mirror of https://github.com/msberends/AMR.git
140 lines
6.6 KiB
YAML
140 lines
6.6 KiB
YAML
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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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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push:
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branches:
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- development
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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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schedule:
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# 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: R-code-check
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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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# test all systems against all released versions of R >= 3.0, we support them all!
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- {os: macOS-latest, r: 'devel', allowfail: true}
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- {os: macOS-latest, r: '4.1', allowfail: false}
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- {os: macOS-latest, r: '4.0', allowfail: false}
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- {os: macOS-latest, r: '3.6', allowfail: false}
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- {os: macOS-latest, r: '3.5', allowfail: false}
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- {os: macOS-latest, r: '3.4', allowfail: false}
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- {os: macOS-latest, r: '3.3', allowfail: false}
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- {os: macOS-latest, r: '3.2', allowfail: false}
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- {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: windows-latest, r: 'devel', allowfail: true}
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- {os: windows-latest, r: '4.1', allowfail: false}
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- {os: windows-latest, r: '4.0', allowfail: false}
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- {os: windows-latest, r: '3.6', allowfail: false}
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- {os: windows-latest, r: '3.5', allowfail: false}
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- {os: windows-latest, r: '3.4', allowfail: false}
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- {os: windows-latest, r: '3.3', allowfail: false}
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- {os: windows-latest, r: '3.2', allowfail: false}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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RSPM: ${{ matrix.config.rspm }}
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R_REPOSITORIES: "https://cran.rstudio.com"
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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@v2
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- uses: r-lib/actions/setup-pandoc@v1
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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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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- name: show file list
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run: ls -lh
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shell: bash
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- name: Install dependencies
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if: always()
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run: |
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install.packages("remotes", repos = c("https://cloud.r-project.org", "https://cran.rstudio.com"))
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remotes::install_local("data-raw/AMR_latest.tar.gz", dependencies = TRUE)
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shell: Rscript {0}
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- name: Show session info
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if: always()
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run: |
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options(width = 100)
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utils::sessionInfo()
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as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
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shell: Rscript {0}
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- uses: r-lib/actions/check-r-package@v1
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env:
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_R_CHECK_CRAN_INCOMING_: false
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_R_CHECK_FORCE_SUGGESTS_: false
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_R_CHECK_DEPENDS_ONLY_: true
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_R_CHECK_LENGTH_1_CONDITION_: verbose
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_R_CHECK_LENGTH_1_LOGIC2_: verbose
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R_RUN_TINYTEST: true
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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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- name: Show unit tests output
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if: always()
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run: find check -name 'tinytest.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Upload check results
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if: always()
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uses: actions/upload-artifact@main
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with:
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name: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-artifacts
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path: check
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