iohub` uses [Hypothesis](https://hypothesis.readthedocs.io/en/latest/index.html)
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### Code style
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We use [pre-commit](https://pre-commit.com/) to sort imports with [isort](https://github.com/PyCQA/isort), format code with [black](https://black.readthedocs.io/en/stable/), and lint with [flake8](https://github.com/PyCQA/flake8) automatically prior to each commit. To minimize test errors when submitting pull requests, please install pre-commit in your environment as follows:
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We use [prek](https://github.com/j178/prek) (a faster [pre-commit](https://pre-commit.com/) runner) to automatically format and lint code prior to each commit. To minimize test errors when submitting pull requests, install the hooks:
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179+
```bash
180+
uvx prek install
181+
```
182+
183+
> `uvx` runs tools in isolated, cached environments, no binaries added to your PATH and no dependencies installed in your project venv.
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To run manually:
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163187
```bash
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pre-commit install
188+
uvx prek run # run on staged files only
189+
uvx prek run --all-files # run on all files
165190
```
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When these packages are executed within the project root directory, they should automatically use the [project settings](./pyproject.toml).
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When these tools are executed within the project root directory, they should automatically use the [project settings](./pyproject.toml).
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[NumPy style docstrings](https://numpydoc.readthedocs.io/en/latest/format.html) are used for API documentation.

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