Merge pull request #110 from OxfordIHTM/rock-lee #133
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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") | |
| ) | |
| 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 | |