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Standardize pyproject and relax dependencies (#54)
* Use standardized pyproject instead of poetry * Relax dependency pins for upstream libraries * Bump poetry version * Add dynamic version and remove generated version * Add __version__.py to gitignore * Replace poetry sections with uv (supporting setuptools-scm) * fix: set activate-environment * Use uv for running docs
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‎.github/workflows/pull-docs.yml‎

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@@ -8,55 +8,28 @@ jobs:
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strategy:
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matrix:
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python-version: [ "3.11" ]
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poetry-version: [ "1.8.3" ]
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steps:
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# ======
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# Checkout, set up python
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# Checkout, set up python and uv
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# ======
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- name: Check out
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uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/checkout@v5
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- name: Install the latest version of uv
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uses: astral-sh/setup-uv@v7
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with:
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python-version: ${{ matrix.python-version }}
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# ======
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# Install and configure poetry from cache
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# ======
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- name: Load cached Poetry installation
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id: cached-poetry
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uses: actions/cache@v4
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with:
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path: ~/.local # the path depends on the OS
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key: poetry-${{ matrix.poetry-version }}
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- name: Install poetry
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if: steps.cached-poetry.outputs.cache-hit != 'true'
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uses: snok/install-poetry@v1
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with:
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version: ${{ matrix.poetry-version }}
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virtualenvs-create: true
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virtualenvs-in-project: true
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# ======
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# Load cached venv if cache exists
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# Install dependencies if cache does not exist
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# ======
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- name: Load cached venv
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id: cached-poetry-dependencies-docs
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uses: actions/cache@v4
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with:
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path: .venv
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key: docs-${{ matrix.python-version }}-${{ matrix.poetry-version }}-${{ hashFiles('**/poetry.lock') }}
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activate-environment: true
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- name: Install dependencies
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if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
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run: poetry install --no-interaction -E docs
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run: uv pip install .[docs]
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# ======
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# Install Pandoc
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# ======
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- name: Use pandoc (external to Poetry)
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uses: nikeee/setup-pandoc@v1
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# uses: docker://pandoc/latex:2.9
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- run: pip install pandoc
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- run: uv pip install pandoc
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# ======
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# Run test suite
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# ======
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- name: Make docs
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run: poetry run sphinx-build docs docs/_build
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run: uv run sphinx-build docs docs/_build

‎.github/workflows/push-test.yml‎

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@@ -9,112 +9,53 @@ jobs:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.9"]
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poetry-version: ["1.2.1"]
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python-version: ["3.9", "3.10", "3.11", "3.12"]
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steps:
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# ======
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# Checkout, set up python
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# Checkout, set up python and uv
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# ======
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- name: Check out
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uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/checkout@v5
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- name: Install the latest version of uv
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uses: astral-sh/setup-uv@v7
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with:
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python-version: ${{ matrix.python-version }}
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# ======
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# Install and configure poetry
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# ======
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- name: Load cached Poetry installation
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id: cached-poetry
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uses: actions/cache@v4
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with:
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path: ~/.local # the path depends on the OS
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key: poetry-${{ matrix.poetry-version }}
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- name: Install Poetry
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if: steps.cached-poetry.outputs.cache-hit != 'true'
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uses: snok/install-poetry@v1
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with:
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version: ${{ matrix.poetry-version }}
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virtualenvs-create: true
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virtualenvs-in-project: true
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# ======
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# Load cached venv if cache exists
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# Install dependencies if cache does not exist
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# ======
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- name: Load cached venv
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id: cached-poetry-dependencies-dev
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uses: actions/cache@v4
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with:
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path: .venv
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key: dev-${{ matrix.python-version }}-${{ matrix.poetry-version }}-${{ hashFiles('**/poetry.lock') }}
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activate-environment: true
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- name: Install dependencies
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if: steps.cached-poetry-dependencies-dev.outputs.cache-hit != 'true'
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run: poetry install --no-interaction -E dev
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run: uv pip install .[dev]
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# ======
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# Run test suite
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# TODO: output code coverage, --cov=<project-dir> --cov-report=xml
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# https://github.com/marketplace/actions/install-poetry-action#codecov-upload
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# ======
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- name: Run tests
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run: poetry run pytest
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run: pytest
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benchmarks:
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name: ASV Benchmarks
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needs: test
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runs-on: ubuntu-22.04
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strategy:
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matrix:
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python-version: ["3.9"]
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poetry-version: ["1.2.1"]
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python-version: ["3.9", "3.10", "3.11", "3.12"]
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steps:
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# ======
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# Checkout, set up python
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# ======
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- name: Check out
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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: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/checkout@v5
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- name: Install the latest version of uv
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uses: astral-sh/setup-uv@v7
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with:
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python-version: ${{ matrix.python-version }}
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# ======
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# Install and configure poetry
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# ======
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- name: Load cached Poetry installation
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id: cached-poetry
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uses: actions/cache@v4
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with:
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path: ~/.local # the path depends on the OS
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key: poetry-${{ matrix.poetry-version }}
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- name: Install Poetry
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if: steps.cached-poetry.outputs.cache-hit != 'true'
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uses: snok/install-poetry@v1
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with:
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version: ${{ matrix.poetry-version }}
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virtualenvs-create: true
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virtualenvs-in-project: true
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# ======
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# Load cached venv if cache exists
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# Install dependencies if cache does not exist
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# ======
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- name: Load cached venv
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id: cached-poetry-dependencies-dev
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uses: actions/cache@v4
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with:
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path: .venv
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key: dev-${{ matrix.python-version }}-${{ matrix.poetry-version }}-${{ hashFiles('**/poetry.lock') }}
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activate-environment: true
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- name: Install dependencies
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if: steps.cached-poetry-dependencies-dev.outputs.cache-hit != 'true'
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run: poetry install --no-interaction -E dev
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run: uv pip install .[dev]
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# ======
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# Compare benchmarks between master and PR, and fail if any get worse
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# ======
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- name: Setup ASV
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run: |
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pip install asv
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cd asv_bench
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asv machine --yes
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- name: Check regression

‎.github/workflows/release.yml‎

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@@ -15,40 +15,24 @@ jobs:
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strategy:
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matrix:
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python-version: ["3.9"]
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poetry-version: ["1.2.1"]
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steps:
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# ======
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# Checkout, set up python
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# Checkout, set up python and uv
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# ======
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- name: Checkout source
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uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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- name: Check out
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uses: actions/checkout@v5
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- name: Install the latest version of uv
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uses: astral-sh/setup-uv@v7
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with:
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python-version: ${{ matrix.python-version }}
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# ======
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# Install poetry
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# ======
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- name: Install Poetry
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uses: snok/install-poetry@v1
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with:
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version: ${{ matrix.poetry-version }}
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virtualenvs-create: true
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virtualenvs-in-project: true
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# ======
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# Install dependencies
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# ======
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- name: Install dependencies
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run: poetry install --no-interaction --no-root
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activate-environment: true
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# ======
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# Build and upload package to Test-PyPI
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# Null API token? "There is no pypi-token.testpypi setting."
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# Test?
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# poetry config repositories.testpypi https://test.pypi.org/legacy/
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# poetry config pypi-token.testpypi ${{ secrets.TEST_PYPI_TOKEN }}
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# poetry publish --no-interaction --build -r testpypi
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# uv build
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# uv publish --repository testpypi --token ${{ secrets.TEST_PYPI_TOKEN }}
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# =====
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- name: Upload package
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run: |
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poetry config pypi-token.pypi ${{ secrets.PYPI_TOKEN }}
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poetry publish --no-interaction --build
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uv build
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uv publish --token ${{ secrets.PYPI_TOKEN }}
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‎.gitignore‎

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.installed.cfg
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*.egg
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MANIFEST
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# generated by setuptools-scm
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__version__.py
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# PyInstaller
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# Usually these files are written by a python script from a template

‎derivative/__version__.py‎

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This file was deleted.

‎pyproject.toml‎

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@@ -1,44 +1,51 @@
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[build-system]
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requires = ["poetry-core>=1.1.0"]
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build-backend = "poetry.core.masonry.api"
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requires = ["setuptools", "setuptools-scm"]
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build-backend = "setuptools.build_meta"
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[tool.poetry]
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[tool.setuptools.packages.find]
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where = ["."]
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include = ["derivative*"]
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[project]
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name = "derivative"
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version = "0.6.3"
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dynamic = ["version"]
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description = "Numerical differentiation in python."
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repository = "https://github.com/andgoldschmidt/derivative"
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documentation = "https://derivative.readthedocs.io/"
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keywords = ["differentiation", "derivative", "gradient", "prime"]
13+
readme = "README.rst"
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requires-python = ">=3.9"
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license-files = ["LICENSE.rst"]
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authors = [
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"Andy Goldschmidt <andygold@uchicago.edu>",
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"Markus Quade <info@markusqua.de>",
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"Jacob Stevens-Haas <jmsh@uw.edu>"
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{ name = "Andy Goldschmidt", email = "andygold@uchicago.edu" },
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{ name = "Markus Quade", email = "info@markusqua.de" },
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{ name = "Jacob Stevens-Haas", email = "jmsh@uw.edu" },
20+
]
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keywords = ["differentiation", "derivative", "gradient", "prime"]
22+
dependencies = [
23+
"numpy>=1.18.3",
24+
"scipy>=1.4.1",
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"scikit-learn>=1.0.0",
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"importlib-metadata>=7.1.0",
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"spectral-derivatives>=0.8",
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]
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license = "MIT"
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readme = "README.rst"
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[tool.poetry.dependencies]
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python = "^3.9"
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numpy = ">=1.18.3"
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scipy = "^1.4.1"
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scikit-learn = "^1"
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importlib-metadata = ">=7.1.0"
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spectral-derivatives = ">=0.8"
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# docs
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sphinx = {version = "7.2.6", optional = true}
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nbsphinx = {version = "^0.9.5", optional = true}
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matplotlib = {version = "^3.2.1", optional = true}
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ipython = {version = "^8.0.0, !=8.7.0, !=8.18.1", optional = true}
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ipykernel = {version = "^6.0.0", optional = true}
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[project.optional-dependencies]
31+
docs = [
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"sphinx==7.2.6",
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"nbsphinx==0.9.5",
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"matplotlib",
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"ipython",
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"ipykernel",
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]
38+
dev = [
39+
"asv",
40+
"pytest>=7",
41+
]
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# dev
36-
asv = {version = "^0.6", optional = true}
37-
pytest = {version = ">=7", optional = true}
43+
[project.urls]
44+
Repository = "https://github.com/andgoldschmidt/derivative"
45+
Documentation = "https://derivative.readthedocs.io/"
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39-
[tool.poetry.extras]
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docs = ["sphinx", "nbsphinx", "matplotlib", "ipython", "ipykernel"]
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dev = ["asv", "pytest"]
47+
[tool.setuptools_scm]
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write_to = "derivative/__version__.py"
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43-
[tool.poetry.plugins.'derivative.hyperparam_opt']
50+
[project.entry-points."derivative.hyperparam_opt"]
4451
"kalman.default" = "derivative.utils:_default_kalman"

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