support R 4.5

.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" = "*"

.github/recipe/variant_r43.yaml → .github/recipe/variant_r45.yaml

@@ -1,2 +1,2 @@
 r_base:
-  - 4.3
+  - 4.5

.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

.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 }}