GA: Split out package-check job from coverage jobs

.github/workflows/check-python.yml

@@ -88,25 +88,3 @@ jobs:
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-
-    - name: Generate coverage report
-      if: matrix.config.python == '3.10'
-      run: |
-        pip install pytest-cov
-        cd python
-        pytest --cov=port4me ## output summarize in GitHub logs
-        pytest --cov=port4me --cov-report=xml:coverage.xml
-        ## AD HOC: Make reported paths relative to the root of repository
-        sed -i  's/filename="/filename="python\/port4me\//g' coverage.xml
-
-        
-    - name: Upload Coverage to Codecov
-      if: matrix.config.python == '3.10'
-      uses: codecov/codecov-action@v3
-      with:
-        env_vars: OS,PYTHON
-        files: python/coverage.xml
-        fail_ci_if_error: true
-        flags: python
-        name: codecov-umbrella-python
-        verbose: true      

.github/workflows/check-r.yml

@@ -64,8 +64,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           working-directory: r
-          extra-packages: any::rcmdcheck any::covr any::jsonlite
-          needs: check coverage
+          extra-packages: any::rcmdcheck any::jsonlite
 
       - name: Install port4me
         run: |
@@ -123,13 +122,3 @@ jobs:
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check
-
-      - name: Test coverage
-        if: matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'release'
-        run: |
-          setwd("r")
-          ## relative_path = ".." => reported files r/R/*.R, r/src/*.{c,h}
-          coverage <- covr::package_coverage(relative_path = "..", quiet = FALSE)
-          print(coverage)
-          covr::codecov(coverage = coverage, flags = "r", quiet = FALSE)  ## Upload to codecov
-        shell: Rscript {0}

.github/workflows/coverage-python.yml

@@ -0,0 +1,64 @@
+on:
+  push:
+    paths:
+      - 'python/**/*'
+      - .github/workflows/check-python.yml
+  pull_request:
+    paths:
+      - 'python/**/*'
+      - .github/workflows/check-python.yml
+
+name: "Python checks"
+
+permissions:
+  contents: read
+
+jobs:
+  check:
+    if: "! contains(github.event.head_commit.message, '[ci skip]')"
+
+    timeout-minutes: 5
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: 3.10
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+
+    - name: Install port4me
+      run: |
+        cd python/
+        pip install .
+        
+    - name: Session information
+      run: |
+        python -c "import os; print('EUID='+str(os.geteuid()))"
+        python --version
+        python -m port4me --version
+
+    - name: Generate coverage report
+      run: |
+        pip install pytest-cov
+        cd python
+        pytest --cov=port4me ## output summarize in GitHub logs
+        pytest --cov=port4me --cov-report=xml:coverage.xml
+        ## AD HOC: Make reported paths relative to the root of repository
+        sed -i  's/filename="/filename="python\/port4me\//g' coverage.xml
+        
+    - name: Upload Coverage to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        env_vars: OS,PYTHON
+        files: python/coverage.xml
+        fail_ci_if_error: true
+        flags: python
+        name: codecov-umbrella-python
+        verbose: true      

.github/workflows/coverage-r.yml

@@ -0,0 +1,71 @@
+on:
+  push:
+    paths:
+      - 'r/**/*'
+      - .github/workflows/check-r.yml
+  pull_request:
+    paths:
+      - 'r/**/*'
+      - .github/workflows/check-r.yml
+
+name: "R checks"
+
+jobs:
+  check:
+    if: "! contains(github.event.head_commit.message, '[ci skip]')"    
+
+    timeout-minutes: 10
+
+    runs-on: ubuntu-latest
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      ## R CMD check
+      _R_CHECK_CRAN_INCOMING_: false
+      _R_CHECK_MATRIX_DATA_: true
+      _R_CHECK_SUGGESTS_ONLY_: true
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-tinytex@v2
+
+      - name: Install system dependencies (Linux)
+        if: runner.os == 'Linux'
+        run: sudo apt-get install -y tidy
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          working-directory: r
+          extra-packages: any::rcmdcheck any::covr any::jsonlite
+          needs: check coverage
+
+      - name: Install port4me
+        run: |
+          cd r/
+          Rscript -e "install.packages('.', repos = NULL, type = 'source')"
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          capabilities()
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: |
+          setwd("r")
+          ## relative_path = ".." => reported files r/R/*.R, r/src/*.{c,h}
+          coverage <- covr::package_coverage(relative_path = "..", quiet = FALSE)
+          print(coverage)
+          covr::codecov(coverage = coverage, flags = "r", quiet = FALSE)  ## Upload to codecov
+        shell: Rscript {0}