update + debug workflows

CDDLeiden · Jan 8, 2024 · 0642a7f · 0642a7f
1 parent 0d41b6a
commit 0642a7f
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Showing 2 changed files with 37 additions and 22 deletions.
diff --git a/.github/workflows/dev_ci.yml b/.github/workflows/dev_ci.yml
@@ -30,17 +30,22 @@ jobs:
 
     - name: Install Clustal Omega and MAFFT
       run: |
+        export $HOME_DIR=$PWD
+        ls -la
+        echo "$PWD" >> $GITHUB_PATH
         if [ "${{ runner.os }}" = "macOS" ]; then
-          wget http://www.clustal.org/omega/clustal-omega-1.2.3-macosx -O clustalo && chmod +x clustalo
-          echo "$PWD" >> $GITHUB_PATH
-          brew install mafft && unset MAFFT_BINARIES
+        wget http://www.clustal.org/omega/clustal-omega-1.2.3-macosx -O clustalo && chmod +x clustalo
+        brew install mafft && unset MAFFT_BINARIES
         elif [ "${{ 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
-          export PATH=$PATH:$PWD/mafft-linux64/mafftdir/bin/:$PWD
-          export MAFFT_BINARIES=$PWD/mafft-linux64/mafftdir/libexec/
+        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 "$PWD/mafft-linux64/mafftdir/bin/" >> $GITHUB_PATH
+        export MAFFT_BINARIES=$PWD/mafft-linux64/mafftdir/libexec/
         fi
-        echo "$PWD" >> $GITHUB_PATH
+        echo 'PATH, and GITHUB_PATH:'
+        echo $PATH
+        echo $GITHUB_PATH
+        ls -la
         clustalo --version  # For debugging clustalo version
         mafft --version  # For debugging mafft version
 
@@ -53,10 +58,14 @@ jobs:
         python -m pip install jupyterlab
         python -m pip freeze # For debugging environment
     
-    - name: Run tests
-      run: pytest qsprpred
+    - name: Run pytest
+      run: pytest -xv qsprpred # -x: stop on first failure, -v: verbose
 
-    - name: Run notebooks
-      run: |
-        cd clitest && ./run.sh
-        cd ../tutorial && ./run_all.sh
+    - name: Test CLI
+      run: cd test_cli && ./run.sh && cd "$HOME_DIR"
+
+    - name: Test Tutorials
+      run: cd test_tutorial && ./run.sh && cd "$HOME_DIR"
+
+    - name: Test Consistency
+      run: cd test_consistency && ./run.sh && cd "$HOME_DIR"
diff --git a/.github/workflows/pre_merge_ci.yml b/.github/workflows/pre_merge_ci.yml
@@ -24,7 +24,7 @@ jobs:
         python-version: '3.10'
 
     - name: Cache Python dependencies
-      uses: actions/cache@v4
+      uses: actions/cache@v3
       with:
         path: ~/.cache/pip
         key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
@@ -33,10 +33,12 @@ jobs:
 
     - name: Install Clustal Omega and MAFFT
       run: |
+        export $HOME_DIR=$PWD
         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
-        export PATH=$PATH:$PWD/mafft-linux64/mafftdir/bin/:$PWD
+        echo "$PWD/mafft-linux64/mafftdir/bin/" >> $GITHUB_PATH
         export MAFFT_BINARIES=$PWD/mafft-linux64/mafftdir/libexec/
+        echo $PWD >> $GITHUB_PATH
         clustalo --version  # For debugging clustalo version
         mafft --version  # For debugging mafft version
 
@@ -49,10 +51,14 @@ jobs:
         python -m pip install jupyterlab
         python -m pip freeze # For debugging environment
     
-    - name: Run tests
-      run: pytest qsprpred
+    - name: Run pytest
+      run: pytest -xv qsprpred # -x: stop on first failure, -v: verbose
 
-    - name: Run notebooks
-      run: |
-        cd clitest && ./run.sh
-        cd ../tutorial && ./run_all.sh
+    - name: Test CLI
+      run: cd test_cli && ./run.sh && cd "$HOME_DIR"
+
+    - name: Test Tutorials
+      run: cd test_tutorial && ./run.sh && cd "$HOME_DIR"
+
+    - name: Test Consistency
+      run: cd test_consistency && ./run.sh && cd "$HOME_DIR"