Update functional CI

CDDLeiden · Jan 8, 2024 · 0d4c498 · 0d4c498
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commit 0d4c498
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Showing 2 changed files with 43 additions and 17 deletions.
diff --git a/.github/workflows/dev_ci.yml b/.github/workflows/dev_ci.yml
@@ -31,16 +31,22 @@ jobs:
     - name: Install Clustal Omega, MAFFT & add to PATH
       run: |
         export HOME_DIR=$PWD
+        echo "HOME_DIR=$PWD" >> $GITHUB_ENV # used later in the workflow
         if [ "${{ runner.os }}" = "macOS" ]; then
         wget http://www.clustal.org/omega/clustal-omega-1.2.3-macosx -O clustalo && chmod +x clustalo
         brew install mafft && unset MAFFT_BINARIES
+        echo "$HOME_DIR" >> $GITHUB_PATH # make clustalo available in the next steps
         elif [ "${{ runner.os }}" = "Linux" ]; then
         wget http://www.clustal.org/omega/clustalo-1.2.4-Ubuntu-x86_64 -O clustalo && chmod +x clustalo
         wget https://mafft.cbrc.jp/alignment/software/mafft-7.520-linux.tgz -O mafft.tgz && tar -xzvf mafft.tgz && chmod +x mafft-linux64/mafftdir/bin/mafft
         echo "MAFFT_BINARIES=$PWD/mafft-linux64/mafftdir/libexec/" >> $GITHUB_ENV
         echo "$HOME_DIR/mafft-linux64/mafftdir/bin/" >> $GITHUB_PATH
+        echo "$HOME_DIR" >> $GITHUB_PATH # make clustalo available in the next steps
+        elif [ "${{ runner.os }}" = "Windows" ]; then
+        choco install clustal-omega mafft
+        echo "::add-path::$env:ProgramFiles\Clustal Omega"
+        echo "::add-path::$env:ProgramFiles\MAFFT"
         fi
-        echo "$HOME_DIR" >> $GITHUB_PATH
 
     - name: Print Clustal Omega & MAFFT versions
       run: |
@@ -49,21 +55,28 @@ jobs:
 
     - name: Install dependencies
       run: |
-        python --version
+        python -c "print('Python version: ' + '$(python --version)')"
+        python -c "import platform; print('System info: ', platform.system(), platform.release())" # For debugging OS version
         python -m pip install ".[full]"  --no-cache-dir
         python -c "import qsprpred; print(qsprpred.__version__)" # For debugging package version
         python -m pip install pytest
         python -m pip install jupyterlab
         python -m pip freeze # For debugging environment
     
     - name: Run pytest
-      run: pytest -xv qsprpred # -x: stop on first failure, -v: verbose
+      run: pytest -xv qsprpred --junitxml=$HOME_DIR/test_report.xml # -x: stop on first failure, -v: verbose
+
+    - name: Publish Test Report
+      uses: mikepenz/action-junit-report@v4
+      if: success() || failure() # always run even if the previous step fails
+      with:
+        report_paths: 'test_report.xml'
 
     - name: Test CLI
-      run: cd testing/test_cli && ./run.sh && cd "$HOME_DIR"
+      run: cd testing/test_cli && ./run.sh
 
     - name: Test Tutorials
-      run: cd testing/test_tutorial && ./run.sh && cd "$HOME_DIR"
+      run: cd testing/test_tutorial && ./run.sh
 
     - name: Test Consistency
-      run: cd testing/test_consistency && ./run.sh && cd "$HOME_DIR"
+      run: cd testing/test_consistency && ./run.sh
diff --git a/.github/workflows/pre_merge_ci.yml b/.github/workflows/pre_merge_ci.yml
@@ -31,33 +31,46 @@ jobs:
         restore-keys: |
           ${{ runner.os }}-pip-
 
-    - name: Install Clustal Omega and MAFFT
+    - name: Install Clustal Omega, MAFFT & add to PATH
       run: |
+        export HOME_DIR=$PWD
+        echo "HOME_DIR=$PWD" >> $GITHUB_ENV # used later in the workflow
         wget http://www.clustal.org/omega/clustalo-1.2.4-Ubuntu-x86_64 -O clustalo && chmod +x clustalo
         wget https://mafft.cbrc.jp/alignment/software/mafft-7.520-linux.tgz -O mafft.tgz && tar -xzvf mafft.tgz && chmod +x mafft-linux64/mafftdir/bin/mafft
+        echo "MAFFT_BINARIES=$PWD/mafft-linux64/mafftdir/libexec/" >> $GITHUB_ENV
         echo "$HOME_DIR/mafft-linux64/mafftdir/bin/" >> $GITHUB_PATH
-        export MAFFT_BINARIES=$HOME_DIR/mafft-linux64/mafftdir/libexec/
-        echo $HOME_DIR >> $GITHUB_PATH
-        clustalo --version  # For debugging clustalo version
-        mafft --version  # For debugging mafft version
+        echo "$HOME_DIR" >> $GITHUB_PATH # make clustalo available in the next steps
 
+    - name: Print Clustal Omega & MAFFT versions
+      run: |
+          clustalo --version  # For debugging clustalo version
+          mafft --version  # For debugging mafft version
+  
     - name: Install dependencies
       run: |
-        python --version
-        python -m pip install ".[full]" 
+        python -c "print('Python version: ' + '$(python --version)')"
+        python -c "import platform; print('System info: ', platform.system(), platform.release())" # For debugging OS version
+        python -c "import platform; print(platform.system(), platform.release())" # For debugging OS version
+        python -m pip install ".[full]"
         python -c "import qsprpred; print(qsprpred.__version__)" # For debugging package version
         python -m pip install pytest
         python -m pip install jupyterlab
         python -m pip freeze # For debugging environment
     
     - name: Run pytest
-      run: pytest -xv qsprpred # -x: stop on first failure, -v: verbose
+      run: pytest -xv qsprpred --junitxml=$HOME_DIR/test_report.xml # -x: stop on first failure, -v: verbose
+
+    - name: Publish Test Report
+      uses: mikepenz/action-junit-report@v4
+      if: success() || failure() # always run even if the previous step fails
+      with:
+        report_paths: 'test_report.xml'
 
     - name: Test CLI
-      run: cd testing/test_cli && ./run.sh && cd "$HOME_DIR"
+      run: cd testing/test_cli && ./run.sh
 
     - name: Test Tutorials
-      run: cd testing/test_tutorial && ./run.sh && cd "$HOME_DIR"
+      run: cd testing/test_tutorial && ./run.sh
 
     - name: Test Consistency
-      run: cd testing/test_consistency && ./run.sh && cd "$HOME_DIR"
+      run: cd testing/test_consistency && ./run.sh