improve data cleaning code for BirdLife data #254
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| # For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. | |
| # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions | |
| on: | |
| schedule: | |
| - cron: 0 0 * * 1 # schedule to run at midnight on Monday each week | |
| push: | |
| branches: | |
| - main | |
| - master | |
| pull_request: | |
| branches: | |
| - main | |
| - master | |
| name: Ubuntu | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: ubuntu-20.04, r: 'release'} | |
| - {os: ubuntu-20.04, r: 'devel'} | |
| - {os: ubuntu-20.04, r: 'devel', pkgs: 'depends only'} | |
| env: | |
| _R_REMOTES_NO_ERRORS_FROM_WARNINGS_: true | |
| _R_CHECK_FORCE_SUGGESTS_: false | |
| _R_CHECK_TIMINGS_: 10 | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| GGMAP_KEY: ${{ secrets.GGMAP_STADIAMAPS_API_KEY }} | |
| CI: true | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| use-public-rspm: true | |
| - name: Install system dependencies | |
| run: | | |
| sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable | |
| sudo apt update | |
| sudo apt-get install \ | |
| libgdal-dev libgeos-dev libproj-dev gdal-bin grass \ | |
| libgmp3-dev libmpfr-dev libudunits2-dev \ | |
| libharfbuzz-dev libfribidi-dev | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache-version: 4 | |
| extra-packages: | | |
| any::covr | |
| any::rcmdcheck | |
| any::remotes | |
| cran/XML | |
| cran/dotCall64 | |
| prepr=?ignore | |
| link2GI=?ignore | |
| rgrass=?ignore | |
| smoothr=?ignore | |
| OpenMPController=?ignore | |
| needs: | | |
| check | |
| coverage | |
| - name: Install spatial R packages | |
| run: | | |
| options(repos = "https://cloud.r-project.org/") | |
| install.packages("sf") | |
| install.packages("terra") | |
| install.packages("lwgeom") | |
| install.packages("link2GI") | |
| install.packages("rgrass") | |
| install.packages("smoothr") | |
| remotes::install_github("prioritizr/prepr") | |
| shell: Rscript {0} | |
| - name: Session information | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| - name: Set R environmental variables | |
| run: | | |
| echo GGMAP_STADIAMAPS_API_KEY="$GGMAP_KEY" >> ~/.Renviron | |
| shell: bash | |
| - name: Environmental variables | |
| if: matrix.config.pkgs == 'depends only' | |
| run: | | |
| echo "_R_CHECK_DEPENDS_ONLY_=true" >> $GITHUB_ENV | |
| - uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| args: 'c("--no-manual", "--as-cran", "--no-build-vignettes")' | |
| upload-snapshots: true | |
| - name: Show testthat output | |
| if: always() | |
| run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Test coverage | |
| if: runner.os == 'Linux' && matrix.config.r == 'release' | |
| run: | | |
| cov <- covr::package_coverage( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") | |
| ) | |
| covr::to_cobertura(cov) | |
| shell: Rscript {0} | |
| - uses: codecov/codecov-action@v4 | |
| if: runner.os == 'Linux' && matrix.config.r == 'release' | |
| with: | |
| fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} | |
| file: ./cobertura.xml | |
| plugin: noop | |
| disable_search: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |