mirror of https://github.com/msberends/AMR.git
104 lines
4.3 KiB
YAML
104 lines
4.3 KiB
YAML
# ==================================================================== #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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on:
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pull_request:
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# run in each PR in this repo
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branches: '**'
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push:
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branches: '**'
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schedule:
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# also run a schedule everyday at 1 AM.
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# this is to check that all dependencies are still available (see R/zzz.R)
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- cron: '0 1 * * *'
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name: check-recent
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jobs:
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R-code-check:
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runs-on: ${{ matrix.config.os }}
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continue-on-error: ${{ matrix.config.allowfail }}
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name: ${{ matrix.config.os }} (R-${{ 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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# current development version, check all major OSes:
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- {os: macOS-latest, r: 'devel', allowfail: false}
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- {os: windows-latest, r: 'devel', allowfail: false}
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- {os: ubuntu-latest, r: 'devel', allowfail: false}
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# current 'release' version, check all major OSes:
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- {os: macOS-latest, r: '4.3', allowfail: false}
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- {os: windows-latest, r: '4.3', allowfail: false}
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- {os: ubuntu-latest, r: '4.3', allowfail: false}
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# older versions (see also check-old.yaml for even older versions):
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- {os: ubuntu-latest, r: '4.2', allowfail: false}
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- {os: ubuntu-latest, r: '4.1', allowfail: false}
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- {os: ubuntu-latest, r: '4.0', allowfail: false}
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- {os: ubuntu-latest, r: '3.6', allowfail: false} # when a new R releases, this one has to move to check-old.yaml
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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@v3
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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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# use RStudio Package Manager to quickly install packages
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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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env:
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_R_CHECK_LENGTH_1_CONDITION_: verbose
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_R_CHECK_LENGTH_1_LOGIC2_: verbose
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# during 'R CMD check', R_LIBS_USER will be overwritten, so:
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R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
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R_RUN_TINYTEST: true
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- name: Show tinytest output
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if: always()
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run: |
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find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
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shell: bash
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