Merge pull request #140 from StoXProject/release1.4

Release1.4

Author: edvinf

Diff for: .github/workflows/check-full.yaml

@@ -2,9 +2,13 @@ on:
   push:
     branches:
       - master
+      - develop
+      - testing
   pull_request:
     branches:
       - master
+      - develop
+      - testing
 
 name: R-CMD-check
 
@@ -21,27 +25,15 @@ jobs:
         config:
         # for windows and mac all builds are pushed to drat repo on merge to master (except pre-release builds), except 'next'
 
-        # 2023-08-23 fails, not getting Reca. Because it is not built yet for macos and next or 4.3.
-          #- {os: macOS-latest,   r: 'next', pkgext: '.tgz'}
-          #- {os: macOS-latest,   r: '4.3', pkgext: '.tgz'}
-          
-          - {os: macOS-latest,   r: '4.2', pkgext: '.tgz'}
-          - {os: macOS-latest,   r: '4.1',  pkgext: '.tgz'}
-          - {os: macOS-latest,   r: '4.0',     pkgext: '.tgz'}
+          - {os: macOS-latest,   r: 'next', pkgext: '.tgz'} # will be tested without suggests
+          - {os: macOS-latest,   r: '4.3', pkgext: '.tgz'} # will be tested without suggests
 
-          # 2023-08-23 fails, not getting Reca. Because it is not built yet for windows and next or 4.3.
           - {os: windows-latest, r: 'next', pkgext: '.zip'} 
           - {os: windows-latest, r: '4.3', pkgext: '.zip'}
-          
-          - {os: windows-latest, r: '4.2', pkgext: '.zip'}
-          - {os: windows-latest, r: '4.1',  pkgext: '.zip'}
-          - {os: windows-latest, r: '4.0',     pkgext: '.zip',    rspm: "https://cloud.r-project.org"}
 
           - {os: ubuntu-latest,  r: 'next', pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"}
-          - {os: ubuntu-22.04,   r: '4.2',  pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"}
-          # 4.1 is pushed to drat repo on merge to master for ubunutu (except pre-release builds), update script if 4.1 is taken out
-          - {os: ubuntu-20.04,   r: '4.1',  pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"}
-          - {os: ubuntu-20.04,   r: '4.0',     pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"}
+          # 4.3 is pushed to drat repo on merge to master for ubunutu (except pre-release builds), update script if 4.3 is taken out
+          - {os: ubuntu-22.04,   r: '4.3',  pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -50,11 +42,15 @@ jobs:
 
     steps:
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Do autorelease increment, tagging, and environment setup
-        if: github.event_name == 'push' && github.ref == 'refs/heads/master'
+        if: github.event_name == 'push'
         run: |
+          curl "https://raw.githubusercontent.com/StoXProject/unstableRepo/main/scripts/checktag-actions.sh" --output unstableRepo_checktag.sh
+          curl "https://raw.githubusercontent.com/StoXProject/unstableRepo/main/scripts/deploy-actions.sh" --output unstableRepo_deploy.sh
+          chmod +x ./unstableRepo_checktag.sh ./unstableRepo_deploy.sh
+          . unstableRepo_checktag.sh
           curl "https://raw.githubusercontent.com/StoXProject/testingRepo/main/scripts/checktag-actions.sh" --output testingRepo_checktag.sh
           curl "https://raw.githubusercontent.com/StoXProject/testingRepo/main/scripts/deploy-actions.sh" --output testingRepo_deploy.sh
           chmod +x ./testingRepo_checktag.sh ./testingRepo_deploy.sh
@@ -74,23 +70,9 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-          rtools-version: ${{ matrix.config.rtools }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
-
-      - name: Anticipate Bintray shutdown
-        if: runner.os == 'macOS'
-        run: |
-          brew update
-        shell: bash
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Anticipate Bintray shutdown
-        if: runner.os == 'macOS'
-        run: |
-          brew update
-        shell: bash
-
       - name: Query dependencies
         run: |
           install.packages('remotes')
@@ -100,7 +82,7 @@ jobs:
 
       - name: Cache R packages
         if: runner.os != 'Windows'
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
@@ -114,22 +96,26 @@ jobs:
             eval sudo $cmd
           done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
 
-      - name: Install MacOS dependencies
+      - name: Install MacOS system dependencies
         if: runner.os == 'macOS'
         run: |
-          rm -f '/usr/local/bin/gfortran'
-          rm -f '/usr/local/bin/2to3'
-          rm -f '/usr/local/bin/2to3-3.11'
-          rm -f '/usr/local/bin/idle3'
-          rm -f '/usr/local/bin/idle3.11'
-          rm -f '/usr/local/bin/pydoc3'
-          rm -f '/usr/local/bin/pydoc3.11'
-          rm -f '/usr/local/bin/python3'
-          rm -f '/usr/local/bin/python3.11'
-          rm -f '/usr/local/bin/python3-config'
-          rm -f '/usr/local/bin/python3.11-config'
+          # gfortran may not exist in a period after a new R minor release:
+          gfortranFile='/usr/local/bin/gfortran'
+          if [ -f "$gfortranFile" ] ; then
+            rm "$gfortranFile"
+          fi
+          rm '/usr/local/bin/2to3'
+          rm '/usr/local/bin/2to3-3.11'
+          rm '/usr/local/bin/idle3.11'
+          rm '/usr/local/bin/idle3'
+          rm '/usr/local/bin/pydoc3'
+          rm '/usr/local/bin/python3'
+          rm '/usr/local/bin/python3-config'
+          rm '/usr/local/bin/pydoc3.11'
+          rm '/usr/local/bin/python3.11'
+          rm '/usr/local/bin/python3.11-config'
           export HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=false # This prevents Homebrew from re-installing R, which will lead to .Platform$pkgType = "source".
-          brew install gdal
+          brew install gdal udunits
         shell: bash
 
       - name: Prepare for dependencies on Linux
@@ -159,31 +145,75 @@ jobs:
           }
         shell: Rscript {0}
 
+        #
+        # Install Reca (awlays from prod repo)
+        #
+      - name: Install Reca 
+        run: |
+          remotes::install_cran("Reca", repos = c("https://stoxproject.github.io/repo/", "https://cloud.r-project.org/"))
+        shell: Rscript {0}
+
+
 
       - name: Install CRANdependencies
         run: |
-          remotes::install_cran("rcmdcheck")
-          #remotes::install_cran("git2r")
-          remotes::install_cran("drat")
-          remotes::install_cran("sessioninfo")
+          install.packages(c("rcmdcheck", "git2r", "sessioninfo", "knitr", "remotes"))
+          
+          # Using the latest drat that supports big sur (after inputs from us). 
+          # When the next drat appears on CRAN this can be changed to install from CRAN:
+          remotes::install_github(repo = 'eddelbuettel/drat', dependencies = FALSE)
+            
+        shell: Rscript {0}
+        
+        #
+        # Install StoX dependencies, corresponding to release status (unstable, pre-release or release)
+        #
+      - name: Install R package dependencies from the unstableRepo
+        if: (github.event_name == 'push' && github.ref_name == 'develop') || (github.event_name == 'pull_request' && github.base_ref == 'develop')
+        run: |
+          remotes::install_deps(dependencies = TRUE, repos = c("https://stoxproject.github.io/unstableRepo/", "https://cloud.r-project.org/"))
+        shell: Rscript {0}
+
+      - name: Install R package dependencies from the testingRepo
+        if: (github.event_name == 'push' && github.ref_name == 'testing') || (github.event_name == 'pull_request' && github.base_ref == 'testing')
+        run: |
+          remotes::install_deps(dependencies = TRUE, repos = c("https://stoxproject.github.io/testingRepo/", "https://cloud.r-project.org/"))
+        shell: Rscript {0}
+
+      - name: Install R package dependencies from the official repo
+        if: (github.event_name == 'push' && github.ref_name == 'master') || (github.event_name == 'pull_request' && github.base_ref == 'master')
+        run: |
+          remotes::install_deps(dependencies = TRUE, repos = c("https://stoxproject.github.io/repo/", "https://cloud.r-project.org/"))
         shell: Rscript {0}
 
+        
       - name: Session info
         run: |
           options(width = 100)
           pkgs <- installed.packages()[, "Package"]
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
-      - name: Check
+     # turn off testing of suggestions for configurations where Reca is not provided in StoX package repositories
+      - name: Check without suggest-dependencies
+        if: runner.os == 'macOS'
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+          _R_CHECK_FORCE_SUGGESTS_ : false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Check with suggest-dependencies
+        if: runner.os != 'macOS'
         env:
           _R_CHECK_CRAN_INCOMING_: false
+          _R_CHECK_FORCE_SUGGESTS_ : true
         run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
         shell: Rscript {0}
 
-      - name: Show testthat output
+      - name: Show test output
         if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        run: find check -name 'tinytest.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload check results
@@ -193,39 +223,72 @@ jobs:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check
 
-      - name: Build package source archive
-        if: runner.os == 'Linux' && matrix.config.r == '4.1' && github.event_name == 'push' && github.ref == 'refs/heads/master'
+      - name: Build package source archive from branches develop, testing and master
+        if: runner.os == 'Linux' && matrix.config.r == '4.3' && github.event_name == 'push' && (github.ref_name == 'master' || github.ref_name == 'testing' || github.ref_name == 'develop')
         run: |
           pkgbuild::build(".", dest_path = ".", binary = FALSE)
           system(paste0("PKG_FREL=", Sys.getenv("PKG_FILE"), " >> ", Sys.getenv("GITHUB_ENV")))
         shell: Rscript {0}
 
-      - name: Build package binary archive
-        if: (runner.os == 'Windows' || runner.os == 'macOS') && github.event_name == 'push' && github.ref == 'refs/heads/master'
+      - name: Build package binary archive from branches develop, testing and master for Windows and macOS (this builds also on matrix.config.r = release, which can or can not be a duplicate)
+        if: (runner.os == 'Windows' || runner.os == 'macOS') && github.event_name == 'push' && (github.ref_name == 'master' || github.ref_name == 'testing' || github.ref_name == 'develop')
         run: |
           pkgbuild::build(".", dest_path = ".", binary = TRUE)
+          print("PKG_FILE")
+          print(Sys.getenv("PKG_FILE"))
+          print("PKG_FREL")
+          print(Sys.getenv("PKG_FREL"))
           file.copy(Sys.getenv("PKG_FILE"), Sys.getenv("PKG_FREL"))
         shell: Rscript {0}
 
-        # Upload to drat repo only for one version (4.1) on Linux, and only for all the specifically given R versions for macOS and Windows (not next). Next is included to detect errors immediatelly when the new R is patched:
-      - name: Upload to DRAT repo
-        if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.1') ) && github.event_name == 'push' && github.ref == 'refs/heads/master'
+    ## 5a. Upload to the official (DRAT) repo, but only from the master branch. Here we skip the matrix.config.r = release, as a new StoX release should be ready shortly after each R minor release and listed specifically in the matrix.config:
+      - name: Upload to the official (DRAT) repo
+        if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.3') ) && github.event_name == 'push' && github.ref_name == 'master'
         env:
           BUILD_NUMBER: ${{ github.sha  }}
           DRAT_DEPLOY_TOKEN: ${{ secrets.DRAT_DEPLOY_TOKEN }}
         run: . repo_deploy.sh
         shell: bash
 
-      - name: Upload to DRAT testingRepo
-        if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.1') ) && github.event_name == 'push' && github.ref == 'refs/heads/master'
+
+      ## 5b. Upload to the (DRAT) testingRepo, but only from the testing branch. Here we skip the matrix.config.r = release, as a new StoX release should be ready shortly after each R minor release and listed specifically in the matrix.config:
+      - name: Upload to the testing (DRAT) repo
+        if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.3') ) && github.event_name == 'push' && github.ref_name == 'testing'
         env:
           BUILD_NUMBER: ${{ github.sha  }}
           DRAT_DEPLOY_TOKEN: ${{ secrets.DRAT_DEPLOY_TOKEN }}
         run: . testingRepo_deploy.sh
         shell: bash
 
-      - name: Create release and upload files
-        if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.1') ) && github.event_name == 'push' && github.ref == 'refs/heads/master'
+
+      ## 5c. Upload to the (DRAT) unstableRepo, but only from the develop branch. Here we skip the matrix.config.r = release, as a new StoX release should be ready shortly after each R minor release and listed specifically in the matrix.config:
+      - name: Upload to the unstable (DRAT) repo
+        if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.3') ) && github.event_name == 'push' && github.ref_name == 'develop'
+        env:
+          BUILD_NUMBER: ${{ github.sha  }}
+          DRAT_DEPLOY_TOKEN: ${{ secrets.DRAT_DEPLOY_TOKEN }}
+        run: . unstableRepo_deploy.sh
+        shell: bash
+
+
+
+      ###############################
+      #### 6. Release on GitHub: ####
+      ###############################
+      
+      - name: Create release on GitHub and upload files for testing branch
+        if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.3') ) && github.event_name == 'push' && github.ref_name == 'testing'
+        uses: ncipollo/release-action@v1
+        with:
+          allowUpdates: true
+          commit: testing
+          tag: ${{ env.FINAL_TAG }}
+          name: ${{ env.FINAL_TAG }}
+          artifacts: ${{ env.PKG_REPO }}/${{ env.PKG_FREL }}
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Create release on GitHub and upload files for master branch
+        if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.3') ) && github.event_name == 'push' && github.ref_name == 'master'
         uses: ncipollo/release-action@v1
         with:
           allowUpdates: true

Diff for: .github/workflows/test-coverage.yaml

@@ -2,8 +2,7 @@ on:
   push:
     branches:
       - master
-  pull_request:
-    branches:
+      - testing
       - develop
 
 name: test-coverage
@@ -29,14 +28,55 @@ jobs:
           install.packages('remotes')
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
         shell: Rscript {0}
-
+        
       - name: Install MacOS dependencies
         if: runner.os == 'macOS'
         run: |
           rm -f '/usr/local/bin/gfortran'
-          brew install udunits proj
+          rm -f '/usr/local/bin/2to3'
+          rm -f '/usr/local/bin/2to3-3.11'
+          rm -f '/usr/local/bin/idle3'
+          rm -f '/usr/local/bin/idle3.11'
+          rm -f '/usr/local/bin/pydoc3'
+          rm -f '/usr/local/bin/pydoc3.11'
+          rm -f '/usr/local/bin/python3'
+          rm -f '/usr/local/bin/python3.11'
+          rm -f '/usr/local/bin/python3-config'
+          rm -f '/usr/local/bin/python3.11-config'
+          export HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=false # This prevents Homebrew from re-installing R, which will lead to .Platform$pkgType = "source".
+          brew install gdal
         shell: bash
 
+        #
+        # Install Reca (awlays from prod repo)
+        #
+      - name: Install Reca 
+        run: |
+          remotes::install_cran("Reca", repos = c("https://stoxproject.github.io/repo/", "https://cloud.r-project.org/"))
+        shell: Rscript {0}
+
+
+        #
+        # Install StoX dependencies, corresponding to release status (unstable, pre-release or release)
+        #
+      - name: Install R package dependencies from the unstableRepo
+        if: (github.event_name == 'push' && github.ref_name == 'develop') || (github.event_name == 'pull_request' && github.base_ref == 'develop')
+        run: |
+          remotes::install_deps(dependencies = TRUE, repos = c("https://stoxproject.github.io/unstableRepo/", "https://cloud.r-project.org/"))
+        shell: Rscript {0}
+
+      - name: Install R package dependencies from the testingRepo
+        if: (github.event_name == 'push' && github.ref_name == 'testing') || (github.event_name == 'pull_request' && github.base_ref == 'testing')
+        run: |
+          remotes::install_deps(dependencies = TRUE, repos = c("https://stoxproject.github.io/testingRepo/", "https://cloud.r-project.org/"))
+        shell: Rscript {0}
+
+      - name: Install R package dependencies from the official repo
+        if: (github.event_name == 'push' && github.ref_name == 'master') || (github.event_name == 'pull_request' && github.base_ref == 'master')
+        run: |
+          remotes::install_deps(dependencies = TRUE, repos = c("https://stoxproject.github.io/repo/", "https://cloud.r-project.org/"))
+        shell: Rscript {0}
+
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)