Release 1.5.0

.dockerignore

@@ -0,0 +1,33 @@
+.git
+.github
+.claude
+.venv
+.venv-*
+venv
+env
+__pycache__
+*.py[cod]
+*.egg-info
+dist
+build
+.pytest_cache
+.mypy_cache
+.coverage
+htmlcov
+*.pt
+*.pth
+data
+ignore
+ignore.py
+test_library_out*
+test_verify_*
+readme_advanced_results
+readme_example_results
+src/tests/test_files/test_output
+*.tsv
+*.code-workspace
+.vscode
+.env
+plan.md
+ROADMAP.md
+src/tests

.github/QUICK_SETUP.md

@@ -6,7 +6,7 @@
 ```
 GitHub Repository → Settings → Environments → New environment
 Name: testpypi
-Protection rules: 
+Protection rules:
   - Deployment branches: test
   - Save protection rules
 ```

.github/bioconda_submission_guide.md

@@ -59,7 +59,7 @@ about:
   license_file: LICENSE
   summary: Pipeline for Easy Protein Embedding
   description: |
-    PEPE (Pipeline for Easy Protein Embedding) is a tool for extracting 
+    PEPE (Pipeline for Easy Protein Embedding) is a tool for extracting
     embeddings and attention matrices from protein sequences using pre-trained models.
   doc_url: https://github.com/csi-greifflab/pepe-cli#readme
   dev_url: https://github.com/csi-greifflab/pepe-cli
@@ -71,7 +71,7 @@ extra:
 
 ## Step-by-Step Submission
 
-1.  **Fork Bioconda Recipes**: 
+1.  **Fork Bioconda Recipes**:
     - Go to [bioconda/bioconda-recipes](https://github.com/bioconda/bioconda-recipes) and fork it.
 2.  **Clone your fork**:
     ```bash

.github/conda/meta.yaml

@@ -12,12 +12,12 @@ build:
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.10
     - pip
     - setuptools
     - wheel
   run:
-    - python >=3.8
+    - python >=3.10
     - pytorch >=1.9.0
     - transformers >=4.20.0
     - sentencepiece

.github/workflows/publish-main-branch-trusted.yml

@@ -13,49 +13,49 @@ jobs:
       id-token: write  # Required for trusted publishing
       contents: write  # Required for creating releases
       pull-requests: read
-    
+
     steps:
     - uses: actions/checkout@v5
-    
+
     - name: Set up Python
       uses: actions/setup-python@v6
       with:
         python-version: '3.10'
-    
+
     - name: Install build dependencies
       run: |
         python3 -m pip install --upgrade pip
         pip install build
-    
+
     - name: Clean build artifacts
       run: |
         # Remove any cached files that might interfere with the build
         find . -name "__pycache__" -type d -exec rm -rf {} + || true
         find . -name "*.pyc" -type f -delete || true
         rm -rf dist/ build/ *.egg-info/ src/*.egg-info/ || true
-    
+
     - name: Verify version for main branch
       run: |
         # Extract metadata directly from __init__.py (avoids importing package deps like torch)
         CURRENT_VERSION=$(grep -m1 '__version__ = ' src/pepe/__init__.py | sed 's/__version__ = "\(.*\)"/\1/')
         PACKAGE_NAME=$(grep -m1 '__package_name__ = ' src/pepe/__init__.py | sed 's/__package_name__ = "\(.*\)"/\1/')
         MODULE_NAME=$(grep -m1 '__module_name__ = ' src/pepe/__init__.py | sed 's/__module_name__ = "\(.*\)"/\1/')
-        
+
         # Check if version contains -dev or -test (should not be in main branch)
         if [[ "$CURRENT_VERSION" == *"-dev"* ]] || [[ "$CURRENT_VERSION" == *"-test"* ]]; then
           echo "❌ Error: Version $CURRENT_VERSION contains development/test suffix"
           echo "Main branch should have a clean version number (e.g., 1.0.0, 1.2.3)"
           exit 1
         fi
-        
+
         echo "✅ Version validation passed: $CURRENT_VERSION"
         echo "Package name: $PACKAGE_NAME"
         echo "Module name: $MODULE_NAME"
         grep "__version__" src/pepe/__init__.py
-    
+
     - name: Build package
       run: python3 -m build
-    
+
     - name: Verify build artifacts
       run: |
         echo "📦 Build artifacts created:"
@@ -68,13 +68,13 @@ jobs:
           file "$file"
           echo "SHA256: $(sha256sum "$file" | cut -d' ' -f1)"
         done
-    
+
     - name: Publish to PyPI (Trusted Publishing)
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
         verbose: true
         skip_existing: true
-    
+
     - name: Output installation command
       run: |
         PACKAGE_NAME=$(grep -m1 '__package_name__ = ' src/pepe/__init__.py | sed 's/__package_name__ = "\(.*\)"/\1/')
@@ -84,7 +84,7 @@ jobs:
         echo "pip install \"$PACKAGE_NAME==$CURRENT_VERSION\""
         echo "Or for the latest version:"
         echo "pip install \"$PACKAGE_NAME\""
-    
+
     - name: Wait for package availability
       run: |
         echo "Waiting for package to be available on PyPI..."
@@ -106,10 +106,10 @@ jobs:
           echo "Attempt $i failed, retrying in 30s..."
           sleep 30
         done
-        
+
         # Verify installation
         pip list | grep -i pepe
-        
+
         # Test basic import
         python3 -c "import $MODULE_NAME; print('Package imported successfully')"
 
@@ -132,34 +132,41 @@ jobs:
 
         echo "🎉 Package verification completed successfully!"
         echo "Package $PACKAGE_NAME version $CURRENT_VERSION is now available on PyPI!"
-
+
+    - name: Upload dist artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: dist-packages
+        path: dist/
+        retention-days: 1
+
     - name: Get version for release
       id: get_version
       run: |
         VERSION=$(grep -m1 '__version__ = ' src/pepe/__init__.py | sed 's/__version__ = "\(.*\)"/\1/')
         echo "version=$VERSION" >> $GITHUB_OUTPUT
-    
+
     - name: Create GitHub Release
       uses: softprops/action-gh-release@v3
       with:
         tag_name: v${{ steps.get_version.outputs.version }}
         name: Release v${{ steps.get_version.outputs.version }}
         body: |
           Release of pepe-cli version ${{ steps.get_version.outputs.version }}
-          
+
           ## Installation
-          
+
           ### From PyPI (Recommended)
           ```bash
           pip install pepe-cli==${{ steps.get_version.outputs.version }}
           ```
-          
+
           ### From GitHub Release
           Download the wheel file and install:
           ```bash
           pip install pepe_cli-${{ steps.get_version.outputs.version }}-py3-none-any.whl
           ```
-          
+
         files: |
           dist/*.whl
           dist/*.tar.gz
@@ -174,7 +181,7 @@ jobs:
     needs: build-and-publish-main
     steps:
       - uses: actions/checkout@v5
-      
+
       - name: Set up Conda
         uses: conda-incubator/setup-miniconda@v4
         with:
@@ -207,3 +214,110 @@ jobs:
           fi
           echo "Found package: $PACKAGE_PATH"
           anaconda -t $ANACONDA_TOKEN upload --label main $PACKAGE_PATH
+
+  publish-docker:
+    runs-on: ubuntu-latest
+    needs: build-and-publish-main
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Get version
+        id: version
+        run: |
+          VERSION=$(grep -m1 '__version__ = ' src/pepe/__init__.py | sed 's/__version__ = "\(.*\)"/\1/')
+          echo "version=$VERSION" >> $GITHUB_OUTPUT
+          echo "image=ghcr.io/csi-greifflab/pepe-cli" >> $GITHUB_OUTPUT
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to GHCR
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          push: true
+          tags: |
+            ghcr.io/csi-greifflab/pepe-cli:${{ steps.version.outputs.version }}
+            ghcr.io/csi-greifflab/pepe-cli:latest
+          labels: |
+            org.opencontainers.image.source=${{ github.repository }}
+            org.opencontainers.image.version=${{ steps.version.outputs.version }}
+            org.opencontainers.image.title=pepe-cli
+
+      - name: Verify container CLI
+        run: |
+          docker pull ghcr.io/csi-greifflab/pepe-cli:${{ steps.version.outputs.version }}
+          docker run --rm ghcr.io/csi-greifflab/pepe-cli:${{ steps.version.outputs.version }} --help
+
+      - name: Output Docker pull command
+        run: |
+          echo "Docker image published to GHCR:"
+          echo "docker pull ghcr.io/csi-greifflab/pepe-cli:${{ steps.version.outputs.version }}"
+
+  create-release:
+    runs-on: ubuntu-latest
+    needs: [build-and-publish-main, publish-docker]
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Get version for release
+        id: get_version
+        run: |
+          VERSION=$(grep -m1 '__version__ = ' src/pepe/__init__.py | sed 's/__version__ = "\(.*\)"/\1/')
+          echo "version=$VERSION" >> $GITHUB_OUTPUT
+
+      - name: Download dist artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist-packages
+          path: dist/
+
+      - name: Create GitHub Release
+        uses: softprops/action-gh-release@v3
+        with:
+          tag_name: v${{ steps.get_version.outputs.version }}
+          name: Release v${{ steps.get_version.outputs.version }}
+          body: |
+            Release of pepe-cli version ${{ steps.get_version.outputs.version }}
+
+            ## Installation
+
+            ### From PyPI (Recommended)
+            ```bash
+            pip install pepe-cli==${{ steps.get_version.outputs.version }}
+            ```
+
+            ### From GitHub Release
+            Download the wheel file and install:
+            ```bash
+            pip install pepe_cli-${{ steps.get_version.outputs.version }}-py3-none-any.whl
+            ```
+
+            ### From GHCR (Docker)
+            ```bash
+            docker pull ghcr.io/csi-greifflab/pepe-cli:${{ steps.get_version.outputs.version }}
+            docker run --rm -v "$PWD:/data" --user "$(id -u):$(id -g)" \
+              ghcr.io/csi-greifflab/pepe-cli:${{ steps.get_version.outputs.version }} \
+              --model_name esm2_t6_8M_UR50D --fasta_path /data/sequences.fasta --output_path /data/out --extract_embeddings mean_pooled
+            ```
+
+          files: |
+            dist/*.whl
+            dist/*.tar.gz
+          draft: false
+          prerelease: false
+          generate_release_notes: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}