(v2.1.1.9078) 12 new formatting formats for antibiogram(), prepare …
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| # ==================================================================== # | |
| # TITLE: # | |
| # AMR: An R Package for Working with Antimicrobial Resistance Data # | |
| # # | |
| # SOURCE CODE: # | |
| # https://github.com/msberends/AMR # | |
| # # | |
| # PLEASE CITE THIS SOFTWARE AS: # | |
| # Berends MS, Luz CF, Friedrich AW, et al. (2022). # | |
| # AMR: An R Package for Working with Antimicrobial Resistance Data. # | |
| # Journal of Statistical Software, 104(3), 1-31. # | |
| # https://doi.org/10.18637/jss.v104.i03 # | |
| # # | |
| # Developed at the University of Groningen and the University Medical # | |
| # Center Groningen in The Netherlands, in collaboration with many # | |
| # colleagues from around the world, see our website. # | |
| # # | |
| # This R package is free software; you can freely use and distribute # | |
| # it for both personal and commercial purposes under the terms of the # | |
| # GNU General Public License version 2.0 (GNU GPL-2), as published by # | |
| # the Free Software Foundation. # | |
| # We created this package for both routine data analysis and academic # | |
| # research and it was publicly released in the hope that it will be # | |
| # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # | |
| # # | |
| # Visit our website for the full manual and a complete tutorial about # | |
| # how to conduct AMR data analysis: https://msberends.github.io/AMR/ # | |
| # ==================================================================== # | |
| on: | |
| push: | |
| branches: '**' | |
| pull_request: | |
| branches: '**' | |
| name: code-coverage | |
| jobs: | |
| code-coverage: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| CODECOV_TOKEN: ${{secrets.CODECOV_TOKEN}} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: release | |
| # use RStudio Package Manager to quickly install packages | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::covr | |
| - name: Test coverage | |
| env: | |
| R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }} | |
| R_RUN_TINYTEST: true | |
| run: | | |
| x <- covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/zz_deprecated.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R")) | |
| print(x) | |
| shell: Rscript {0} |