test PR

pixi.toml → .github/environment/pixi.toml

@@ -1,4 +1,4 @@
-[workspace]
+[project]
 name = "r-pecotmr"
 channels = ["dnachun", "conda-forge", "bioconda"]
 platforms = ["linux-64", "osx-arm64"]
@@ -16,75 +16,28 @@ bioccheck = "cd $GITHUB_WORKSPACE; R -e 'BiocCheck::BiocCheck()'"
 use_major_version = "cd $GITHUB_WORKSPACE; R -e 'usethis::use_version(which = \"major\", push = FALSE)'"
 use_minor_version = "cd $GITHUB_WORKSPACE; R -e 'usethis::use_version(which = \"minor\", push = FALSE)'"
 use_patch_version = "cd $GITHUB_WORKSPACE; R -e 'usethis::use_version(which = \"patch\", push = FALSE)'"
-pkgdown_build = "cd $GITHUB_WORKSPACE; R -e 'devtools::install(upgrade = \"never\"); pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)'"
-
-[feature.r43]
-dependencies = {"r-base" = "4.3.*"}
+pkgdown_build = "cd $GITHUB_WORKSPACE; R -e 'pkgdown::build_site_github_pages(new_process = FALSE, install = TRUE)'"
 
 [feature.r44]
 dependencies = {"r-base" = "4.4.*"}
 
+[feature.r45]
+dependencies = {"r-base" = "4.5.*"}
+
 [environments]
-r43 = {features = ["r43"]}
 r44 = {features = ["r44"]}
+r45 = {features = ["r45"]}
 
 [target.linux-64.dependencies]
 "gcc" = "*"
 
 [dependencies]
-# Bioconductor dependencies
-"bioconductor-bioccheck" = "*"
-"bioconductor-iranges" = "*"
-"bioconductor-qvalue" = "*"
-"bioconductor-s4vectors" = "*"
-"bioconductor-snpstats" = "*"
-
-# Core R dependencies (from Imports)
-"r-bigsnpr" = "*"
-"r-bigstatsr" = "*"
-"r-coda" = "*"
-"r-coloc" = "*"
-"r-colocboost" = "*"
-"r-dofuture" = "*"
-"r-dplyr" = "*"
-"r-flashier" = "*"
-"r-fsusier" = "*"
-"r-furrr" = "*"
-"r-future" = "*"
-"r-gbj" = "*"
-"r-glmnet" = "*"
-"r-harmonicmeanp" = "*"
-"r-magrittr" = "*"
-"r-mashr" = "*"
-"r-matrixstats" = "*"
-"r-mr.mash.alpha" = "*"
-"r-mvsusier" = "*"
-"r-pgenlibr" = "*"
-"r-purrr" = "*"
-"r-qgg" = "*"
-"r-quadprog" = "*"
-"r-quantreg" = "*"
-"r-rcpp" = "*"
-"r-rcpparmadillo" = "*"
-"r-readr" = "*"
-"r-rfast" = "*"
-"r-rlang" = "*"
-"r-stringr" = "*"
-"r-susier" = "*"
-"r-tibble" = "*"
-"r-tidyr" = "*"
-"r-vctrs" = "*"
-"r-vroom" = "*"
-"r-xicor" = "*"
-
-# Suggested dependencies (testing and documentation)
-"r-knitr" = "*"
-"r-rmarkdown" = "*"
-"r-testthat" = "*"
-
-# Development tools
+# "bioconductor-bioccheck" = "*"
 "r-covr" = "*"
 "r-devtools" = "*"
+"r-knitr" = "*"
+"r-markdown" = "*"
 "r-pkgdown" = "*"
 "r-rcmdcheck" = "*"
+"r-testthat" = "*"
 "r-tidyverse" = "*"

.github/recipe/recipe.yaml

@@ -42,11 +42,10 @@ requirements:
     - r-gbj
     - r-glmnet
     - r-harmonicmeanp
-    - r-knitr
     - r-magrittr
     - r-mashr
     - r-matrixstats
-    - r-mr.mash.alpha
+    - r-mr.mashr
     - r-mvsusier
     - r-pgenlibr
     - r-purrr
@@ -58,10 +57,8 @@ requirements:
     - r-readr
     - r-rfast
     - r-rlang
-    - r-rmarkdown
     - r-stringr
     - r-susier
-    - r-testthat
     - r-tibble
     - r-tidyr
     - r-vctrs
@@ -87,11 +84,10 @@ requirements:
     - r-gbj
     - r-glmnet
     - r-harmonicmeanp
-    - r-knitr
     - r-magrittr
     - r-mashr
     - r-matrixstats
-    - r-mr.mash.alpha
+    - r-mr.mashr
     - r-mvsusier
     - r-pgenlibr
     - r-purrr
@@ -103,10 +99,8 @@ requirements:
     - r-readr
     - r-rfast
     - r-rlang
-    - r-rmarkdown
     - r-stringr
     - r-susier
-    - r-testthat
     - r-tibble
     - r-tidyr
     - r-vctrs

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

@@ -11,4 +11,4 @@ c_stdlib:
   - if: osx
     then: macosx_deployment_target
 r_base:
-  - 4.3
+  - 4.5

.github/workflows/ci.yml

@@ -1,7 +1,6 @@
 name: Continuous Integration
 
 on:
-  workflow_dispatch:
   pull_request:
     paths-ignore:
       - .gitignore
@@ -13,30 +12,32 @@ concurrency:
 
 jobs:
   ci:
-    name: ${{ matrix.platform }} / ${{ matrix.environment }}
+    name: CI (${{ matrix.platform }} / ${{ matrix.environment }})
     runs-on: ${{ matrix.runner }}
-    timeout-minutes: 30
     env:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
     strategy:
       fail-fast: false
       matrix:
-        runner: [ubuntu-latest, macos-14]
-        environment: ["r43", "r44"]
+        runner: [ubuntu-latest, macos-latest]
+        environment: ["r44", "r45"]
         include:
           - runner: ubuntu-latest
             platform: linux-64
-          - runner: macos-14
+          - runner: macos-latest
             platform: osx-arm64
-
+    
     steps:
-      - name: Checkout
+      - name: Checkout pull request branch
         uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
 
-      - name: Copy pixi manifest
+      - name: Create TOML from recipe
         run: |
+          .github/workflows/create_toml_from_yaml.sh ${GITHUB_WORKSPACE}
           mkdir /tmp/pixi
-          cp ${GITHUB_WORKSPACE}/pixi.toml /tmp/pixi
+          mv ${GITHUB_WORKSPACE}/pixi.toml /tmp/pixi
 
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0.9.4
@@ -46,10 +47,15 @@ jobs:
       - name: Run unit tests
         run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml devtools_test
 
-      - name: R CMD check
-        if: matrix.runner == 'ubuntu-latest' && matrix.environment == 'r44'
-        run: 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
+
+      #- name: Run R CMD CHECK
+        #run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml rcmdcheck
+
+      #- name: Run BiocCheckGitClone
+        #run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml bioccheck_git_clone
+
+      #- name: Run BiocCheck
+        #run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml bioccheck