Dev

.github/workflows/ci.yml

@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - main
+      - dev
   pull_request:
     branches:
       - main
@@ -17,78 +18,52 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.12']
-    
+        python-version: ['3.9', '3.14']
+
     steps:
-    - uses: actions/checkout@v4
-    
+    - uses: actions/checkout@v6
+
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       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@v4
+      uses: actions/cache@v5
       with:
-        path: ./src/
+        path: ${{ github.workspace }}/src/
         key: ${{ runner.os }}-src-grch37
         restore-keys: |
           ${{ runner.os }}-src-
-    
+
     - name: Download GRCh37.tar.gz if not present
       run: |
-        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/
+        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/
         fi
-    
+
     - name: Install package with tests
       run: |
         pip install .[tests]
-    
+
     - name: Install genome
       run: |
-        python install_genome.py ${{ github.workspace }}/src/
-    
+        SigProfilerMatrixGenerator install GRCh37 --local_genome ${{ github.workspace }}/src/
+
     - name: Run unit tests
       run: |
-        pytest tests
-
+        pip install pytest
+        pytest -s -rw tests
+
     - name: Run integration test
       run: |
         python3 test.py
-
-    - name: Build and push Docker image
-      if: github.ref == 'refs/heads/main' && github.event_name == 'push' && matrix.python-version == '3.12'
-      run: |
-        echo "Starting Docker deployment to GHCR for sigprofilersuite..."
-
-        VERSION_TAG=$(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"

.github/workflows/docs.yml

@@ -0,0 +1,55 @@
+name: Docs
+
+on:
+  push:
+    branches:
+      - master
+      - dev
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: github-pages
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Configure Pages
+        uses: actions/configure-pages@v5
+
+      - name: Install docs dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install mkdocs mkdocs-material pymdown-extensions
+
+      - name: Build site
+        run: |
+          mkdocs build --clean
+
+      - name: Upload Pages artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: site
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: build
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@v4
+

.github/workflows/release.yml

@@ -0,0 +1,125 @@
+name: Create Release from setup.py
+
+on:
+  pull_request:
+    types:
+      - closed
+    branches:
+      - main
+
+jobs:
+  release:
+    if: github.event.pull_request.merged == true
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write
+
+    outputs:
+      version: ${{ steps.get_version.outputs.VERSION }}
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.14"
+
+      - name: Upgrade pip, setuptools, packaging and install git-cliff
+        run: |
+          python -m pip install --upgrade pip setuptools packaging
+          pip install git-cliff
+
+      - name: Extract version from setup.py
+        id: get_version
+        run: |
+          VERSION=$(python setup.py --version)
+          echo "VERSION=$VERSION" >> $GITHUB_OUTPUT
+
+      - name: Get latest release tag
+        id: get_last_release
+        run: |
+          latest=$(curl -s \
+            -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
+            https://api.github.com/repos/${{ github.repository }}/releases/latest \
+            | jq -r '.tag_name // "v0.0.0"' | sed 's/^v//')
+          echo "LATEST_RELEASE=$latest" >> $GITHUB_ENV
+
+      - name: Check release version
+        run: |
+          echo "New version: ${{ steps.get_version.outputs.VERSION }}"
+          echo "Latest release: $LATEST_RELEASE"
+          python - <<EOF
+          from packaging.version import parse
+
+          new_version = parse("${{ steps.get_version.outputs.VERSION }}")
+          latest_version = parse("$LATEST_RELEASE")
+
+          if new_version <= latest_version:
+              raise SystemExit(f"Error: New version ({new_version}) is not higher than latest release ({latest_version})")
+          EOF
+
+      - name: Generate release notes and update CHANGELOG.md
+        run: |
+          git-cliff --unreleased --strip all --tag "v${{ steps.get_version.outputs.VERSION }}" > RELEASE_NOTES.md
+          git-cliff --unreleased --tag "v${{ steps.get_version.outputs.VERSION }}" --prepend CHANGELOG.md
+
+      - name: Commit and push CHANGELOG.md
+        run: |
+          git config user.name "github-actions"
+          git config user.email "github-actions@github.com"
+          git add CHANGELOG.md
+          git commit -m "chore: update CHANGELOG.md for v${{ steps.get_version.outputs.VERSION }}"
+          git push origin HEAD:main
+
+      - name: Create Git tag
+        run: |
+          git tag v${{ steps.get_version.outputs.VERSION }}
+          git push origin v${{ steps.get_version.outputs.VERSION }}
+
+      - name: Create GitHub Release
+        uses: softprops/action-gh-release@v2
+        with:
+          tag_name: v${{ steps.get_version.outputs.VERSION }}
+          body_path: RELEASE_NOTES.md
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+  sync-dev:
+    needs: release
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write
+      pull-requests: write
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Merge main into a sync branch off dev
+        run: |
+          git config user.name "github-actions"
+          git config user.email "github-actions@github.com"
+          git fetch origin main dev
+          git checkout -b sync/main-into-dev-${{ github.run_id }} origin/dev
+          git merge origin/main --no-edit
+
+      - name: Push sync branch
+        run: git push origin sync/main-into-dev-${{ github.run_id }}
+
+      - name: Open PR into dev
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          gh pr create \
+            --base dev \
+            --head sync/main-into-dev-${{ github.run_id }} \
+            --title "chore: sync main into dev after v${{ needs.release.outputs.version }}" \
+            --body "Automated sync of \`main\` into \`dev\` after release v${{ needs.release.outputs.version }}."