fix lint and ruff issues

## Description
<!-- Brief description of the changes -->

## Type of Change
- [ ] Bug fix
- [ ] New feature
- [ ] Breaking change
- [ ] Documentation

## Testing
- [ ] Tests pass locally
- [ ] New tests added (if applicable)

## Related Issues
Closes #

Author: houman1359

.github/.git-blame-ignore-revs

@@ -1,2 +1,2 @@
 # Migrate code style to Black
-c2e17898e9b907384b4e8669828e1efbc9efdc77
+c2e17898e9b907384b4e8669828e1efbc9efdc77

.github/workflows/benchmark.yml.disabled

@@ -10,26 +10,26 @@ on:
 jobs:
   benchmark:
     runs-on: ubuntu-latest
-    
+
     steps:
     - uses: actions/checkout@v4
-    
+
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
         python-version: '3.10'
-    
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install -e .
         pip install pytest-benchmark memory-profiler
-    
+
     - name: Run benchmarks
       run: |
         pytest tests/benchmarks/ -v --benchmark-only --benchmark-save=benchmark
         python scripts/run_benchmarks.py
-    
+
     - name: Upload benchmark results
       uses: actions/upload-artifact@v4
       with:

.github/workflows/black.yml.disabled

@@ -9,4 +9,4 @@ jobs:
       - uses: actions/checkout@v4
       - uses: psf/black@stable
         with:
-          options: "--line-length 150"
+          options: "--line-length 150"

.github/workflows/dependency-update.yml

@@ -8,24 +8,24 @@ on:
 jobs:
   update-dependencies:
     runs-on: ubuntu-latest
-    
+
     steps:
     - uses: actions/checkout@v4
-    
+
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
         python-version: '3.10'
-    
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install pip-tools
-    
+
     - name: Update requirements
       run: |
         pip-compile requirements.in --upgrade --output-file requirements.txt
-    
+
     - name: Create Pull Request
       uses: peter-evans/create-pull-request@v5
       with:
@@ -34,7 +34,7 @@ jobs:
         title: 'Automated dependency updates'
         body: |
           This PR contains automated dependency updates.
-          
+
           Please review the changes and test before merging.
         branch: dependency-updates
         delete-branch: true

.github/workflows/deploy-docs.yml.disabled

@@ -15,21 +15,21 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      
+
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
           python-version: '3.10'
-          
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install mkdocs mkdocs-material pymdown-extensions
-          
+
       - name: Prepare documentation
         run: |
           chmod +x prepare_docs.sh
           ./prepare_docs.sh
-          
+
       - name: Deploy documentation
-        run: mkdocs gh-deploy --force 
+        run: mkdocs gh-deploy --force

.github/workflows/docs.yml

@@ -10,28 +10,28 @@ jobs:
   docs:
     runs-on: ubuntu-latest
     timeout-minutes: 20
-    
+
     steps:
     - uses: actions/checkout@v4
-    
+
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
         python-version: '3.10'
-    
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install -e .
         pip install sphinx sphinx-rtd-theme sphinx-autodoc-typehints myst-parser sphinx-copybutton
-    
+
     - name: Build documentation
       run: |
         cd docs/
         make html
-    
+
     - name: Upload documentation
       uses: actions/upload-artifact@v4
       with:
         name: documentation
-        path: docs/_build/html/
+        path: docs/_build/html/

.github/workflows/gpu-test.yml.disabled

@@ -10,28 +10,28 @@ on:
 jobs:
   gpu-test:
     runs-on: ubuntu-latest
-    
+
     steps:
     - uses: actions/checkout@v4
-    
+
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
         python-version: '3.10'
-    
+
     - name: Install CUDA dependencies
       run: |
         wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-keyring_1.0-1_all.deb
         sudo dpkg -i cuda-keyring_1.0-1_all.deb
         sudo apt-get update
         sudo apt-get -y install cuda-toolkit-12-0
-    
+
     - name: Install Python dependencies
       run: |
         python -m pip install --upgrade pip
         pip install -e .
         pip install pytest pytest-cov
-    
+
     - name: Run GPU tests
       run: |
         python -c "import torch; print(f'CUDA available: {torch.cuda.is_available()}')"

.github/workflows/lint.yml

@@ -10,29 +10,29 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     timeout-minutes: 15
-    
+
     steps:
     - uses: actions/checkout@v4
-    
+
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
         python-version: '3.10'
-    
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install -e .
         pip install "black==25.9.0" isort flake8 mypy ruff
-    
+
     - name: Run black (code formatting)
       run: black --check --diff src/alignment/ tests/ scripts/
-    
+
     - name: Run isort (import sorting)
       run: isort --check-only --diff --profile black src/alignment/ tests/ scripts/
-    
+
     - name: Run flake8 (linting)
       run: flake8 src/alignment/ tests/ scripts/ --max-line-length=100 --ignore=E203,W503 || echo "Flake8 has warnings"
-    
+
     - name: Run mypy (type checking)
       run: mypy src/alignment/ --ignore-missing-imports --no-strict-optional || echo "Type checking has warnings"

.github/workflows/pages.yml.disabled

@@ -43,4 +43,4 @@ jobs:
           path: './docs/build/html'
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v4 
+        uses: actions/deploy-pages@v4

.github/workflows/pre-commit.yml

@@ -10,26 +10,26 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     timeout-minutes: 15
-    
+
     steps:
     - uses: actions/checkout@v4
-    
+
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
         python-version: '3.10'
-    
+
     - name: Install pre-commit
       run: |
         python -m pip install --upgrade pip
         pip install pre-commit
-    
+
     - name: Cache pre-commit
       uses: actions/cache@v4
       with:
         path: ~/.cache/pre-commit
         key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
-    
+
     - name: Run pre-commit
       uses: pre-commit/action@v3.0.0
       continue-on-error: true