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Jelmer Bot
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add github actions
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‎.github/workflows/Docs.yml‎

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name: Documentation
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concurrency:
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group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
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cancel-in-progress: true
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on:
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push:
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branches:
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- main
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workflow_dispatch:
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jobs:
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pages:
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runs-on: ubuntu-20.04
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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permissions:
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pages: write
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id-token: write
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steps:
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- id: deployment
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uses: sphinx-notes/pages@v3
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with:
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cache: True
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documentation_path: ./doc
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requirements_path: ./doc/requirements.txt

‎.github/workflows/Publish.yml‎

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name: Publish Python Package
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concurrency:
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group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
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cancel-in-progress: true
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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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jobs:
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publish_pypi:
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name: Publish to PyPi
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runs-on: ubuntu-20.04
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permissions:
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# IMPORTANT: this permission is mandatory for trusted publishing
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id-token: write
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environment:
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name: pypi
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url: https://pypi.org/p/multi_mst
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steps:
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- name: Setup Python
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uses: actions/setup-python@v4
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with:
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python-version: 3.9
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- name: Install dependencies
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run: |
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pip install -U wheelhouse_uploader pyyaml
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- name: Download wheels and sdist
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uses: dawidd6/[email protected]
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with:
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github_token: ${{ secrets.PUSH_TOKEN }}
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workflow: Wheels.yml
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workflow_conclusion: success
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branch: main
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path: .
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- name: Move files to dist
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run: |
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mkdir dist
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mv sdist/* dist/
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mv wheels/* dist/
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- name: Publish package to (Test)PyPI
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uses: pypa/[email protected]
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# Comment lines below to publish to PyPi instead of test PyPi
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# with:
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# repository-url: https://test.pypi.org/legacy/

‎.github/workflows/Tests.yml‎

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name: Tests
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concurrency:
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group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
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cancel-in-progress: true
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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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branches:
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- main
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workflow_dispatch:
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jobs:
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build_sdist:
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name: Build sdist
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runs-on: ubuntu-20.04
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outputs:
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SDIST_NAME: ${{ steps.sdist.outputs.SDIST_NAME }}
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steps:
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- uses: actions/checkout@v3
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with:
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fetch-depth: 0
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- uses: actions/setup-python@v4
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name: Install python
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with:
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python-version: 3.9
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cache: 'pip'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r requirements.txt
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pip install twine flake8
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- name: Lint with flake8
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run: |
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# stop the build if there are Python syntax errors or undefined names
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flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
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- name: Build sdist
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id: sdist
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run: |
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python setup.py sdist
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python ci/export_sdist_name.py
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- name: Check README rendering for PyPI
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run: twine check dist/*
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- name: Upload sdist result
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uses: actions/upload-artifact@v3
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with:
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name: sdist
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path: dist/*.tar.gz
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if-no-files-found: error
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build_wheels:
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name: Build wheel for cp${{ matrix.python }}-${{ matrix.platform_id }}-${{ matrix.manylinux_image }}
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needs: build_sdist
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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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include:
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- os: windows-latest
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python: 39
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platform_id: win_amd64
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- os: windows-latest
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python: 310
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platform_id: win_amd64
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- os: windows-latest
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python: 311
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platform_id: win_amd64
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# Linux 64 bit manylinux2014
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- os: ubuntu-latest
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python: 39
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platform_id: manylinux_x86_64
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manylinux_image: manylinux2014
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- os: ubuntu-latest
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python: 310
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platform_id: manylinux_x86_64
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manylinux_image: manylinux2014
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- os: ubuntu-latest
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python: 311
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platform_id: manylinux_x86_64
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manylinux_image: manylinux2014
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# MacOS x86_64
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- os: macos-latest
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python: 39
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platform_id: macosx_x86_64
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- os: macos-latest
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python: 310
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platform_id: macosx_x86_64
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- os: macos-latest
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python: 311
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platform_id: macosx_x86_64
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steps:
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- name: Download sdist
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uses: actions/download-artifact@v3
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with:
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name: sdist
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path: dist/
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- name: Setup Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.9' # update once build dependencies are available
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- name: Build and Test wheels
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uses: pypa/cibuildwheel@51f5c7fe68ff24694d5a6ac0eb3ad476ddd062a8 # v2.13.0
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with:
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package-dir: dist/${{ needs.build_sdist.outputs.SDIST_NAME }}
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env:
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CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
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CIBW_ARCHS: all
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CIBW_MANYLINUX_X86_64_IMAGE: ${{ matrix.manylinux_image }}
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CIBW_MANYLINUX_I686_IMAGE: ${{ matrix.manylinux_image }}
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CIBW_TEST_REQUIRES: pytest matplotlib pandas networkx
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CIBW_TEST_COMMAND: pytest {package}/tests
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CIBW_BUILD_VERBOSITY: 1
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- name: Store artifacts
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uses: actions/upload-artifact@v3
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with:
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name: wheels
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path: wheelhouse/*.whl
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if-no-files-found: ignore
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‎MANIFEST.in‎

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include LICENSE
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include MANIFEST.in
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include requirements.txt
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recursive-include docs *
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recursive-exclude docs/_build *
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recursive-include doc *
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recursive-exclude doc/_build *
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recursive-include notebooks *.ipynb *.py
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recursive-include notebooks/data *
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recursive-exclude notebooks/data/generated *
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recursive-exclude notebooks/.ipynb_checkpoints *
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recursive-exclude notebooks/**/.ipynb_checkpoints *
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recursive-exclude notebooks/images *

‎ci/export_sdist_name.py‎

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#!/usr/bin/env python3
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"""
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Determine the name of the sdist and export to GitHub output named SDIST_NAME.
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To run:
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$ python3 -m build --sdist
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$ ./ci/determine_sdist_name.py
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"""
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import os
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from pathlib import Path
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import sys
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paths = [p.name for p in Path("dist").glob("*.tar.gz")]
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if len(paths) != 1:
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sys.exit(f"Only a single sdist is supported, but found: {paths}")
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print(paths[0])
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with open(os.environ["GITHUB_OUTPUT"], "a") as f:
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f.write(f"SDIST_NAME={paths[0]}\n")

‎doc/requirements.txt‎

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ipykernel
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nbsphinx
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numpydoc
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sphinx_rtd_theme

‎multi_mst/k_mst/k_mst.py‎

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clean_data = X
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kwargs = self.get_params()
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print(kwargs, self.umap_kwargs)
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self.mst_indices_, self.mst_distances_, self._umap = kMST(
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clean_data, umap_kwargs=self.umap_kwargs, **kwargs
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)

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