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⬆️ Opt fully into uv
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‎.github/dependabot.yml‎

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version: 2
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updates:
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- package-ecosystem: pip
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- package-ecosystem: uv
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directory: "/"
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schedule:
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interval: weekly
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day: friday
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time: "18:00"
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timezone: Europe/Amsterdam
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open-pull-requests-limit: 20
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reviewers:
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- jsnel
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assignees:
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- jsnel
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- s-weigand
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# Maintain dependencies for GitHub Actions
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- package-ecosystem: "github-actions"
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directory: "/"

‎.github/requirements_min.txt‎

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‎.github/workflows/integration-tests.yml‎

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uses: actions/setup-python@v6
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with:
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python-version: "3.10"
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- name: Install pyglotaran-extras
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- name: Install uv
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uses: astral-sh/setup-uv@v4
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- name: Install dependencies
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run: |
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pip install wheel
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pip install -r requirements_pinned.txt
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pip install .
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uv sync --frozen --no-default-groups
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- name: ${{ matrix.example_name }}
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id: example-run

‎.github/workflows/test.yml‎

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docs:
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name: Build Docs
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- name: Check out repo
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uses: actions/checkout@v6
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- name: Setup docs env same as on RTD
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uses: mamba-org/setup-micromamba@v2
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uses: actions/checkout@v4
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- name: Set up Python 3.10
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uses: actions/setup-python@v5
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with:
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environment-file: docs/environment.yml
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cache-environment: true
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python-version: "3.10"
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- name: Install asdf package manager
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uses: asdf-vm/actions/setup@v4
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- name: Install pandoc
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run: |
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asdf plugin add pandoc
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asdf install pandoc latest
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- name: Install uv
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uses: astral-sh/setup-uv@v4
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- name: Install just
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run: |
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uv tool install rust-just
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- name: Install dependencies
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run: |
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uv sync --frozen --group docs
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- name: Show installed dependencies
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run: pip freeze
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run: |
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uv tree
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- name: Build docs
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run: just docs/html
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docs-link:
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name: Check Doc Links
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- name: Check out repo
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uses: actions/checkout@v6
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- name: Setup docs env same as on RTD
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uses: mamba-org/setup-micromamba@v2
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uses: actions/checkout@v4
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- name: Set up Python 3.10
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uses: actions/setup-python@v5
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with:
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environment-file: docs/environment.yml
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cache-environment: true
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python-version: "3.10"
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- name: Install asdf package manager
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uses: asdf-vm/actions/setup@v4
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- name: Install pandoc
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run: |
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asdf plugin add pandoc
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asdf install pandoc latest
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- name: Install uv
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uses: astral-sh/setup-uv@v4
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- name: Install just
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run: |
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uv tool install rust-just
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- name: Install dependencies
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run: |
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uv sync --frozen --group docs
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- name: Show installed dependencies
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run: pip freeze
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run: |
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uv tree
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- name: Build docs
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- name: Check links in docs
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run: just docs/linkcheck
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test:
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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@v4
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- name: Install dependencies
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run: |
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python -m pip install -U pip wheel
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python -m pip install -r requirements_pinned.txt
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python -m pip install -U ".[test]"
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uv sync --frozen --group test
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- name: Run tests
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run: python -m pytest --nbval --cov=pyglotaran_extras --cov-report term --cov-report xml --cov-config pyproject.toml tests
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run: uv run pytest --nbval --cov=pyglotaran_extras --cov-report term --cov-report xml --cov-config pyproject.toml tests
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- name: Codecov Upload
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continue-on-error: true
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with:
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python-version: "3.10"
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- name: Install uv
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uses: astral-sh/setup-uv@v4
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- name: Install dependencies
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run: |
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python -m pip install -U pip wheel
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python -m pip install -r requirements_pinned.txt
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python -m pip install -U ".[test]"
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python -m pip install git+https://github.com/glotaran/pyglotaran
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uv sync --frozen --group test
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uv add git+https://github.com/glotaran/pyglotaran
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- name: Show installed dependencies
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run: pip freeze
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run: uv tree
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- name: Run tests
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run: python -m pytest --nbval --cov=pyglotaran_extras --cov-report term --cov-report xml --cov-config pyproject.toml tests
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run: uv run pytest --nbval --cov=pyglotaran_extras --cov-report term --cov-report xml --cov-config pyproject.toml tests
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- name: Codecov Upload
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continue-on-error: true
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with:
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python-version: "3.10"
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- name: Install uv
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uses: astral-sh/setup-uv@v4
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- name: Install dependencies
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run: |
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python -m pip install -U pip wheel
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python -m pip install -r .github/requirements_min.txt
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python -m pip install -e ".[test]"
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uv sync --group test --resolution lowest
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- name: Show installed dependencies
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run: pip freeze
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run: uv tree
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- name: Run tests
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run: python -m pytest --nbval --cov=./ --cov-report term --cov-report xml --cov-config pyproject.toml tests
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run: uv run pytest --nbval --cov=./ --cov-report term --cov-report xml --cov-config pyproject.toml tests
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- name: Codecov Upload
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continue-on-error: true
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uses: actions/setup-python@v6
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with:
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python-version: "3.10"
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- name: Install dependencies
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run: python -m pip install -U hatch
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- name: Install uv
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uses: astral-sh/setup-uv@v4
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- name: Build dist
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run: hatch build
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run: uv build
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- name: Publish package
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uses: pypa/gh-action-pypi-publish@v1.13.0

‎.ruff-notebooks.toml‎

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]
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[lint.isort]
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required-imports = []
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required-imports = [ ]
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force-single-line = false

‎.ruff.toml‎

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# Covered by formatter
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"ISC001",
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]
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external = ["DOC"]
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external = [ "DOC" ]
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# Allow unused variables when underscore-prefixed.
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dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
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[lint.per-file-ignores]
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"tests/*" = ["ARG001"]
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"tests/data/*" = ["INP", "D"]
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"tests/*" = [ "ARG001" ]
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"tests/data/*" = [ "INP", "D" ]
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"tests/data/config/run_load_config_on_import.py" = [
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"I002", # from __future__ import annotations
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]
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[lint.isort]
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required-imports = ["from __future__ import annotations"]
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known-first-party = ["pyglotaran_extras"]
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required-imports = [ "from __future__ import annotations" ]
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known-first-party = [ "pyglotaran_extras" ]
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force-single-line = true
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[lint.pydocstyle]

‎.taplo.toml‎

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[formatting]
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align_comments = true
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array_auto_collapse = false
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compact_arrays = false

‎docs/environment.yml‎

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‎pyproject.toml‎

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"version",
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]
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dependencies = [
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"cycler>=0.10",
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"docstring-parser>=0.16",
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"matplotlib>=3.3",
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"numpy>=1.22",
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"packaging>=23.1",
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"pydantic>=2.7",
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"pyglotaran>=0.7",
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"ruamel-yaml>=0.18.6",
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"tabulate>=0.8.9",
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"xarray>=2022.3",
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"cycler==0.12.1",
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"docstring-parser==0.17",
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"matplotlib==3.10.8",
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"numpy==2.2.6",
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"packaging==26",
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"pydantic==2.12.5",
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"pyglotaran==0.7.4",
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"ruamel-yaml==0.19.1",
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"tabulate==0.9",
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"xarray==2025.6.1",
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]
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optional-dependencies.dev = [
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"pyglotaran-extras[docs,test]",
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urls.Changelog = "https://pyglotaran-extras.readthedocs.io/en/latest/changelog.html"
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urls.Documentation = "https://pyglotaran-extras.readthedocs.io"
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urls."GloTarAn Ecosystem" = "https://glotaran.org"
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urls.Homepage = "https://github.com/glotaran/pyglotaran-extras"
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urls.Source = "https://github.com/glotaran/pyglotaran-extras"
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urls.Tracker = "https://github.com/glotaran/pyglotaran-extras/issues"
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[dependency-groups]
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dev = [ { include-group = "docs" }, { include-group = "test" } ]
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test = [
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"coverage[toml]",
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"jsonschema>=4.22",
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"nbval>=0.9.6",
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"pluggy>=0.7",
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"pytest>=3.7.1",
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"pytest-cov>=2.5.1",
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]
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optional-dependencies.docs = [
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docs = [
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"autodoc-pydantic>=2.2",
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"jupyterlab>=3",
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"myst-nb>=1.1.1", # notebook docs
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"sphinx-last-updated-by-git>=0.3",
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"sphinxcontrib-mermaid>=0.9.2",
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optional-dependencies.test = [
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"coverage[toml]",
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"jsonschema>=4.22",
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"nbval>=0.9.6",
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"pluggy>=0.7",
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"pytest>=3.7.1",
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"pytest-cov>=2.5.1",
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]
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urls.Changelog = "https://pyglotaran-extras.readthedocs.io/en/latest/changelog.html"
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urls.Documentation = "https://pyglotaran-extras.readthedocs.io"
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urls."GloTarAn Ecosystem" = "https://glotaran.org"
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urls.Homepage = "https://github.com/glotaran/pyglotaran-extras"
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urls.Source = "https://github.com/glotaran/pyglotaran-extras"
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urls.Tracker = "https://github.com/glotaran/pyglotaran-extras/issues"
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[tool.hatch.version]
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path = "pyglotaran_extras/__init__.py"

‎readthedocs.yml‎

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version: 2
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formats: all
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sphinx:
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configuration: docs/conf.py
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build:
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os: ubuntu-lts-latest
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os: ubuntu-24.04
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tools:
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python: "mambaforge-latest"
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conda:
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environment: docs/environment.yml
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python: "3.13"
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jobs:
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pre_create_environment:
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- asdf plugin add uv
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- asdf install uv latest
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- asdf plugin add pandoc
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- asdf install pandoc latest
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create_environment:
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- uv venv "${READTHEDOCS_VIRTUALENV_PATH}"
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install:
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- UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen --group docs

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