Revert/pr200 pr201

.github/workflows/ci.yml

@@ -4,7 +4,6 @@ on:
   push:
     branches:
       - main
-      - dev
   pull_request:
     branches:
       - main
@@ -18,52 +17,78 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.14']
-
+        python-version: ['3.9', '3.12']
+    
     steps:
-    - uses: actions/checkout@v6
-
+    - uses: actions/checkout@v4
+    
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-
+    
     - name: Install system dependencies
       run: |
         sudo apt-get update
         sudo apt-get install -y poppler-utils
-
+    
     - name: Upgrade pip, setuptools, and packaging
       run: |
         python -m pip install --upgrade pip setuptools packaging
-
+    
     - name: Cache src directory
-      uses: actions/cache@v5
+      uses: actions/cache@v4
       with:
-        path: ${{ github.workspace }}/src/
+        path: ./src/
         key: ${{ runner.os }}-src-grch37
         restore-keys: |
           ${{ runner.os }}-src-
-
+    
     - name: Download GRCh37.tar.gz if not present
       run: |
-        if [ ! -f ${{ github.workspace }}/src/GRCh37.tar.gz ]; then
-          wget --connect-timeout=10 --tries=20 ftp://alexandrovlab-ftp.ucsd.edu/pub/tools/SigProfilerMatrixGenerator/GRCh37.tar.gz -P ${{ github.workspace }}/src/
+        if [ ! -f ./src/GRCh37.tar.gz ]; then
+          wget --connect-timeout=10 --tries=20 ftp://alexandrovlab-ftp.ucsd.edu/pub/tools/SigProfilerMatrixGenerator/GRCh37.tar.gz -P ./src/
         fi
-
+    
     - name: Install package with tests
       run: |
         pip install .[tests]
-
+    
     - name: Install genome
       run: |
-        SigProfilerMatrixGenerator install GRCh37 --local_genome ${{ github.workspace }}/src/
-
+        python install_genome.py ${{ github.workspace }}/src/
+    
     - name: Run unit tests
       run: |
-        pip install pytest
-        pytest -s -rw tests
-
+        pytest tests
+
     - name: Run integration test
       run: |
         python3 test.py
+
+    - name: Build and push Docker image
+      if: github.ref == 'refs/heads/main' && github.event_name == 'push' && matrix.python-version == '3.12'
+      run: |
+        echo "Starting Docker deployment to GHCR for sigprofilersuite..."
+
+        VERSION_TAG=$(grep "VERSION = " setup.py | cut -d'"' -f2)
+
+        # Get the repository name and convert it to lowercase
+        REPO_NAME=$(basename ${{ github.repository }} | tr '[:upper:]' '[:lower:]')
+        IMAGE_NAME="ghcr.io/sigprofilersuite/$REPO_NAME"
+
+        echo "Building version: $VERSION_TAG for image: $IMAGE_NAME"
+
+        echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io \
+          --username "${{ github.actor }}" \
+          --password-stdin
+
+        docker build \
+          --build-arg COMMIT_SHA=${{ github.sha }} \
+          -t $IMAGE_NAME:$VERSION_TAG \
+          -t $IMAGE_NAME:latest .
+
+        docker push $IMAGE_NAME:$VERSION_TAG
+        docker push $IMAGE_NAME:latest
+
+        echo "Docker deployment to GHCR successful"