Test using composite actions

pharmpy · Nov 30, 2023 · 0936e37 · 0936e37
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commit 0936e37
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diff --git a/.github/actions/check-pharmr/action.yml b/.github/actions/check-pharmr/action.yml
@@ -0,0 +1,157 @@
+name: Set up pharmr
+
+inputs:
+  as-release:
+    required: true
+    type: boolean
+
+runs:
+  using: "composite"
+  steps:
+    - uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: "release"
+
+    - uses: r-lib/actions/setup-pandoc@v2
+
+    - name: Query dependencies
+      working-directory: pharmr_repo
+      run: |
+        install.packages('remotes')
+        saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+      shell: Rscript {0}
+
+    - uses: actions/setup-python@v2
+      with:
+          python-version: "3.11"
+
+    - name: Restore R package cache
+      if: runner.os != 'Windows'
+      uses: actions/cache@v2
+      with:
+        path: ${{ env.R_LIBS_USER }}
+        key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+        restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+    - name: Install system dependencies
+      working-directory: pharmr_repo
+      if: runner.os == 'Linux'
+      run: |
+        while read -r cmd
+        do
+          eval sudo $cmd
+        done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+        sudo apt install libcurl4-openssl-dev
+
+    - name: Install png (temporary)
+      working-directory: pharmr_repo
+      if: runner.os == 'Windows'
+      run: |
+        install.packages('png', repos='https://mran.microsoft.com/snapshot/2022-11-27')
+      shell: Rscript {0}
+
+    - name: Install R packages
+      working-directory: pharmr_repo
+      run: |
+        remotes::install_deps(dependencies = TRUE)
+        remotes::install_cran("rcmdcheck")
+        install.packages('reticulate')
+        install.packages('devtools')
+        install.packages('promises')
+        remotes::install_local(force=TRUE)
+      shell: Rscript {0}
+
+    - name: Checkout Pharmpy
+      uses: actions/checkout@v3
+      with:
+        repository: pharmpy/pharmpy
+        path: pharmpy_repo
+        fetch-depth: 0
+
+    - name: Set up Pharmpy release version
+      working-directory: pharmpy_repo
+      if: ${{ inputs.as-release == true }}
+      run: |
+        git checkout -b release_latest "$(git rev-list --tags --max-count=1)"
+
+    - id: get_pharmpy_version
+      working-directory: pharmpy_repo
+      if: ${{ inputs.as-release == true && runner.os == 'Linux'}}
+      run: |
+        echo "pharmpy_version=`git describe --tags`" >> $GITHUB_OUTPUT 
+
+    - name: Install Pharmpy in venv
+      working-directory: pharmpy_repo
+      if: runner.os != 'Windows'
+      run: |
+        python3 -m venv pharmpy_venv
+        source pharmpy_venv/bin/activate
+        pip install .
+
+    - name: Install Pharmpy in venv
+      working-directory: pharmpy_repo
+      if: runner.os == 'Windows'
+      run: |
+        python -m venv pharmpy_venv
+        pharmpy_venv\Scripts\activate
+        pip install .
+
+    - name: Start Pharmpy venv
+      working-directory: pharmr_repo
+      run: |
+        reticulate::py_discover_config()
+        venv_path = file.path('..', 'pharmpy_repo', 'pharmpy_venv')
+        if(.Platform$OS.type == "unix") {
+            venv_path = file.path(venv_path, 'bin')
+        } else {
+            venv_path = file.path(venv_path, 'Scripts')          
+        }
+        reticulate::use_python(venv_path)
+        pharmr::print_pharmpy_version()
+      shell: Rscript {0}
+
+    - name: Update DESCRIPTION and documentation
+      working-directory: pharmr_repo/deploy
+      run: |
+        venv_path = file.path('..', '..', 'pharmpy_repo', 'pharmpy_venv')
+        if(.Platform$OS.type == "unix") {
+            venv_path = file.path(venv_path, 'bin')
+        } else {
+            venv_path = file.path(venv_path, 'Scripts')          
+        }
+        reticulate::use_python(venv_path)
+        
+        pharmpy <- reticulate::import("pharmpy")
+        pharmpy_version <- pharmpy$`__version__`
+        desc::desc_set('Version', pharmpy_version)
+        desc::desc_set('Date', Sys.Date())
+        
+        reticulate::py_run_file('build_functions.py')
+        devtools::document()
+      shell: Rscript {0}
+
+    - name: Check pharmr
+      working-directory: pharmr_repo
+      env:
+        _R_CHECK_CRAN_INCOMING_REMOTE_: false
+      run: |
+        venv_path = file.path('..', 'pharmpy_repo', 'pharmpy_venv')
+        if(.Platform$OS.type == "unix") {
+            venv_path = file.path(venv_path, 'bin')
+        } else {
+            venv_path = file.path(venv_path, 'Scripts')          
+        }
+        reticulate::use_python(venv_path)
+        pharmr::print_pharmpy_version()
+        options(crayon.enabled = TRUE)
+        rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "warning", check_dir = "check")
+      shell: Rscript {0}
+
+    - name: Upload check results
+      if: failure()
+      uses: actions/upload-artifact@main
+      with:
+        name: results-cran
+        path: check
diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
@@ -5,62 +5,71 @@ on:
 name: Deploy pharmr
 
 jobs:
-  check-pharmr:
-    uses: pharmpy/pharmr/.github/workflows/main.yaml@main
-    with:
-      as-release: true
-
   deploy:
     runs-on: ubuntu-20.04
-    needs: check-pharmr
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - name: Download pharmr repo artifact
-        uses: actions/download-artifact@master
+      - name: Checkout pharmr
+        uses: actions/checkout@v3
         with:
-          name: pharmr_repo
           path: pharmr_repo
 
-      - name: Set up git config
+      - name: Switch branch (remove when in main)
         working-directory: pharmr_repo
-        run: |
-          git config --local user.name "github-actions[bot]"
-          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+        run:
+          git switch use-composite-actions
+
+      - uses: ./.github/actions/check-pharmr
+        with:
+          as-release: true
 
-      - name: Add changes to DESCRIPTION and documentation
+      - name: Check git
         working-directory: pharmr_repo
-        run: |
-          git add DESCRIPTION
-          git add NAMESPACE
-          git add R/functions_wrapper.R
-          git add man/
+        run:
           git status
 
-      - name: Check if any files have been staged
-        working-directory: pharmr_repo
-        run: |
-          if [[ "$(git diff --name-only --cached | wc -c)" != "0" ]]; then
-            echo "has_been_updated=true" >> $GITHUB_ENV
-          else
-            echo "has_been_updated=false" >> $GITHUB_ENV
-          fi
 
-      - name: Commit and push changes, tag version
-        if: ${{ env.has_been_updated == 'true' }}
-        working-directory: pharmr_repo
-        run: |
-          echo "Committing changes"
-          git commit -m "Update DESCRIPTION/documentation"
-          echo "Tag version"
-          git tag "${{ needs.check-pharmr.outputs.pharmpy_version }}"
-          echo "Push changes"
-          git push https://$USERNAME:[email protected]/pharmpy/pharmr.git
-          echo "push tags"
-          git push --tags https://$USERNAME:[email protected]/pharmpy/pharmr.git
-        env:
-          REPO_KEY: ${{secrets.ACCESS_TOKEN}}
-          USERNAME: github-actions[bot]
+
+#      - name: Set up git config
+#        working-directory: pharmr_repo
+#        run: |
+#          git config --local user.name "github-actions[bot]"
+#          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+#
+#      - name: Add changes to DESCRIPTION and documentation
+#        working-directory: pharmr_repo
+#        run: |
+#          git add DESCRIPTION
+#          git add NAMESPACE
+#          git add R/functions_wrapper.R
+#          git add man/
+#          git status
+#
+#      - name: Check if any files have been staged
+#        working-directory: pharmr_repo
+#        run: |
+#          if [[ "$(git diff --name-only --cached | wc -c)" != "0" ]]; then
+#            echo "has_been_updated=true" >> $GITHUB_ENV
+#          else
+#            echo "has_been_updated=false" >> $GITHUB_ENV
+#          fi
+#
+#      - name: Commit and push changes, tag version
+#        if: ${{ env.has_been_updated == 'true' }}
+#        working-directory: pharmr_repo
+#        run: |
+#          echo "Committing changes"
+#          git commit -m "Update DESCRIPTION/documentation"
+#          echo "Tag version"
+#          git tag "${{ needs.check-pharmr.outputs.pharmpy_version }}"
+#          echo "Push changes"
+#          git push https://$USERNAME:[email protected]/pharmpy/pharmr.git
+#          echo "push tags"
+#          git push --tags https://$USERNAME:[email protected]/pharmpy/pharmr.git
+#        env:
+#          REPO_KEY: ${{secrets.ACCESS_TOKEN}}
+#          USERNAME: github-actions[bot]