AMR/.github/workflows/codecovr.yaml

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
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# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# 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 #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
# 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. #
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# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
on:
push:
branches:
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- premaster
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- master
pull_request:
branches:
- master
name: code-coverage
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jobs:
code-coverage:
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runs-on: macOS-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@v1
with:
r-version: release
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- uses: r-lib/actions/setup-pandoc@master
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- name: Restore cached R packages
# this step will add the step 'Post Restore cached R packages' on a succesful run
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uses: actions/cache@v1
with:
path: ${{ env.R_LIBS_USER }}
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key: macOS-latest-r-release-v4
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- name: Unpack AMR and install R dependencies
run: |
tar -xf data-raw/AMR_latest.tar.gz
Rscript -e "source('data-raw/_install_deps.R')"
shell: bash
- name: Show session info
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run: |
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options(width = 100)
utils::sessionInfo()
as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
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shell: Rscript {0}
- name: Test coverage
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env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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run: |
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library(AMR)
library(tinytest)
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library(covr)
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source_files <- list.files("R", pattern = ".R$", full.names = TRUE)
test_files <- list.files("inst/tinytest", full.names = TRUE)
cov <- file_coverage(source_files = source_files, test_files = test_files, parent_env = asNamespace("AMR"), 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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attr(cov, which = "package") <- list(path = ".") # until https://github.com/r-lib/covr/issues/478 is solved
codecov(coverage = cov, quiet = FALSE)
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shell: Rscript {0}