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scottgigantescottgigante
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Merge pull request #195 from KrishnaswamyLab/dev
MAGIC v3.0
2 parents 0a4f0c6 + c72c463 commit 136169c

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‎.github/ISSUE_TEMPLATE/question.md‎

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assignees: ''
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‎.github/workflows/deploy.yml‎

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name: Publish Python distributions to PyPI
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on:
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push:
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branches:
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- 'master'
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- 'test_deploy'
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tags:
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- '*'
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jobs:
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build-n-publish:
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name: Build and publish Python distributions to PyPI
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@master
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- name: Set up Python 3.7
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uses: actions/setup-python@v2
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with:
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python-version: 3.7
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- name: Install pypa/build
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run: >-
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cd python &&
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python -m
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pip install
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build
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--user &&
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cd ..
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- name: Build a binary wheel and a source tarball
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run: >-
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cd python &&
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python -m
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build
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--sdist
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--wheel
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--outdir dist/
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. &&
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cd ..
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- name: Publish distribution to Test PyPI
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uses: pypa/gh-action-pypi-publish@master
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with:
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skip_existing: true
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password: ${{ secrets.test_pypi_password }}
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repository_url: https://test.pypi.org/legacy/
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- name: Publish distribution to PyPI
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if: startsWith(github.ref, 'refs/tags')
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uses: pypa/gh-action-pypi-publish@master
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with:
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password: ${{ secrets.pypi_password }}

‎.github/workflows/pre-commit.yml‎

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name: pre-commit
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on:
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push:
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branches-ignore:
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- 'master'
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jobs:
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pre-commit:
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runs-on: ubuntu-latest
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steps:
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- name: Cancel Previous Runs
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uses: styfle/cancel-workflow-action@0.6.0
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with:
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access_token: ${{ github.token }}
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- name: Set up environment
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run: |
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echo "UBUNTU_VERSION=`grep DISTRIB_RELEASE /etc/lsb-release | sed 's/.*=//g'`" >> $GITHUB_ENV
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mkdir -p .local/R/site-packages
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echo "R_LIBS_USER=`pwd`/.local/R/site-packages" >> $GITHUB_ENV
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- name: Install system dependencies
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if: runner.os == 'Linux'
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run: |
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sudo apt-get update -qq
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sudo apt-get install -y libcurl4-openssl-dev
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: "3.8"
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architecture: "x64"
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- name: Cache pre-commit
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uses: actions/cache@v2
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with:
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path: ~/.cache/pre-commit
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key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}-
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- name: Run pre-commit
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uses: pre-commit/action@v2.0.0
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- name: Cache R packages
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uses: actions/cache@v2
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if: startsWith(runner.os, 'Linux')
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with:
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path: ${{env.R_LIBS_USER}}
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key: precommit-${{env.UBUNTU_VERSION}}-renv-${{ hashFiles('Rmagic/.pre-commit.r_requirements.txt') }}-${{ hashFiles('Rmagic/DESCRIPTION') }}-
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restore-keys: |
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precommit-${{env.UBUNTU_VERSION}}-renv-${{ hashFiles('Rmagic/.pre-commit.r_requirements.txt') }}-
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precommit-${{env.UBUNTU_VERSION}}-renv-
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- name: Install R packages
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run: |
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if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv")
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con = file("Rmagic/.pre-commit.r_requirements.txt", "r")
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while ( length(pkg <- readLines(con, n = 1)) > 0 ) {
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renv::install(pkg)
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}
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close(con)
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if (!require("devtools")) install.packages("devtools", repos="http://cloud.r-project.org")
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devtools::install_dev_deps("./Rmagic", upgrade=TRUE)
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devtools::install("./Rmagic")
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shell: Rscript {0}
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- name: Run pre-commit for R
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run: |
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cd Rmagic
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git init
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git add *
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pre-commit run --all-files
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rm -rf .git
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cd ..
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- name: Commit files
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if: failure()
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run: |
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git checkout -- .github/workflows
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if [[ `git status --porcelain --untracked-files=no` ]]; then
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git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
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git config --local user.name "github-actions[bot]"
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git commit -m "pre-commit" -a
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fi
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- name: Push changes
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if: failure()
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uses: ad-m/github-push-action@master
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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branch: ${{ github.ref }}

‎.github/workflows/run_tests.yml‎

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name: Unit Tests
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on:
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push:
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branches-ignore:
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- 'test_deploy'
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pull_request:
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branches:
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- '*'
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jobs:
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test_python:
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runs-on: ${{ matrix.config.os }}
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if: "!contains(github.event.head_commit.message, 'ci skip')"
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strategy:
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fail-fast: false
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matrix:
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config:
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- {name: '3.9', os: ubuntu-latest, python: '3.9' }
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- {name: '3.8', os: ubuntu-latest, python: '3.8' }
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- {name: '3.7', os: ubuntu-latest, python: '3.7' }
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- {name: '3.6', os: ubuntu-latest, python: '3.6' }
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steps:
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- name: Cancel Previous Runs
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uses: styfle/cancel-workflow-action@0.6.0
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with:
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access_token: ${{ github.token }}
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- name: Check Ubuntu version
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run: |
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echo "UBUNTU_VERSION=`grep DISTRIB_RELEASE /etc/lsb-release | sed 's/.*=//g'`" >> $GITHUB_ENV
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- uses: actions/checkout@v2
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.config.python }}
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- name: Cache Python packages
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uses: actions/cache@v2
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with:
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path: ${{ env.pythonLocation }}
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key: ${{runner.os}}-pip-${{ env.pythonLocation }}-${{ hashFiles('python/setup.py') }}
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restore-keys: ${{runner.os}}-pip-${{ env.pythonLocation }}-
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- name: Install package & dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -U wheel setuptools
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pip install -U ./python[test]
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python -c "import magic"
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- name: Run Python tests
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run: |
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cd python
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nose2 -vvv
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cd ..
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- name: Build docs
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run: |
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cd python
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pip install .[doc]
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cd doc
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make html
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cd ../..
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- name: Coveralls
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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COVERALLS_SERVICE_NAME: github
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run: |
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coveralls
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- name: Upload check results on fail
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if: failure()
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uses: actions/upload-artifact@master
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with:
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name: ${{ matrix.config.name }}_results
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path: check
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test_r:
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runs-on: ${{ matrix.config.os }}
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if: "!contains(github.event.head_commit.message, 'ci skip')"
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strategy:
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fail-fast: false
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matrix:
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config:
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- {name: 'devel', os: ubuntu-latest, r: 'devel' }
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- {name: 'release', os: ubuntu-latest, r: 'release' }
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steps:
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- name: Cancel Previous Runs
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uses: styfle/cancel-workflow-action@0.6.0
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with:
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access_token: ${{ github.token }}
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- name: Set up environment
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run: |
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echo "UBUNTU_VERSION=`grep DISTRIB_RELEASE /etc/lsb-release | sed 's/.*=//g'`" >> $GITHUB_ENV
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mkdir -p .local/R/site-packages
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echo "R_LIBS_USER=`pwd`/.local/R/site-packages" >> $GITHUB_ENV
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- uses: actions/checkout@v2
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: "3.8"
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- name: Install system dependencies
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if: runner.os == 'Linux'
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run: |
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sudo apt-get update -qq
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sudo apt-get install -y libcurl4-openssl-dev pandoc
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- name: Cache Python packages
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uses: actions/cache@v2
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with:
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path: ${{ env.pythonLocation }}
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key: ${{runner.os}}-pip-${{ env.pythonLocation }}-${{ hashFiles('python/setup.py') }}
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restore-keys: ${{runner.os}}-pip-${{ env.pythonLocation }}-
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- name: Install package & dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -U wheel setuptools
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pip install -U ./python
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python -c "import magic"
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- name: Set up R
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id: setup-r
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uses: r-lib/actions/setup-r@v1
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with:
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r-version: ${{ matrix.config.r }}
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- name: Cache R packages
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uses: actions/cache@v2
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if: startsWith(runner.os, 'Linux')
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with:
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path: ${{env.R_LIBS_USER}}
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key: test-${{env.UBUNTU_VERSION}}-renv-${{ steps.setup-r.outputs.installed-r-version }}-${{ hashFiles('Rmagic/DESCRIPTION') }}-
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restore-keys: |
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test-${{env.UBUNTU_VERSION}}-renv-${{ steps.setup-r.outputs.installed-r-version }}-
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- name: Install R packages
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run: |
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if (!require("devtools")) install.packages("devtools", repos="http://cloud.r-project.org")
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devtools::install_dev_deps("./Rmagic", upgrade=TRUE)
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devtools::install("./Rmagic")
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shell: Rscript {0}
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- name: Install tinytex
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uses: r-lib/actions/setup-tinytex@v1
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- name: Run R tests
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run: |
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cd Rmagic
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R CMD build .
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R CMD check --as-cran *.tar.gz
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cd ..
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- name: Upload check results on fail
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if: failure()
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uses: actions/upload-artifact@master
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with:
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name: ${{ matrix.config.name }}_results
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path: check

‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v3.3.0
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hooks:
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- id: check-yaml
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- id: end-of-file-fixer
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- id: trailing-whitespace
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exclude: \.(ai|gz)$
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- repo: https://github.com/timothycrosley/isort
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rev: 5.6.4
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hooks:
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- id: isort
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- repo: https://github.com/psf/black
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rev: 20.8b1
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hooks:
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- id: black
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args: ['--target-version', 'py36']
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- repo: https://github.com/pre-commit/mirrors-autopep8
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rev: v1.5.4
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hooks:
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- id: autopep8
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- repo: https://gitlab.com/pycqa/flake8
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rev: 3.8.4
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hooks:
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- id: flake8
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additional_dependencies: ['hacking']

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