first implementation

Author: haeussma

.github/workflows/ci.yml

@@ -0,0 +1,74 @@
+name: CI
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    
+    - name: Install poetry
+      uses: abatilo/actions-poetry@v2
+    
+    - name: Configure poetry
+      run: |
+        poetry config virtualenvs.create true
+        poetry config virtualenvs.in-project true
+    
+    - name: Cache poetry dependencies
+      uses: actions/cache@v3
+      with:
+        path: .venv
+        key: venv-${{ runner.os }}-${{ matrix.python-version }}-${{ hashFiles('**/poetry.lock') }}
+    
+    - name: Install dependencies
+      run: poetry install
+    
+    - name: Run tests
+      run: poetry run pytest -v
+    
+    - name: Run linting
+      run: |
+        poetry run black --check .
+        poetry run isort --check-only .
+    
+    - name: Test import and basic functionality
+      run: poetry run python test_warnings_fixed.py
+
+  build:
+    runs-on: ubuntu-latest
+    needs: test
+    
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.x"
+    
+    - name: Install poetry
+      uses: abatilo/actions-poetry@v2
+    
+    - name: Build package
+      run: poetry build
+    
+    - name: Check build artifacts
+      run: |
+        ls -la dist/
+        poetry run pip install dist/*.whl
+        poetry run python -c "from structure_align import StructuralAligner; print('✅ Package installed and imports successfully')" 

.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.x"
+    - name: Install poetry
+      uses: abatilo/actions-poetry@v2
+    - name: Configure poetry
+      run: poetry config virtualenvs.create false
+    - name: Install dependencies
+      run: poetry install --only=main
+    - name: Build package
+      run: poetry build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/structure-align
+    permissions:
+      id-token: write
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: >-
+      Sign the Python 🐍 distribution 📦 with Sigstore
+      and upload them to GitHub Release
+    needs:
+    - publish-to-pypi
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write
+      id-token: write
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Sign the dists with Sigstore
+      uses: sigstore/gh-action-sigstore-python@v1.2.3
+      with:
+        inputs: >-
+          ./dist/*.tar.gz
+          ./dist/*.whl
+    - name: Create GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      run: >-
+        gh release upload
+        '${{ github.ref_name }}' dist/**
+        --repo '${{ github.repository }}'