Merge branch 'release/0.7.0'

HenrikBengtsson · Jan 15, 2024 · 4f6ce09 · 4f6ce09
2 parents 2fdffa3 + c573760
commit 4f6ce09
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diff --git a/.github/workflows/check-bash.yml b/.github/workflows/check-bash.yml
@@ -1,4 +1,12 @@
-on: [push, pull_request]
+on:
+  push:
+    paths:
+      - 'bash/**/*'
+      - .github/workflows/check-bash.yml
+  pull_request:
+    paths:
+      - 'bash/**/*'
+      - .github/workflows/check-bash.yml
 
 name: "Bash checks"
 
@@ -9,41 +17,51 @@ jobs:
   check:
     if: "! contains(github.event.head_commit.message, '[ci skip]')"
 
-    timeout-minutes: 10
+    timeout-minutes: 5
 
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+#          - {os: macOS-latest  }
+          - {os: ubuntu-latest }
+          - {os: ubuntu-20.04 }
 
     steps:
     - name: Checkout git repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
-    - name: Install dependencies
+    - name: ShellCheck
+      if: runner.os == 'Linux'
       run: |
-        curl -L -O https://github.com/bats-core/bats-core/archive/refs/tags/v1.7.0.tar.gz && tar xf v1.7.0.tar.gz
-        curl -L -O https://github.com/bats-core/bats-support/archive/refs/tags/v0.3.0.tar.gz && tar xf v0.3.0.tar.gz
-        curl -L -O https://github.com/bats-core/bats-assert/archive/refs/tags/v2.0.0.tar.gz && tar xf v2.0.0.tar.gz
         curl -L -O https://github.com/koalaman/shellcheck/releases/download/v0.9.0/shellcheck-v0.9.0.linux.x86_64.tar.xz
         tar Jxf shellcheck-v0.9.0.linux.x86_64.tar.xz
         mv shellcheck-v0.9.0/shellcheck .
-
-    - name: Session information
-      run: |
-        PATH="$PWD:$PATH" shellcheck --version
-        BATS_SUPPORT_HOME=bats-support-0.3.0 BATS_ASSERT_HOME=bats-assert-2.0.0 PATH="bats-core-1.7.0/bin:$PATH" bats --version
-
-    - name: ShellCheck
-      run: |
         export PATH="$PWD:$PATH"
         cd bash/
         shellcheck --version
         shellcheck incl/*.bash
         shellcheck -x port4me
-
-    - name: Check with Bats
+        (cd tests; shellcheck -x *.bats)
+        
+    - name: Check
       run: |
+        echo "SHELL=${SHELL}"
+        bash --version
+        command -v bash
+        command -v kill || true
+        command -v timeout || true
+        curl -L -O https://github.com/bats-core/bats-core/archive/refs/tags/v1.10.0.tar.gz && tar xf v1.10.0.tar.gz
+        curl -L -O https://github.com/bats-core/bats-support/archive/refs/tags/v0.3.0.tar.gz && tar xf v0.3.0.tar.gz
+        curl -L -O https://github.com/bats-core/bats-assert/archive/refs/tags/v2.1.0.tar.gz && tar xf v2.1.0.tar.gz
         export BATS_SUPPORT_HOME=$PWD/bats-support-0.3.0
-        export BATS_ASSERT_HOME=$PWD/bats-assert-2.0.0
-        export PATH=$PWD/bats-core-1.7.0/bin:$PATH
+        export BATS_ASSERT_HOME=$PWD/bats-assert-2.1.0
+        export PATH=$PWD/bats-core-1.10.0/bin:$PATH
+        export PATH=$PWD/bash:$PATH
         bats --version
-        cd bash/tests/
-        bats *.bats
+        cd bash/
+        make check-cli
diff --git a/.github/workflows/check-python.yml b/.github/workflows/check-python.yml
@@ -1,4 +1,12 @@
-on: [push, pull_request]
+on:
+  push:
+    paths:
+      - 'python/**/*'
+      - .github/workflows/check-python.yml
+  pull_request:
+    paths:
+      - 'python/**/*'
+      - .github/workflows/check-python.yml
 
 name: "Python checks"
 
@@ -9,29 +17,36 @@ jobs:
   check:
     if: "! contains(github.event.head_commit.message, '[ci skip]')"
 
-    timeout-minutes: 10
+    timeout-minutes: 5
 
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (Python ${{ matrix.config.python }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest,  python: '3.7'  }
+          - {os: ubuntu-latest,  python: '3.8'  }
+          - {os: ubuntu-latest,  python: '3.9'  }
+          - {os: ubuntu-latest,  python: '3.10' }
+          - {os: ubuntu-latest,  python: '3.11' }
+          - {os: ubuntu-latest,  python: '3.12' }
+          - {os: macOS-latest,   python: '3.11' }
+          - {os: windows-latest, python: '3.11' }
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
-    - name: Set up Python 3.10
+    - name: Set up Python
       uses: actions/setup-python@v3
       with:
-        python-version: "3.10"
+        python-version: ${{ matrix.config.python }}
 
     - name: Install dependencies
       run: |
-        curl -L -O https://github.com/bats-core/bats-core/archive/refs/tags/v1.7.0.tar.gz && tar xf v1.7.0.tar.gz
-        curl -L -O https://github.com/bats-core/bats-support/archive/refs/tags/v0.3.0.tar.gz && tar xf v0.3.0.tar.gz
-        curl -L -O https://github.com/bats-core/bats-assert/archive/refs/tags/v2.0.0.tar.gz && tar xf v2.0.0.tar.gz
-        curl -L -O https://github.com/koalaman/shellcheck/releases/download/v0.9.0/shellcheck-v0.9.0.linux.x86_64.tar.xz
         python -m pip install --upgrade pip
-        pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        tar Jxf shellcheck-v0.9.0.linux.x86_64.tar.xz
-        mv shellcheck-v0.9.0/shellcheck .
 
     - name: Install port4me
       run: |
@@ -40,28 +55,35 @@ jobs:
         
     - name: Session information
       run: |
-        PATH="$PWD:$PATH" shellcheck --version
+        python -c "import os; print('EUID='+str(os.geteuid()))"
         python --version
         python -m port4me --version
 
+    - name: Test with pytest
+      run: |
+        pip install pytest
+        pytest
+
+    - name: Check CLI
+      if: runner.os != 'Windows'
+      run: |
+        curl -L -O https://github.com/bats-core/bats-core/archive/refs/tags/v1.10.0.tar.gz && tar xf v1.10.0.tar.gz
+        curl -L -O https://github.com/bats-core/bats-support/archive/refs/tags/v0.3.0.tar.gz && tar xf v0.3.0.tar.gz
+        curl -L -O https://github.com/bats-core/bats-assert/archive/refs/tags/v2.1.0.tar.gz && tar xf v2.1.0.tar.gz
+        export BATS_SUPPORT_HOME=$PWD/bats-support-0.3.0
+        export BATS_ASSERT_HOME=$PWD/bats-assert-2.1.0
+        export PATH=$PWD/bats-core-1.10.0/bin:$PATH
+        bash --version
+        bats --version
+        cd python/
+        make check-cli
+
     - name: Lint with flake8
       run: |
+        pip install flake8
         cd python/
         flake8 --version
         # stop the build if there are Python syntax errors or undefined names
         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: Test with pytest
-      run: |
-        pytest
-
-    - name: Check with Bats
-      run: |
-        export BATS_SUPPORT_HOME=$PWD/bats-support-0.3.0
-        export BATS_ASSERT_HOME=$PWD/bats-assert-2.0.0
-        export PATH=$PWD/bats-core-1.7.0/bin:$PATH
-        bats --version
-        cd python/tests/
-        bats *.bats
diff --git a/.github/workflows/R-CMD-check.yaml → .github/workflows/check-r.yml b/.github/workflows/R-CMD-check.yaml → .github/workflows/check-r.yml
@@ -1,29 +1,39 @@
-on: [push, pull_request]
+on:
+  push:
+    paths:
+      - 'r/**/*'
+      - .github/workflows/check-r.yml
+  pull_request:
+    paths:
+      - 'r/**/*'
+      - .github/workflows/check-r.yml
 
 name: "R checks"
 
 jobs:
-  R-CMD-check:
+  check:
     if: "! contains(github.event.head_commit.message, '[ci skip]')"    
 
-    timeout-minutes: 30
+    timeout-minutes: 10
 
     runs-on: ${{ matrix.config.os }}
 
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    name: ${{ matrix.config.os }} (R ${{ matrix.config.r }})
 
     strategy:
       fail-fast: false
       matrix:
         config:
           - {os: windows-latest, r: 'devel'    }
           - {os: windows-latest, r: 'release'  }
-          - {os: macOS-latest,   r: 'devel'    }
+          - {os: windows-latest, r: 'oldrel'  }
+#          - {os: macOS-latest,   r: 'devel'    }
           - {os: macOS-latest,   r: 'release'  }
-          - {os: ubuntu-20.04,   r: 'devel'    }
-          - {os: ubuntu-20.04,   r: 'release'  }
-          - {os: ubuntu-20.04,   r: 'oldrel'   }
-          - {os: ubuntu-20.04,   r: '4.0'      }
+#          - {os: macOS-latest,   r: 'oldrel'   }
+          - {os: ubuntu-latest,  r: 'devel'    }
+          - {os: ubuntu-latest,  r: 'release'  }
+          - {os: ubuntu-latest,  r: 'oldrel'   }
+          - {os: ubuntu-latest,  r: '3.6'      }
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
@@ -36,7 +46,7 @@ jobs:
       _R_CHECK_SUGGESTS_ONLY_: true
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -49,12 +59,17 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           working-directory: r
-          extra-packages: any::rcmdcheck
-          needs: check
+          extra-packages: any::rcmdcheck any::jsonlite
+
+      - name: Install port4me
+        run: |
+          cd r/
+          Rscript -e "install.packages('.', repos = NULL, type = 'source')"
 
       - name: Session info
         run: |
@@ -64,7 +79,7 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
-      - name: Check (!Windows)
+      - name: Check
         if: runner.os != 'Windows'
         run: |
           rcmdcheck::rcmdcheck(
@@ -75,7 +90,7 @@ jobs:
           )
         shell: Rscript {0}
 
-      - name: Check (Windows)
+      - name: Check (MS Windows)
         if: runner.os == 'Windows'
         run: |
           rcmdcheck::rcmdcheck(
@@ -86,6 +101,21 @@ jobs:
           )
         shell: Rscript {0}
 
+      - name: Check CLI
+        if: runner.os != 'Windows'
+        run: |
+          curl -L -O https://github.com/bats-core/bats-core/archive/refs/tags/v1.10.0.tar.gz && tar xf v1.10.0.tar.gz
+          curl -L -O https://github.com/bats-core/bats-support/archive/refs/tags/v0.3.0.tar.gz && tar xf v0.3.0.tar.gz
+          curl -L -O https://github.com/bats-core/bats-assert/archive/refs/tags/v2.1.0.tar.gz && tar xf v2.1.0.tar.gz
+          export BATS_SUPPORT_HOME=$PWD/bats-support-0.3.0
+          export BATS_ASSERT_HOME=$PWD/bats-assert-2.1.0
+          export PATH=$PWD/bats-core-1.10.0/bin:$PATH
+          bash --version
+          bats --version
+          cd r/
+          make check-cli
+
+
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@v3

diff --git a/.github/workflows/coverage-python.yml b/.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 test coverage"
+
+permissions:
+  contents: read
+
+jobs:
+  coverage:
+    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