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‎.fuse_hidden00100aa400000007‎

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‎.github/workflows/CI.yml‎

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# This file is autogenerated by maturin v1.8.3
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# To update, run
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#
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# maturin generate-ci github
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#
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name: CI
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on:
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push:
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branches:
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- main
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- master
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tags:
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- '*'
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pull_request:
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workflow_dispatch:
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permissions:
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contents: read
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jobs:
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linux:
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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: ubuntu-22.04
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target: x86_64
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- runner: ubuntu-22.04
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target: x86
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- runner: ubuntu-22.04
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target: aarch64
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- runner: ubuntu-22.04
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target: armv7
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- runner: ubuntu-22.04
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target: s390x
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- runner: ubuntu-22.04
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target: 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.x
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- name: Build wheels
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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 --find-interpreter
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sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
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manylinux: auto
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- name: Upload wheels
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uses: actions/upload-artifact@v4
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with:
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name: wheels-linux-${{ matrix.platform.target }}
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path: dist
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musllinux:
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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: ubuntu-22.04
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target: x86_64
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- runner: ubuntu-22.04
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target: x86
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- runner: ubuntu-22.04
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target: aarch64
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- runner: ubuntu-22.04
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target: 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.x
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- name: Build wheels
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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 --find-interpreter
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sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
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manylinux: musllinux_1_2
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- name: Upload wheels
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uses: actions/upload-artifact@v4
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with:
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name: wheels-musllinux-${{ matrix.platform.target }}
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path: dist
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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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- runner: windows-latest
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target: x86
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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.x
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architecture: ${{ matrix.platform.target }}
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- name: Build wheels
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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 --find-interpreter
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sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
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- name: Upload wheels
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uses: actions/upload-artifact@v4
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with:
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name: wheels-windows-${{ matrix.platform.target }}
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path: dist
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macos:
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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: macos-13
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target: x86_64
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- runner: macos-14
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target: 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.x
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- name: Build wheels
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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 --find-interpreter
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sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
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- name: Upload wheels
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uses: actions/upload-artifact@v4
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with:
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name: wheels-macos-${{ matrix.platform.target }}
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path: dist
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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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- name: Build sdist
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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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- name: Upload sdist
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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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release:
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name: Release
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runs-on: ubuntu-latest
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if: ${{ startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch' }}
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needs: [linux, musllinux, windows, macos, sdist]
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permissions:
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# Use to sign the release artifacts
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id-token: write
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# Used to upload release artifacts
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contents: write
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# Used to generate artifact attestation
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attestations: write
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steps:
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- uses: actions/download-artifact@v4
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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: 'wheels-*/*'
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- name: Publish to PyPI
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if: ${{ startsWith(github.ref, 'refs/tags/') }}
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uses: PyO3/maturin-action@v1
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env:
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MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
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with:
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command: upload
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args: --non-interactive --skip-existing wheels-*/*

‎.gitignore‎

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paper/*.aux
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paper/*.bbl
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paper/*.blg
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paper/*.dvi
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paper/*.fdb_latexmk
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paper/*.log
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paper/*.out
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paper/*.pdf
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paper/*.fls
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/target
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# Byte-compiled / optimized / DLL files
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__pycache__/
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.pytest_cache/
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*.py[cod]
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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.venv/
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env/
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bin/
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build/
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develop-eggs/
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dist/
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eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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include/
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man/
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venv/
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*.egg-info/
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.installed.cfg
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*.egg
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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pip-selfcheck.json
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.coverage
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.cache
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nosetests.xml
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coverage.xml
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# Translations
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*.mo
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# Mr Developer
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.mr.developer.cfg
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.project
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.pydevproject
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# Rope
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.ropeproject
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# Django stuff:
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*.log
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*.pot
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.DS_Store
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# Sphinx documentation
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docs/_build/
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# PyCharm
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.idea/
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# VSCode
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.vscode/
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# Pyenv
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.python-version
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Cargo.lock

‎Cargo.toml‎

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[package]
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name = "cr_bayesian_optim"
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version = "0.1.0"
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edition = "2021"
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# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
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[lib]
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name = "cr_bayesian_optim"
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crate-type = ["cdylib"]
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[dependencies]
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cellular_raza = "0.2.3"
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pyo3 = "0.24.0"

‎LICENSE‎

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Copyright 2025 Jonas Pleyer
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Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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‎README.md‎

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# cr_bayesian_optim
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This project combines Bayesian Optimization with Agent-Based simulations of cellular systems done by
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cellular_raza.
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## Usage
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```python
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if __name__ == "__main__":
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print("Hello, World!")
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```
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## Installation
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This project uses [maturin](https://github.com/PyO3/maturin) to install all required dependencies.
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We recommend, to pair this with the [`uv`](https://github.com/astral-sh/uv) package manager.
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### From [pypi](https://pypi.org/)
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```bash
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uv pip install cr_bayesian_optim
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```
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### From Source
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Once you have cloned the repository
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```bash
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git clone https://github.com/jonaspleyer/cr_bayesian_optim
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```
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you should move the respective directory and create a new virtual environment.
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```bash
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cd cr_bayesian_optim
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python -m venv .venv
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```
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Afterwards, activate the environment and install the package.
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```bash
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source .venv/bin/activate
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maturin develop -r --uv
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```

‎paper/LICENSE‎

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MIT License
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Copyright (c) 2020 George Kour
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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
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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‎paper/Makefile‎

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CC:=latexmk
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OPTIONS:=-pdf
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TARGET:=main
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all:
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$(CC) $(OPTIONS) $(TARGET)
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clean:
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rm -f $(TARGET).aux
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rm -f $(TARGET).bbl
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rm -f $(TARGET).blg
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rm -f $(TARGET).dvi
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rm -f $(TARGET).fdb_latexmk
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rm -f $(TARGET).log
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rm -f $(TARGET).out
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rm -f $(TARGET).pdf
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rm -f $(TARGET).fls
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fresh: clean all

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