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Commit 95bd98f

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seweberseweber
committed
Test pairinteraction with dependencies with minimal versions, improve colab compatibility, use dependency groups instead of optional dependencies for development dependencies
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‎.build_requirements.txt‎

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scikit-build-core>=0.9.0
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nanobind>=1.9.0
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typing_extensions>=4.7
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numpy>=1.24
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numpy>=2.0.2
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tbb-devel==2022.0.0; sys_platform != 'darwin'
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mkl-devel==2025.0.1; sys_platform != 'darwin'
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‎.github/actions/setup-uv-all-deps/action.yml‎

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using: "composite"
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steps:
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- name: Install uv
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uses: astral-sh/setup-uv@v6
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uses: astral-sh/setup-uv@v7
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with:
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version: "0.7"
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version: "0.9"
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python-version: ${{ inputs.python-version }}
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enable-cache: true
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cache-dependency-glob: |
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./pyproject.toml
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- name: Install all Python dependencies into a virtual environment
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shell: bash
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run: uv sync --no-install-project --all-extras # always install all dependencies, this simplifies caching
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run: uv sync --no-install-project --group dev # always install all development dependencies, this simplifies caching
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‎.github/actions/setup-uv-build-venv/action.yml‎

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using: "composite"
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steps:
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- name: Install uv
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uses: astral-sh/setup-uv@v6
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uses: astral-sh/setup-uv@v7
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with:
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version: "0.7"
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python-version: 3.12
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‎.github/workflows/documentation.yml‎

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- name: Setup uv project virtual environment
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uses: ./.github/actions/setup-uv-all-deps
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- name: Install PairInteraction into virtual environment
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run: uv pip install .[docs]
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run: uv pip install . --group docs
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- name: Build documentation
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working-directory: docs/
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run: uv run --no-project make html SPHINXOPTS="-W --keep-going" # TODO also use -n in the future
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- name: Setup uv project virtual environment
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uses: ./.github/actions/setup-uv-all-deps
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- name: Install PairInteraction into virtual environment
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run: uv pip install .[docs]
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run: uv pip install . --group docs
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- name: Setup 2nd virtual environment for other PairInteraction versions
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run: |
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uv venv tmp_venv --python=python3.11
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- name: Setup uv project virtual environment
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uses: ./.github/actions/setup-uv-all-deps
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- name: Install PairInteraction into virtual environment
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run: uv pip install -Cbuild-dir=build --config-settings=cmake.define.WITH_COVERAGE=ON .[tests]
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run: uv pip install -Cbuild-dir=build --config-settings=cmake.define.WITH_COVERAGE=ON . --group tests
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- name: Run pytest
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run: uv run --no-project pytest
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- name: Generate Code Coverage HTML report
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- name: Setup uv project virtual environment
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uses: ./.github/actions/setup-uv-all-deps
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- name: Install PairInteraction into virtual environment
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run: uv pip install -e .[tests] # -e is needed for coverage to work
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run: uv pip install -e . --group tests # -e is needed for coverage to work
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- name: Run pytest with coverage
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run: | # also run with --generate-reference to get 100% tests coverage and test the reference generation
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uv run --no-project coverage run --source=src,tests -m pytest
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‎.github/workflows/mypy.yml‎

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- name: Setup uv project virtual environment
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uses: ./.github/actions/setup-uv-all-deps
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- name: Install PairInteraction into virtual environment
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run: uv pip install .[mypy]
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run: uv pip install . --group mypy
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- name: Install the benchmarking tool
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run: uv pip install tools/benchmarking[mypy]
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- name: Install the dbmanager tool
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‎.github/workflows/python-wheel.yml‎

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- name: Install uv
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uses: astral-sh/setup-uv@v7
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with:
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version: "0.7"
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version: "0.9"
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enable-cache: true
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cache-dependency-glob: |
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./pyproject.toml
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./.build_requirements.txt
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- uses: pypa/cibuildwheel@v3.3
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env:
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name: dist-wheel-${{ matrix.os }}
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path: wheelhouse/*.whl
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test-min-deps:
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name: Test with minimum dependency versions
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runs-on: ubuntu-latest
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container:
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image: ghcr.io/pairinteraction/pairinteraction-manylinux:docker
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steps:
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- uses: actions/checkout@v6
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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with:
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version: "0.9"
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python-version: "3.12"
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enable-cache: true
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cache-dependency-glob: |
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./pyproject.toml
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- run: uv sync --group tests --resolution lowest-direct
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- run: uv run --no-sync pytest
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test-install-from-sdist:
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strategy:
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fail-fast: false
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‎.pre-commit-config.yaml‎

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rev: v1.15.0
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hooks:
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- id: mypy
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additional_dependencies: ["numpy >= 1.24", "typing_extensions >= 4.7", "pyside6 >= 6.8.2", "pyside6-stubs >= 6.7.3.0", "pint < 0.25.1", "attrs >= 24.0"] # FIXME: unpin pint when https://github.com/hgrecco/pint/issues/2245 is resolved (see also pyproject.toml)
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additional_dependencies: ["numpy >= 1.24", "typing_extensions >= 4.7", "pyside6 >= 6.8.2", "pyside6-stubs >= 6.7.3.0", "pint >= 0.24.4, < 0.25.1", "attrs >= 24.0"] # FIXME: unpin pint when https://github.com/hgrecco/pint/issues/2245 is resolved (see also pyproject.toml)
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args: ["--ignore-missing-imports"]
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- repo: https://github.com/fsfe/reuse-tool
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‎CMakeLists.txt‎

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this package, consider using the following install command inside \
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the root directory of the repository:
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=====================================================================
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$ pip install .[tests,docs]
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$ pip install . --group tests --group docs
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=====================================================================
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Where the arguments 'tests' (installs dependencies for running tests) \
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and 'docs' (installs dependencies for building the documentation) \
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‎docs/contribute/getting_started.rst‎

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.. code-block:: bash
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pip install -e .[tests,docs]
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pip install -e . --group tests --group docs
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Or, you can build solely the C++ backend using ``cmake``. This manual approach is recommended if you are planning to
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contribute to the C++ backend because it allows for a faster build and more fine-grained control.
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‎docs/installation/advanced/documentation.rst‎

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.. code-block:: bash
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pip install .[docs]
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pip install . --group docs
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In order to build the documentation once, you can run
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