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ulupoMonkeyBreaker
ulupo
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MonkeyBreaker
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Add @MonkeyBreaker's GitHub action for wheel building (#646)
* Merge with latest master, do not delete Azure CI, remove Py36, add Py310 and Apple Silicon * Enable cross-compilation on macOS as done by @MonkeyBreaker in pyflagser and giotto-ph * Linting in test_rips_complex * Bump install-boost version to 2.3.1 (latest) * Bumping cibuildwheel version to 2.9.0 (latest) Co-authored-by: julian <[email protected]>
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‎.github/workflows/wheels.yml

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name: Build Wheels
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# https://docs.github.com/en/actions/learn-github-actions/workflow-syntax-for-github-actions#onworkflow_dispatchinputs
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on :
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workflow_dispatch:
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inputs:
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nightlyRelease:
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description: 'Generates wheels for the nightly release'
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type: boolean
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required: true
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default: false
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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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fail-fast: false
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matrix:
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os: [ubuntu-latest, windows-latest, macos-latest]
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include:
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- os: ubuntu-latest
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boost_install_dir: /home/runner/work
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- os: macos-latest
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boost_install_dir: /Users/runner/work
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- os: windows-latest
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boost_install_dir: D:\
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env:
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BOOST_VERSION: 1.76.0
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steps:
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- uses: actions/checkout@v2
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- name: Change name to giotto-tda-nightly
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if: ${{ github.event.inputs.nightlyRelease == true }}
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run: |
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set -e
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sed -i "s/'giotto-tda'/'giotto-tda-nightly'/1" setup.py
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sed -i 's/"giotto-tda"/"giotto-tda-nightly"/1' setup.py
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sed -i "s/__version__.*/__version__ = '$(Build.BuildNumber)'/1" gtda/_version.py
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shell: bash
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- name: Create directories boost
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run: |
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cd ${{ matrix.boost_install_dir }}
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mkdir -p boost/boost
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cd -
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- name: Cache boost ${{env.BOOST_VERSION}} in ${{ matrix.boost_install_dir }}
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# FIXME For an unknown reason on windows runner, when the cache is hit
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# The compilation fails because it doesn't find some headers
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# I don't know if the cache is corrupted, for the moment hard to debug
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if: ${{ runner.os == 'Linux' || runner.os == 'macOS' }}
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uses: actions/cache@v2
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id: cache-boost
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with:
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# Set the default path as the path to cache
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path: ${{ matrix.boost_install_dir }}/boost/boost
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# Use the version as the key to only cache the correct version
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key: 1-boost-${{env.BOOST_VERSION}}
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- name: Install boost ${{env.BOOST_VERSION}}
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uses: MarkusJx/[email protected]
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id: install-boost
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if: steps.cache-boost.outputs.cache-hit != 'true'
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with:
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boost_version: ${{env.BOOST_VERSION}}
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boost_install_dir: ${{ matrix.boost_install_dir }}
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- name: Build wheels
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uses: pypa/[email protected]
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env:
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# Specify which Python versions to build wheels
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# https://cibuildwheel.readthedocs.io/en/stable/options/#build-skip
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CIBW_BUILD: "cp37-* cp38-* cp39-* cp310-*"
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# Skip 32 bit architectures, musllinux, and i686, and macOS x86_64 wheels for CP3.8 -- CP3.10
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CIBW_SKIP: "*-win32 *-musllinux_x86_64 *_i686 cp38-macosx_x86_64 cp39-macosx_x86_64 cp310-macosx_x86_64"
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CIBW_BEFORE_BUILD_WINDOWS: python -m pip install cmake && python -m pip install --upgrade pip setuptools && sed -i $'s/\r$//' README.rst && python -m pip install delvewheel
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CIBW_BEFORE_BUILD_LINUX: python -m pip install cmake && python -m pip install --upgrade pip setuptools
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CIBW_BEFORE_BUILD_MACOS: python -m pip install cmake && python -m pip install --upgrade pip setuptools
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CIBW_TEST_COMMAND: python -m pytest --pyargs gtda
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# nbformat is needed by plotly: https://github.com/plotly/plotly.py/issues/2159
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CIBW_TEST_REQUIRES: pytest hypothesis pandas nbformat
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CIBW_ENVIRONMENT_WINDOWS: BOOST_ROOT='${{ matrix.boost_install_dir }}boost\boost'
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CIBW_ENVIRONMENT_MACOS: BOOST_ROOT='${{ matrix.boost_install_dir }}/boost'
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CIBW_ENVIRONMENT_LINUX: BOOST_ROOT=/host${{ matrix.boost_install_dir }}/boost
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CIBW_ENVIRONMENT_PASS_LINUX: BOOST_ROOT
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CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: "delvewheel repair -vv -w {dest_dir} {wheel}"
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CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
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# Should generate universal2 wheels for CP3.8 -- CP3.10
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CIBW_ARCHS_MACOS: x86_64 universal2
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- uses: actions/upload-artifact@v2
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name: Upload wheels
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with:
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path: ./wheelhouse/*.whl

‎doc/contributing/index.rst

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This page contains a summary of what one needs to do to contribute.
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..
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toctree::
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.. toctree::
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:maxdepth: 2
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:hidden:
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‎gtda/externals/__init__.py

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from .modules.gtda_bottleneck import bottleneck_distance
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from .modules.gtda_wasserstein import wasserstein_distance
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from .python import SparseRipsComplex, CechComplex, CubicalComplex, \
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PeriodicCubicalComplex, SimplexTree, WitnessComplex, StrongWitnessComplex
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from .python import RipsComplex, SparseRipsComplex, CechComplex, \
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CubicalComplex, PeriodicCubicalComplex, SimplexTree, WitnessComplex, \
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StrongWitnessComplex
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__all__ = [
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'bottleneck_distance',
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'wasserstein_distance',
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'RipsComplex',
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'SparseRipsComplex',
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'CechComplex',
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'CubicalComplex',

‎gtda/externals/python/tests/test_rips_complex.py

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from .. import RipsComplex, SparseRipsComplex
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""" Test comes from
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"""Test comes from
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https://github.com/GUDHI/gudhi-devel/blob/master/src/python/test/test_rips_complex.py
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"""
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def test_empty_rips():
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rips_complex = RipsComplex()
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del(rips_complex)
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del rips_complex
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def test_sparse_filtered_rips_from_points():

‎setup.py

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cmake_args += [f"-DCMAKE_BUILD_TYPE={cfg}"]
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build_args += ["--", "-j2"]
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if sys.platform.startswith("darwin"):
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# Cross-compile support for macOS - respect ARCHFLAGS if set
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archs = re.findall(r"-arch (\S+)", os.environ.get("ARCHFLAGS", ""))
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if archs:
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cmake_args += \
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["-DCMAKE_OSX_ARCHITECTURES={}".format(";".join(archs))]
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env = os.environ.copy()
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env["CXXFLAGS"] = f"{env.get('CXXFLAGS', '')} -DVERSION_INFO="\
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f"\\'{self.distribution.get_version()}\\'"

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