diff --git a/.github/environment/pixi.toml b/.github/environment/pixi.toml index 691796b..90f5821 100644 --- a/.github/environment/pixi.toml +++ b/.github/environment/pixi.toml @@ -10,7 +10,8 @@ libc = { family="glibc", version="2.17" } devtools_document = "R -e 'devtools::document()'" devtools_test = "R -e 'devtools::test()'" codecov = "R -e 'covr::codecov(quiet = FALSE)'" -rcmdcheck = "R -e 'rcmdcheck::rcmdcheck()'" +build = "R -e 'devtools::build()'" +rcmdcheck = "R -e 'pkg <- list.files(\"..\", pattern = \".tar.gz\", full.names = TRUE); rcmdcheck::rcmdcheck(path = pkg[1], args = c(\"--as-cran\"))'" use_major_version = "R -e 'usethis::Use_version(which = \"major\", push = FALSE)'" use_minor_version = "R -e 'usethis::use_version(which = \"minor\", push = FALSE)'" use_patch_version = "R -e 'usethis::use_version(which = \"patch\", push = FALSE)'" @@ -26,7 +27,9 @@ r43 = {features = ["r43"]} r44 = {features = ["r44"]} [dependencies] +"r-ashr" = "*" +"r-covr" = "*" "r-devtools" = "*" +"r-mass" = "*" "r-rcmdcheck" = "*" -"r-covr" = "*" "r-tidyverse" = "*" diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml deleted file mode 100644 index 3d53917..0000000 --- a/.github/workflows/R-CMD-check.yaml +++ /dev/null @@ -1,50 +0,0 @@ - -on: - push: - branches: [main, master] - pull_request: - branches: [main, master] - -name: R-CMD-check - -jobs: - R-CMD-check: - runs-on: ${{ matrix.config.os }} - - name: ${{ matrix.config.os }} (${{ matrix.config.r }}) - - strategy: - fail-fast: false - matrix: - config: - - {os: windows-latest, r: "release"} - - {os: macOS-latest, r: "release"} - - {os: ubuntu-latest, r: "release"} - - env: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - - steps: - - uses: actions/checkout@v2 - - - uses: r-lib/actions/setup-r@v2 - with: - r-version: ${{ matrix.config.r }} - - - uses: r-lib/actions/setup-pandoc@v2 - - - name: Install dependencies - run: | - install.packages(c("remotes", "rcmdcheck", "covr", "testthat")) - remotes::install_deps(dependencies = TRUE) - shell: Rscript {0} - - - name: Check - run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") - shell: Rscript {0} - - - name: Test coverage - run: covr::codecov() - shell: Rscript {0} - diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5637fc9..45ad255 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -33,11 +33,16 @@ jobs: - name: Run unit tests run: pixi run --environment ${{ matrix.environment }} devtools_test - # - name: Check unit test code coverage - # run: pixi run --environment ${{ matrix.environment }} codecov + - name: Run R CMD CHECK + run: | + pixi install --environment ${{ matrix.environment }} + ln -sf $(pwd)/.pixi/envs/default/lib/libhwasan.so.0 $(pwd)/.pixi/envs/default/lib/libhwasan.so + ln -sf $(pwd)/.pixi/envs/${{ matrix.environment }}/lib/libhwasan.so.0 $(pwd)/.pixi/envs/${{ matrix.environment }}/lib/libhwasan.so + pixi run --environment ${{ matrix.environment }} build + pixi run --environment ${{ matrix.environment }} rcmdcheck - #- name: Run R CMD CHECK - #run: pixi run rcmdcheck + - name: Check unit test code coverage + run: pixi run --environment ${{ matrix.environment }} codecov ci_osx-64: name: osx-64 CI @@ -62,8 +67,10 @@ jobs: - name: Run unit tests run: pixi run --environment ${{ matrix.environment }} devtools_test - #- name: Run R CMD CHECK - #run: pixi run rcmdcheck + - name: Run R CMD CHECK + run: | + pixi run --environment ${{ matrix.environment }} build + pixi run --environment ${{ matrix.environment }} rcmdcheck ci_osx-arm64: name: osx-arm64 CI @@ -88,5 +95,7 @@ jobs: - name: Run unit tests run: pixi run --environment ${{ matrix.environment }} devtools_test - #- name: Run R CMD CHECK - #run: pixi run rcmdcheck + - name: Run R CMD CHECK + run: | + pixi run --environment ${{ matrix.environment }} build + pixi run --environment ${{ matrix.environment }} rcmdcheck diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml deleted file mode 100644 index 61d3681..0000000 --- a/.github/workflows/test-coverage.yaml +++ /dev/null @@ -1,28 +0,0 @@ - -on: - push: - branches: [main, master] - pull_request: - branches: [main, master] - -name: test-coverage - -jobs: - test-coverage: - runs-on: ubuntu-latest - - steps: - - uses: actions/checkout@v2 - - - uses: r-lib/actions/setup-r@v2 - - - name: Install dependencies - run: | - install.packages(c("remotes", "covr")) - remotes::install_deps(dependencies = TRUE) - shell: Rscript {0} - - - name: Test coverage - run: covr::codecov() - shell: Rscript {0} - diff --git a/DESCRIPTION b/DESCRIPTION index 0586bef..b0f74b5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -28,8 +28,8 @@ Suggests: testthat (>= 3.0.0), knitr, rmarkdown, - susieR, - ashr + ashr, + MASS VignetteBuilder: knitr Roxygen: list(markdown = TRUE) Config/testthat/edition: 3