pysauce 0.3.2__tar.gz

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Files changed (41) hide show
  1. pysauce-0.3.2/.github/workflows/CI.yml +59 -0
  2. pysauce-0.3.2/.github/workflows/publish.yml +135 -0
  3. pysauce-0.3.2/.gitignore +52 -0
  4. pysauce-0.3.2/CHANGELOG.md +41 -0
  5. pysauce-0.3.2/CITATION.cff +39 -0
  6. pysauce-0.3.2/Cargo.lock +321 -0
  7. pysauce-0.3.2/Cargo.toml +25 -0
  8. pysauce-0.3.2/LICENSE +21 -0
  9. pysauce-0.3.2/PKG-INFO +181 -0
  10. pysauce-0.3.2/README.md +144 -0
  11. pysauce-0.3.2/benchmarks/test_speed.py +70 -0
  12. pysauce-0.3.2/conda/meta.yaml +43 -0
  13. pysauce-0.3.2/examples/01_xi_r.ipynb +330 -0
  14. pysauce-0.3.2/examples/02_redshift_space.ipynb +303 -0
  15. pysauce-0.3.2/examples/03_npoint.ipynb +393 -0
  16. pysauce-0.3.2/pyproject.toml +59 -0
  17. pysauce-0.3.2/python/pysauce/__init__.py +58 -0
  18. pysauce-0.3.2/python/pysauce/_pysauce.pyi +35 -0
  19. pysauce-0.3.2/python/pysauce/analytic.py +87 -0
  20. pysauce-0.3.2/python/pysauce/estimators.py +453 -0
  21. pysauce-0.3.2/python/pysauce/py.typed +0 -0
  22. pysauce-0.3.2/rustfmt.toml +2 -0
  23. pysauce-0.3.2/sauce/binning.rs +274 -0
  24. pysauce-0.3.2/sauce/grid.rs +494 -0
  25. pysauce-0.3.2/sauce/lib.rs +32 -0
  26. pysauce-0.3.2/sauce/npoint.rs +498 -0
  27. pysauce-0.3.2/sauce/pairs.rs +696 -0
  28. pysauce-0.3.2/sauce/python.rs +383 -0
  29. pysauce-0.3.2/sauce/traverse.rs +1073 -0
  30. pysauce-0.3.2/sauce/validate.rs +172 -0
  31. pysauce-0.3.2/tests/reference.py +164 -0
  32. pysauce-0.3.2/tests/test_analytic.py +94 -0
  33. pysauce-0.3.2/tests/test_corrfunc.py +134 -0
  34. pysauce-0.3.2/tests/test_edge_cases.py +287 -0
  35. pysauce-0.3.2/tests/test_estimators.py +378 -0
  36. pysauce-0.3.2/tests/test_geometry_sweep.py +167 -0
  37. pysauce-0.3.2/tests/test_npoint.py +187 -0
  38. pysauce-0.3.2/tests/test_pairs.py +206 -0
  39. pysauce-0.3.2/tests/test_partition_matrix.py +63 -0
  40. pysauce-0.3.2/tests/test_sparse_estimates.py +178 -0
  41. pysauce-0.3.2/tests/test_validation.py +164 -0
pysauce-0.3.2/.github/workflows/CI.yml ADDED
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+ name: CI
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+
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+ on:
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+ push:
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+ branches:
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+ - main
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+ pull_request:
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+ workflow_dispatch:
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+
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+ permissions:
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+ contents: read
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+
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+ jobs:
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+ lint:
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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@v5
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+ with:
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+ python-version: '3.12'
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+ - run: pip install ruff black
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+ - run: ruff check python tests benchmarks
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+ - run: black --check python tests benchmarks
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+ - run: cargo fmt --check
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+ - run: cargo clippy --all-targets -- -D warnings
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+
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+ rust-tests:
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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@v5
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+ id: python
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+ with:
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+ python-version: '3.12'
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+ - name: Run cargo test
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+ env:
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+ PYO3_PYTHON: ${{ steps.python.outputs.python-path }}
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+ LD_LIBRARY_PATH: ${{ env.pythonLocation }}/lib
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+ run: cargo test
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+
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+ python-tests:
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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', '3.10', '3.11', '3.12', '3.13']
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+ steps:
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+ - uses: actions/checkout@v4
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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: Build wheel
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+ uses: PyO3/maturin-action@v1
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+ with:
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+ command: build
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+ args: --release --out dist
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+ container: off
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+ - run: sudo apt-get install -y libgsl-dev # needed to build Corrfunc
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+ - run: pip install dist/pysauce-*.whl pytest pytest-cov Corrfunc
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+ - run: pytest --cov=pysauce --cov-report=term-missing
pysauce-0.3.2/.github/workflows/publish.yml ADDED
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+ name: Publish
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+
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+ on:
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+ push:
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+ tags:
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+ - 'v*'
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+ workflow_dispatch:
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+
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+ jobs:
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+ linux:
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+ runs-on: ubuntu-22.04
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+ strategy:
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+ matrix:
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+ target: [x86_64, x86, aarch64, armv7, s390x, ppc64le]
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+ steps:
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+ - uses: actions/checkout@v4
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+ - uses: actions/setup-python@v5
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+ with:
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+ python-version: '3.9'
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+ - uses: PyO3/maturin-action@v1
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+ with:
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+ target: ${{ matrix.target }}
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+ args: --release --out dist
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+ manylinux: auto
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+ - uses: actions/upload-artifact@v4
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+ with:
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+ name: wheels-linux-${{ matrix.target }}
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+ path: dist
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+
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+ musllinux:
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+ runs-on: ubuntu-22.04
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+ strategy:
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+ matrix:
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+ target: [x86_64, x86, aarch64, armv7]
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+ steps:
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+ - uses: actions/checkout@v4
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+ - uses: actions/setup-python@v5
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+ with:
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+ python-version: '3.9'
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+ - uses: PyO3/maturin-action@v1
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+ with:
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+ target: ${{ matrix.target }}
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+ args: --release --out dist
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+ manylinux: musllinux_1_2
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+ - uses: actions/upload-artifact@v4
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+ with:
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+ name: wheels-musllinux-${{ matrix.target }}
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+ path: dist
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+
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+ windows:
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+ runs-on: ${{ matrix.platform.runner }}
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+ strategy:
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+ matrix:
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+ platform:
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+ - runner: windows-latest
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+ target: x64
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+ python_arch: x64
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+ - runner: windows-latest
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+ target: x86
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+ python_arch: x86
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+ - runner: windows-11-arm
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+ target: aarch64
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+ python_arch: arm64
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+ steps:
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+ - uses: actions/checkout@v4
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+ - uses: actions/setup-python@v5
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+ with:
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+ python-version: '3.11'
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+ architecture: ${{ matrix.platform.python_arch }}
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+ - uses: PyO3/maturin-action@v1
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+ with:
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+ target: ${{ matrix.platform.target }}
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+ args: --release --out dist
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+ - uses: actions/upload-artifact@v4
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+ with:
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+ name: wheels-windows-${{ matrix.platform.target }}
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+ path: dist
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+
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+ macos:
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+ runs-on: macos-latest
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+ strategy:
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+ matrix:
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+ target: [x86_64, aarch64]
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+ steps:
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+ - uses: actions/checkout@v4
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+ - uses: actions/setup-python@v5
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+ with:
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+ python-version: '3.9'
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+ - uses: PyO3/maturin-action@v1
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+ with:
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+ target: ${{ matrix.target }}
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+ args: --release --out dist
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+ - uses: actions/upload-artifact@v4
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+ with:
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+ name: wheels-macos-${{ matrix.target }}
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+ path: dist
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+
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+ sdist:
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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: PyO3/maturin-action@v1
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+ with:
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+ command: sdist
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+ args: --out dist
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+ - uses: actions/upload-artifact@v4
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+ with:
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+ name: wheels-sdist
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+ path: dist
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+
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+ publish:
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+ name: Publish to PyPI
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+ runs-on: ubuntu-latest
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+ needs: [linux, musllinux, windows, macos, sdist]
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+ environment: pypi
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+ permissions:
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+ id-token: write
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+ contents: write
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+ attestations: write
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+ steps:
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+ - uses: actions/download-artifact@v4
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+ with:
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+ merge-multiple: true
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+ path: dist
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+ - name: Generate artifact attestation
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+ uses: actions/attest-build-provenance@v2
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+ with:
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+ subject-path: dist/*
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+ - name: Create GitHub Release
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+ uses: softprops/action-gh-release@v2
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+ with:
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+ files: dist/*
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+ generate_release_notes: true
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+ - name: Publish to PyPI
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+ uses: pypa/gh-action-pypi-publish@release/v1
pysauce-0.3.2/.gitignore ADDED
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+ # Rust
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+ /target
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+ # machine-specific build flags
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+ .cargo/config.toml
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+
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+ # Python
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+ __pycache__/
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+ *.py[cod]
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+ *.so
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+ *.egg-info/
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+ .venv/
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+ venv/
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+ .env
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+ .env.*
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+ build/
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+ dist/
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+ uv.lock
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+
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+ # Tests and linters
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+ .pytest_cache/
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+ .ruff_cache/
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+ .mypy_cache/
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+ .hypothesis/
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+ .coverage
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+ .coverage.*
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+ htmlcov/
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+ .benchmarks/
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+
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+ # Jupyter
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+ .ipynb_checkpoints/
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+
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+ # Editors and OS
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+ .idea/
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+ .vscode/
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+ *.swp
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+ *.swo
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+ *~
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+ .DS_Store
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+
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+ # Batch-job output
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+ slurm-*.out
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+ slurm-*.err
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+ *.log
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+
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+ # Data files
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+ *.npy
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+ *.npz
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+ *.h5
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+ *.hdf5
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+ *.fits
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+ *.pkl
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+ *.parquet
pysauce-0.3.2/CHANGELOG.md ADDED
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+ # Changelog
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+
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+ ## 0.3.2 (2026-11-11)
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+
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+ - `count_npoint` can count one of `n_shards` shares of the work for N >= 3,
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+ to split a calculation across jobs. The shares sum to the full count.
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+ - New `count_pairs_1d_partition_matrix`: pair counts for every pair of
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+ partitions.
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+ - New `count_npoint3_smu` and `compute_npcf3_smu`: triplets binned by longest
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+ side and its orientation to the line of sight.
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+ - The estimators require `N <= m <= k`.
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+ - Faster pair and N-point counting. Counts are unchanged.
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+ - The core was rewritten and is tested against brute force and Corrfunc.
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+
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+ ## 0.3.1 (2026-07-04)
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+
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+ - Fixed the bin lookup for N >= 3: tuples with a diameter close to a bin edge
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+ could be counted in the neighbouring bin. Pair counts were not affected.
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+ - Invalid input raises `ValueError`.
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+ - The GIL is released while counting.
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+ - Package renamed to `pysauce`.
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+
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+ ## 0.3.0 (2026-06-11)
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+
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+ - New `count_npoint3_shape` and `compute_npcf3_shape`: triplets binned by size
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+ and shape.
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+
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+ ## 0.2.0 (2026-05-30)
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+
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+ - `compute_npcf` takes `scale_method` ("scale-up" or "scale-down") and returns
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+ `zeta`, the corrected counts divided by the number of N-tuples.
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+
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+ ## 0.1.1 (2026-05-28)
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+
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+ - `compute_xi_smu` returns the analytic random counts, the multipoles and the
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+ bin centres.
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+
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+ ## 0.1.0 (2026-05-27)
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+
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+ - First release: pair counters in r, (r_p, pi) and (s, mu), the N-tuple
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+ counter, and the sparse-partition estimators.
pysauce-0.3.2/CITATION.cff ADDED
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+ cff-version: 1.2.0
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+ message: "If you use this software, please cite it using the metadata below."
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+ type: software
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+ title: "SaUCE: Sparse and Unbiased Clustering Estimator"
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+ version: 0.3.2
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+ license: MIT
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+ url: "https://github.com/OscarHickman/SaUCE"
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+ repository-code: "https://github.com/OscarHickman/SaUCE"
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+ authors:
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+ - family-names: Hickman
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+ given-names: Oscar
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+ affiliation: "Institute for Computational Cosmology, Durham University"
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+ email: oscar.hickman17@alumni.imperial.ac.uk
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+ keywords:
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+ - cosmology
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+ - galaxy clustering
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+ - correlation functions
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+ - N-body simulations
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+ - astronomy
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+ abstract: >
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+ Correlation function counters for galaxy catalogues drawn from sparse
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+ subsets of periodic N-body simulations. Computes xi(r), xi(s, mu)
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+ multipoles, and high-order N-point functions with unbiased corrections for
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+ statistical under-sampling in m-of-k sparse samples.
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+ references:
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+ - type: article
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+ title: "Less is More: Unbiased Galaxy Clustering from Fewer Merger Trees"
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+ authors:
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+ - family-names: Hickman
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+ given-names: Oscar J.
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+ year: 2026
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+ status: preprint
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+ - type: article
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+ title: "SaUCE for the N-point Correlation Function: Unbiased Higher-Order Galaxy Clustering from Fewer Merger Trees"
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+ authors:
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+ - family-names: Hickman
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+ given-names: Oscar J.
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+ year: 2026
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+ status: in-preparation
pysauce-0.3.2/Cargo.lock ADDED
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+ # This file is automatically @generated by Cargo.
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+ # It is not intended for manual editing.
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pysauce-0.3.2/Cargo.toml ADDED
@@ -0,0 +1,25 @@
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+ [package]
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+ name = "pysauce"
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+ version = "0.3.2"
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+ edition = "2021"
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+ description = "Pair and N-point counters for sparse partitions of periodic simulation boxes"
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+ license = "MIT"
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+ repository = "https://github.com/OscarHickman/SaUCE"
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+ readme = "README.md"
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+
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+ [lib]
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+ name = "_pysauce"
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+ crate-type = ["cdylib"]
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+ path = "sauce/lib.rs"
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+
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+ [dependencies]
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+ # The "extension-module" feature is enabled by maturin (see pyproject.toml) so
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+ # that `cargo test` can link against libpython.
18
+ pyo3 = { version = "0.23", features = ["abi3-py39"] }
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+ numpy = "0.23"
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+ rayon = "1"
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+
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+ [profile.release]
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+ lto = true
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+ panic = "abort"
pysauce-0.3.2/LICENSE ADDED
@@ -0,0 +1,21 @@
1
+ MIT License
2
+
3
+ Copyright (c) 2026 Oscar Hickman
4
+
5
+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
7
+ in the Software without restriction, including without limitation the rights
8
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9
+ copies of the Software, and to permit persons to whom the Software is
10
+ furnished to do so, subject to the following conditions:
11
+
12
+ The above copyright notice and this permission notice shall be included in all
13
+ copies or substantial portions of the Software.
14
+
15
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21
+ SOFTWARE.