diff --git a/.github/environment/pixi.toml b/.github/environment/pixi.toml index 49dd3f0..e0fa583 100644 --- a/.github/environment/pixi.toml +++ b/.github/environment/pixi.toml @@ -1,7 +1,7 @@ [project] name = "r-colocboost" channels = ["dnachun", "conda-forge", "bioconda"] -platforms = ["linux-64", "osx-64", "osx-arm64"] +platforms = ["linux-64", "osx-arm64"] [system-requirements] libc = { family="glibc", version="2.17" } @@ -17,15 +17,15 @@ use_minor_version = "cd $GITHUB_WORKSPACE; R -e 'usethis::use_version(which = \" use_patch_version = "cd $GITHUB_WORKSPACE; R -e 'usethis::use_version(which = \"patch\", push = FALSE)'" pkgdown_build = "cd $GITHUB_WORKSPACE; R -e 'pkgdown::build_site_github_pages(new_process = FALSE, install = TRUE)'" -[feature.r43] -dependencies = {"r-base" = "4.3.*"} - [feature.r44] dependencies = {"r-base" = "4.4.*"} +[feature.r45] +dependencies = {"r-base" = "4.5.*"} + [environments] -r43 = {features = ["r43"]} r44 = {features = ["r44"]} +r45 = {features = ["r45"]} [dependencies] "r-ashr" = "*" diff --git a/.github/recipe/variant_r43.yaml b/.github/recipe/variant_r45.yaml similarity index 50% rename from .github/recipe/variant_r43.yaml rename to .github/recipe/variant_r45.yaml index 21bfbbf..4dc7e20 100644 --- a/.github/recipe/variant_r43.yaml +++ b/.github/recipe/variant_r45.yaml @@ -1,2 +1,2 @@ r_base: - - 4.3 + - 4.5 diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c39d62a..5067579 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -7,17 +7,27 @@ on: - .gitignore - README.md +concurrency: + group: ci-${{ github.ref }} + cancel-in-progress: true + jobs: - ci_linux-64: - name: linux-64 CI - runs-on: ubuntu-latest + ci: + name: CI (${{ matrix.platform }} / ${{ matrix.environment }}) + runs-on: ${{ matrix.runner }} env: CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} strategy: fail-fast: false matrix: - environment: ["r43", "r44"] - + runner: [ubuntu-latest, macos-latest] + environment: ["r44", "r45"] + include: + - runner: ubuntu-latest + platform: linux-64 + - runner: macos-latest + platform: osx-arm64 + steps: - name: Checkout pull request branch uses: actions/checkout@v6 @@ -44,37 +54,5 @@ jobs: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml rcmdcheck - name: Check unit test code coverage + if: matrix.runner == 'ubuntu-latest' && matrix.environment == 'r44' run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml codecov - - ci_osx-arm64: - name: osx-arm64 CI - runs-on: macos-14 - strategy: - fail-fast: false - matrix: - environment: ["r43", "r44"] - - steps: - - name: Checkout pull request branch - uses: actions/checkout@v6 - with: - fetch-depth: 0 - - - name: Create TOML from recipe - run: | - .github/workflows/create_toml_from_yaml.sh ${GITHUB_WORKSPACE} - mkdir /tmp/pixi - mv ${GITHUB_WORKSPACE}/pixi.toml /tmp/pixi - - - name: Setup pixi - uses: prefix-dev/setup-pixi@v0.9.4 - with: - manifest-path: /tmp/pixi/pixi.toml - - - name: Run unit tests - run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml devtools_test - - - name: Run R CMD CHECK - run: | - pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml build - pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml rcmdcheck diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml index c52433a..5fcce1e 100644 --- a/.github/workflows/conda_build.yml +++ b/.github/workflows/conda_build.yml @@ -19,7 +19,7 @@ jobs: strategy: fail-fast: false matrix: - variant: ["r43", "r44"] + variant: ["r44", "r45"] env: ANACONDA_API_KEY: ${{ secrets.ANACONDA_API_TOKEN }}