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kylebittingerkylebittinger
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Merge pull request #20 from PennChopMicrobiomeProgram/use-native-pipe
Use native pipe, fix linting errors, update workflows
2 parents 5d1d5d6 + 59578ac commit 4c63c43

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‎.github/workflows/R-CMD-check.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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branches: [main, master]
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name: R-CMD-check
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jobs:
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R-CMD-check:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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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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- {os: macOS-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'oldrel-1'}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: rcmdcheck
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- uses: r-lib/actions/check-r-package@v2
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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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name: R-CMD-check.yaml
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permissions: read-all
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jobs:
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R-CMD-check:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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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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- {os: macos-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'oldrel-1'}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::rcmdcheck
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needs: check
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- uses: r-lib/actions/check-r-package@v2
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with:
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upload-snapshots: true
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build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

‎.github/workflows/linter.yaml‎

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name: Super-Linter
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on:
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pull_request:
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branches: [ master, main ]
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push:
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branches: [ master, main ]
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jobs:
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lint:
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name: Lint Code Base
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runs-on: ubuntu-latest
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steps:
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- name: Checkout Code
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uses: actions/checkout@v3
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- name: Lint Code Base
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uses: github/super-linter@v4
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env:
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VALIDATE_ALL_CODEBASE: true
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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VALIDATE_R_LINTR: true
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FILTER_REGEX_INCLUDE: R/.*|tests/.*\.R
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name: Lint Code Base
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on:
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push:
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branches: [main]
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pull_request:
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branches: [main]
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jobs:
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run-lint:
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name: Lint Code Base
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runs-on: ubuntu-latest
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steps:
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- name: Checkout Code
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uses: actions/checkout@v4
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with:
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# Full git history is needed for Super-Linter to detect changed files
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fetch-depth: 0
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- name: Super-Linter
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uses: super-linter/super-linter@v7
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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# Enable only R linting (optional; defaults to all languages if omitted)
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VALIDATE_R: true
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# Lint the entire codebase (true) or just changed files (false)
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VALIDATE_ALL_CODEBASE: false
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# Set the default branch (required for diff-based linting)
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DEFAULT_BRANCH: main
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FILTER_REGEX_INCLUDE: R/.*|tests/.*\.R

‎.github/workflows/test-coverage.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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branches: [main, master]
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name: test-coverage
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jobs:
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test-coverage:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: covr
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- name: Test coverage
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run: covr::codecov()
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shell: Rscript {0}
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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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name: test-coverage.yaml
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permissions: read-all
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jobs:
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test-coverage:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::covr, any::xml2
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needs: coverage
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- name: Test coverage
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run: |
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cov <- covr::package_coverage(
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quiet = FALSE,
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clean = FALSE,
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install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
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)
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print(cov)
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covr::to_cobertura(cov)
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shell: Rscript {0}
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- uses: codecov/codecov-action@v5
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with:
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# Fail if error if not on PR, or if on PR and token is given
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fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
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files: ./cobertura.xml
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plugins: noop
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disable_search: true
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token: ${{ secrets.CODECOV_TOKEN }}
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- name: Show testthat output
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if: always()
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run: |
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## --------------------------------------------------------------------
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find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Upload test results
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if: failure()
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uses: actions/upload-artifact@v4
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with:
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name: coverage-test-failures
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path: ${{ runner.temp }}/package

‎DESCRIPTION‎

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License: GPL-3 + file LICENSE
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Encoding: UTF-8
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LazyData: true
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RoxygenNote: 7.3.1
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RoxygenNote: 7.3.3
2020
Imports:
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generics (>= 0.0.2),
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rlang,
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dplyr (>= 1.0.0),
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tibble (>= 3.0.0),
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ape,
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magrittr,
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ggplot2,
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stringr
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Depends:
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R (>= 2.10)
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R (>= 4.1.0)
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Suggests:
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covr,
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testthat

‎NAMESPACE‎

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S3method(plot,pcoaplus)
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S3method(tidy,adonis)
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S3method(tidy,anova.cca)
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export("%>%")
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export(adonisplus)
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export(adonispost)
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export(nmdsplus)
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export(shuffle_within_groups)
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export(tidy)
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importFrom(generics,tidy)
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importFrom(magrittr,"%>%")

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