Sakura #136
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name: check overall workflow | |
on: | |
push: | |
branches: [main, master] | |
pull_request: | |
branches: [main, master] | |
workflow_dispatch: | |
branches: | |
- '*' | |
jobs: | |
check-overall-workflow: | |
runs-on: ubuntu-latest | |
container: rocker/geospatial:4.3.2 | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Install system dependencies | |
run: | | |
apt-get update && apt-get install -y --no-install-recommends \ | |
libxt6 libglpk-dev | |
- name: Install R packages | |
run: | | |
install.packages( | |
c("rmarkdown", "openxlsx", "stringr", "remotes", "here", | |
"lme4", "forcats", "plotly", "patchwork", "kableExtra", | |
"gtsummary", "pubh", "janitor", "arm") | |
) | |
shell: Rscript {0} | |
- name: Check that workflow runs without errors | |
run: | | |
source("sudan_health_nutrition.R") | |
shell: Rscript {0} | |
- name: Check that Rmd file runs without errors | |
run: | | |
rmds <- list.files(path = "reports", pattern = "\\.Rmd$", full.names = TRUE) |> | |
(\(x) x[!stringr::str_detect(string = x, pattern = "case_study")])() | |
if (length(rmds) != 0) { | |
lapply( | |
X = rmds, | |
FUN = rmarkdown::render, | |
output_dir = "docs", | |
knit_root_dir = here::here() | |
) | |
} | |
shell: Rscript {0} | |
- name: Upload Rmarkdown reports | |
uses: actions/upload-artifact@v4 | |
with: | |
name: rmd-output | |
path: docs/*.html | |