mirror of https://github.com/msberends/AMR.git
90 lines
3.7 KiB
YAML
90 lines
3.7 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) 2018-2022 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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name: code-coverage
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jobs:
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code-coverage:
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runs-on: macOS-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: release
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- uses: r-lib/actions/setup-pandoc@v2
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# with:
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# pandoc-version: '2.7.3' # The pandoc version to download (if necessary) and use.
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- name: Query dependencies
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# this will change once a week, so it will cache dependency updates
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run: |
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writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/week-R-version")
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shell: Rscript {0}
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- name: Restore cached R packages
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# this step will add the step 'Post Restore cached R packages' on a succesful run
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uses: actions/cache@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ matrix.config.os }}-${{ hashFiles('.github/week-R-version') }}-v4
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- name: Unpack AMR and install R dependencies
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run: |
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tar -xf data-raw/AMR_latest.tar.gz
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Rscript -e "source('data-raw/_install_deps.R')"
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shell: bash
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- name: Show session info
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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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- name: Test coverage
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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R_RUN_TINYTEST: true
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run: |
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install.packages("covr", repos = "https://cran.rstudio.com/")
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library(AMR)
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library(tinytest)
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x <- covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
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print(x)
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shell: Rscript {0}
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