Merge pull request #377 from Olink-Proteomics/optimization_develop_re…

…ad_npx_to_main

Optimization develop read npx to main

.Rbuildignore

@@ -1,2 +1,3 @@
 ^LICENSE\.md$
-/revdep/
+/revdep/
+^\.github$

.github/workflows/CRAN_check.yaml

@@ -30,7 +30,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

.github/workflows/R-CMD-check.yaml

@@ -12,22 +12,22 @@ jobs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
       # Required as the JSON input file needs to be read
-      - uses: actions/checkout@v2      
+      - uses: actions/checkout@v4
       - id: set-matrix
-        uses: JoshuaTheMiller/conditional-build-matrix@main        
+        uses: JoshuaTheMiller/conditional-build-matrix@main
         with:
-          inputFile: '.github/workflows/matrix_config_check.json' 
+          inputFile: '.github/workflows/matrix_config_check.json'
           filter: '[?runOn==`${{ github.event_name }}` || runOn==`always`]'
           # addInclude: true
 
   R-CMD-check:
     needs: matrix_prep
-    strategy:      
-      fail-fast: false    
-      matrix: ${{fromJson(needs.matrix_prep.outputs.matrix)}}  
+    strategy:
+      fail-fast: false
+      matrix: ${{fromJson(needs.matrix_prep.outputs.matrix)}}
 
     runs-on: ${{ matrix.os }}
-    timeout-minutes: 120       
+    timeout-minutes: 120
 
     name: ${{ matrix.os }} (${{ matrix.r }})
 
@@ -37,119 +37,33 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.r }}
-          use-public-rspm: true            
+          use-public-rspm: true
 
       - uses: r-lib/actions/setup-pandoc@v2
-        with:
-          pandoc-version: '2.18'      
-
+
       - name: Set BioC version
         run: |
           install.packages("remotes")
           forenv <- paste("R_BIOC_VERSION=", as.character(remotes::bioc_version()), sep = "")
-          write(forenv, file = Sys.getenv("GITHUB_ENV"), append = TRUE) # Store current value to ENV          
+          write(forenv, file = Sys.getenv("GITHUB_ENV"), append = TRUE) # Store current value to ENV
         shell: Rscript {0}
 
-
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           working-directory: OlinkAnalyze
-          extra-packages: any::rcmdcheck, pillar
-
-      - name: Install Matrix from source
-        run: |
-          install.packages("Matrix", type="source", repos='http://cran.us.r-project.org')
-        shell: Rscript {0}
-
-      - uses: r-lib/actions/check-r-package@v2
-        with:
-          working-directory: OlinkAnalyze     
-
-
-  R-CMD-check-renv:
-    needs: matrix_prep
-    strategy:      
-      fail-fast: false
-      matrix:
-        config:
-          - {os: ubuntu-22.04,   r: '4.1.3'}
+          extra-packages: any::rcmdcheck
 
-
-    runs-on: ${{ matrix.config.os }}
-    timeout-minutes: 120       
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
-    env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      _R_CHECK_FORCE_SUGGESTS_: false
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
-    steps:
-      - uses: actions/checkout@v2
-
-      - name: Install package
+      - name: Install arrow from r-universe
+        if: matrix.os == 'macOS-latest'
         run: |
-          sudo apt update
-          sudo apt-get -y install libglpk-dev texlive-latex-base \
-             texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: ${{ matrix.config.r }}
-          use-public-rspm: true            
-
-      - uses: r-lib/actions/setup-pandoc@v2
-        with:
-          pandoc-version: '2.18'
-
-      - name: Set RENV_PATHS_ROOT
-        shell: bash
-        run: |
-          echo "RENV_PATHS_ROOT=${{ runner.temp }}/renv" >> $GITHUB_ENV
-          
-      - name: Install and activate renv
-        run: |
-          install.packages("remotes")
-          remotes::install_version("renv", "0.16.0")
-          renv::activate(profile = "r413")
+          install.packages('arrow', repos = c('https://apache.r-universe.dev'))
         shell: Rscript {0}
 
-      - name: Get R and OS version
-        id: get-version
-        run: |
-          cat("os-version=", sessionInfo()$running, "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE)
-          cat("r-version=", R.Version()$version.string, "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE)
-        shell: Rscript {0}
-
-      - name: Restore Renv package cache
-        uses: actions/cache@v3
-        with:
-          path: ${{ env.RENV_PATHS_ROOT }}
-          key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{inputs.cache-version }}-${{ hashFiles('renv.lock') }}
-          restore-keys: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{inputs.cache-version }}-
-
-      - name: Install renv dependencies
-        run: renv::restore()
-        shell: Rscript {0}
-
-      - name: Check package
-        run: |                             
-          check_results <- rcmdcheck::rcmdcheck(error_on = "error",
-                                                path = "OlinkAnalyze", 
-                                                check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Upload check results
-        if: failure() 
-        uses: actions/upload-artifact@v3
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: "check"
-
-
+          working-directory: OlinkAnalyze

.github/workflows/R-CMD-check_docker.yaml

@@ -0,0 +1,54 @@
+on:
+  pull_request:
+    branches:
+      - 'main'
+      - 'develop'
+      - 'optimization_develop'
+      - 'optimization_main'
+
+name: R-CMD-check-docker
+
+jobs:
+  R-CMD-check-docker:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        r_version: ["4.1.3", "4.2.3", "4.3.3"]
+    steps:
+      -
+        name: Checkout
+        uses: actions/checkout@v4
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      -
+        name: Cache Docker layers
+        uses: actions/cache@v4
+        with:
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-buildx-
+      -
+        name: Build docker image
+        uses: docker/build-push-action@v5
+        with:
+          push: false
+          tags: oa:latest
+          cache-from: type=local,src=/tmp/.buildx-cache
+          cache-to: type=local,dest=/tmp/.buildx-cache-new,mode=max
+          file: docker/Dockerfile_for_tests
+          load: true
+          build-args: R_VERSION=${{matrix.r_version}}
+      -
+        name: Run rcmdcheck
+        run: |
+          echo "rcmdcheck::rcmdcheck(path = '/OA', check_dir = '/check', error_on = 'warning')" | docker run -i -v "$(pwd)/OlinkAnalyze":/OA -v "$(pwd)/check":/check oa:latest
+      -
+        name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: docker-r${{ matrix.config.r }}-check-results
+          path: check

.github/workflows/R-CMD-check_no-suggests.yaml

@@ -0,0 +1,60 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+#
+# NOTE: This workflow only directly installs "hard" dependencies, i.e. Depends,
+# Imports, and LinkingTo dependencies. Notably, Suggests dependencies are never
+# installed, with the exception of testthat, knitr, and rmarkdown. The cache is
+# never used to avoid accidentally restoring a cache containing a suggested
+# dependency.
+on: 
+  pull_request:
+    branches:
+      - 'main'
+      - 'develop'
+      - 'optimization_develop'
+      - 'optimization_main'
+
+name: R-CMD-check-hard
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest, r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          working-directory: OlinkAnalyze
+          dependencies: '"hard"'
+          cache: false
+          extra-packages: |
+            any::rcmdcheck
+            any::testthat
+            any::knitr
+            any::rmarkdown
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          working-directory: OlinkAnalyze

.github/workflows/lint.yaml

@@ -0,0 +1,44 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on: 
+  pull_request:
+    branches:
+      - 'main'
+      - 'develop'
+      - 'optimization_develop'
+      - 'optimization_main'
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          packages: any::pak
+
+      - name: install OA
+        run: |
+          pak::pkg_install(c("local::OlinkAnalyze", "lintr", "devtools"))
+        shell: Rscript {0}
+
+      - name: Lint
+        run: |
+          options(lintr.github_annotation_project_dir = "OlinkAnalyze")
+          devtools::load_all(path = "OlinkAnalyze")
+          lintr::lint_package(path = "OlinkAnalyze")
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.github/workflows/matrix_config_check.json

@@ -12,16 +12,16 @@
    {
       "os": "ubuntu-20.04",
       "r": "release",
-      "runOn": "always"
+      "runOn": "pull_request"
    },
    {
-      "os": "ubuntu-20.04",
-      "r": "devel",
-      "runOn": "pull_request"
+      "os": "ubuntu-22.04",
+      "r": "release",
+      "runOn": "always"
    },
    {
-      "os": "ubuntu-20.04",
-      "r": "4.2.0",
+      "os": "ubuntu-22.04",
+      "r": "devel",
       "runOn": "pull_request"
    }
 ]

.github/workflows/render-and-document.yaml

@@ -2,8 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches-ignore:    
-      - 'main'  
+    branches-ignore:
+      - 'main'
+      - 'optimization_main'
 
 name: render-and-document
 
@@ -17,7 +18,7 @@ jobs:
 
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with: 
           fetch-depth: 0
           token: ${{ secrets.PAT }}