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Merge pull request #234 from AviPeltz/master
Fix packaging for cross-platform installs and PyPI readiness
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‎.github/workflows/build.yml‎

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name: Build and Test
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on:
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push:
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branches: [main, master, develop]
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pull_request:
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branches: [main, master]
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jobs:
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test:
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name: Test on ${{ matrix.os }} / Python ${{ matrix.python-version }}
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-latest]
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python-version: ["3.9", "3.10", "3.11", "3.12"]
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steps:
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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@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install build dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build pytest
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- name: Build and install package
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run: |
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pip install .
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- name: Verify binaries are bundled
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run: |
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python -c "from smudgeplot.cli import get_binary_path; print(get_binary_path('hetmers'))"
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python -c "from smudgeplot.cli import get_binary_path; print(get_binary_path('extract_kmer_pairs'))"
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- name: Test CLI
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run: |
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smudgeplot --version
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smudgeplot -h
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smudgeplot hetmers --help
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smudgeplot extract --help
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build-wheels:
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name: Build wheels on ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-latest, macos-13, macos-14] # macos-13=x86, macos-14=arm64
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steps:
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- uses: actions/checkout@v4
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- name: Build wheels
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uses: pypa/[email protected]
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# Config is read from pyproject.toml [tool.cibuildwheel]
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- uses: actions/upload-artifact@v4
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with:
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name: wheels-${{ matrix.os }}
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path: ./wheelhouse/*.whl
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build-sdist:
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name: Build source distribution
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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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run: |
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pip install build
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python -m build --sdist
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- name: Verify sdist doesn't contain binaries
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run: |
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tar -tzf dist/*.tar.gz | grep -E 'bin/(hetmers|extract_kmer_pairs)$' && exit 1 || echo "Good: no binaries in sdist"
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- uses: actions/upload-artifact@v4
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with:
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name: sdist
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path: dist/*.tar.gz
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test-sdist:
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name: Test sdist on ${{ matrix.os }}
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needs: build-sdist
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-latest, macos-latest]
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steps:
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- uses: actions/download-artifact@v4
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with:
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name: sdist
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path: dist
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- name: Set up Python
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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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- name: Install from sdist
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run: |
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pip install dist/*.tar.gz
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- name: Verify binaries are compiled
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run: |
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python -c "from smudgeplot.cli import get_binary_path; print(get_binary_path('hetmers'))"
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python -c "from smudgeplot.cli import get_binary_path; print(get_binary_path('extract_kmer_pairs'))"
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- name: Test compiled binaries execute
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run: |
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smudgeplot hetmers --help
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smudgeplot extract --help

‎.github/workflows/publish.yml‎

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name: Publish to PyPI
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on:
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release:
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types: [published]
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jobs:
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build-wheels:
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name: Build wheels on ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-latest, macos-13, macos-14]
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steps:
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- uses: actions/checkout@v4
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- name: Build wheels
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uses: pypa/[email protected]
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# Config is read from pyproject.toml [tool.cibuildwheel]
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- uses: actions/upload-artifact@v4
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with:
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name: wheels-${{ matrix.os }}
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path: ./wheelhouse/*.whl
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build-sdist:
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name: Build source distribution
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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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run: |
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pip install build
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python -m build --sdist
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- name: Verify sdist doesn't contain binaries
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run: |
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tar -tzf dist/*.tar.gz | grep -E 'bin/(hetmers|extract_kmer_pairs)$' && exit 1 || echo "Good: no binaries in sdist"
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- uses: actions/upload-artifact@v4
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with:
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name: sdist
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path: dist/*.tar.gz
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publish:
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name: Publish to PyPI
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needs: [build-wheels, build-sdist]
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runs-on: ubuntu-latest
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environment: pypi
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permissions:
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id-token: write # Required for trusted publishing
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steps:
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- name: Download all artifacts
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uses: actions/download-artifact@v4
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with:
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path: dist
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merge-multiple: true
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- name: List distribution files
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run: ls -la dist/
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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packages-dir: dist/

‎.gitignore‎

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src/smudgeplot.egg-info
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dist
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.venv
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smudgeplot_dev/
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# Compiled binaries (built during install)
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src/smudgeplot/bin/

‎MANIFEST.in‎

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include LICENSE.md
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include README.md
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include Makefile
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# Include C source files for compilation during install
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recursive-include src/lib *.c *.h
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# Explicitly exclude compiled binaries - they must be built per-platform
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global-exclude src/smudgeplot/bin/*
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prune src/smudgeplot/bin

‎pyproject.toml‎

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[build-system]
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requires = ["setuptools>=61.0"]
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requires = ["setuptools>=61.0", "wheel"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "smudgeplot"
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version = "0.5.1"
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dependencies = [
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"numpy >= 2.2.3",
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"matplotlib >= 3.10.0",
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"pandas >= 2.2.3"
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]
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description = "Inference of ploidy and heterozygosity structure using whole genome sequencing data"
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readme = "README.md"
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license = "Apache-2.0"
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license-files = ["LICENSE.md"]
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keywords = ["smudgeplot", "kmer", "ploidy", "genomics", "bioinformatics"]
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# Relaxed Python version - works with 3.9+
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requires-python = ">=3.9"
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requires-python = ">=3.11.11"
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authors = [
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{name = "Kamil S. Jaron", email = "[email protected]"},
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{name = "Sam Ebdon", email = "[email protected]"},
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]
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# add authors
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maintainers = [
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{name = "Kamil Jaron", email = "[email protected]"},
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{name = "Sam Ebdon", email = "[email protected]"},
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]
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description = "Smudgeplot description"
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readme = "README.md"
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license = "Apache-2.0"
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license-files = ["LICENSE.md"]
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keywords = ["smudgeplot","kmer","ploidy"]
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# Relaxed dependency versions for broader compatibility
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dependencies = [
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"numpy>=1.20.0",
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"matplotlib>=3.4.0",
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"pandas>=1.3.0",
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]
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classifiers = [
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"Development Status :: 3 - Alpha",
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"Programming Language :: Python :: 3"
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"Development Status :: 4 - Beta",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.9",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Operating System :: POSIX :: Linux",
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"Operating System :: MacOS",
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"Intended Audience :: Science/Research",
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"Topic :: Scientific/Engineering :: Bio-Informatics",
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]
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[project.urls]
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Homepage = "https://github.com/KamilSJaron/smudgeplot/tree/sploidyplot_obj"
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Homepage = "https://github.com/KamilSJaron/smudgeplot"
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Documentation = "https://github.com/KamilSJaron/smudgeplot#readme"
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Repository = "https://github.com/KamilSJaron/smudgeplot"
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Issues = "https://github.com/KamilSJaron/smudgeplot/issues"
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[project.scripts]
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smudgeplot = "smudgeplot.cli:main"
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[tool.setuptools]
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package-dir = {"" = "src"}
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include-package-data = true
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[tool.setuptools.packages.find]
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where = ["src"]
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[tool.ruff]
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line-length = 120
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[tool.setuptools.package-data]
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smudgeplot = ["bin/*"]
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[tool.ruff.lint]
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select = [
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"A",
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"ARG",
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"B",
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"BLE",
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"C4",
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"COM",
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"DTZ",
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"E",
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"EM",
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"F",
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"I",
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"ISC",
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"LOG",
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"N",
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"PYI",
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"S",
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"SIM",
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"U",
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]
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ignore = [
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"COM812",
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"C901",
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"LOG015",
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"N803",
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"N806",
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]
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[tool.cibuildwheel]
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# Skip 32-bit, PyPy, musllinux, and Windows (no Windows support for now)
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skip = ["*-win32", "*-win_amd64", "*-manylinux_i686", "pp*", "*-musllinux*"]
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build = ["cp39-*", "cp310-*", "cp311-*", "cp312-*"]
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# Test that the CLI works after building
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test-command = "smudgeplot --version"
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[tool.cibuildwheel.linux]
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# manylinux has gcc available
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before-all = "yum install -y gcc || apt-get update && apt-get install -y gcc || true"
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[tool.cibuildwheel.macos]
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# macOS runners have clang available by default
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# Nothing special needed

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