BioNeuralNet Framework

.github/workflows/python-app.yml

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+name: BioNeuralNet
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: [3.8, 3.9, 3.10]
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install -r requirements-dev.txt
+        # Install CPU-specific dependencies
+        pip install -r requirements-cpu.txt
+
+    - name: Lint with flake8
+      run: |
+        flake8 bioneuralnet tests docs
+
+    - name: Format with black
+      run: |
+        black --check bioneuralnet tests docs
+
+    - name: Run tests with pytest
+      run: |
+        pytest --cov=bioneuralnet --cov-report=xml tests/
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        files: ./coverage.xml
+        flags: unittests
+        name: codecov-umbrella

.gitignore

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+# Python
+*.pyc
 __pycache__/
+*.pyo
+*.pyd
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Sphinx documentation build
+docs/build/
+
+# Virtual environment
+venv/
+ENV/
+env/
+env.bak/
+venv.bak/
 .venv/
-.DS_Store/
+
+# IDE and editor directories
+.vscode/
+.idea/
+*.sublime-project
+*.sublime-workspace
+
+# Logs
+*.log
+
+# OS generated files
+.DS_Store
+Thumbs.db
+
+# Coverage reports
+htmlcov/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+
+# Test reports
+test_report/
+
+# Other
+*.bak
+*.tmp

.pre-commit-config.yml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black
+        language_version: python3
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+        additional_dependencies: [flake8>=6.0.0]
+
+  - repo: local
+    hooks:
+      - id: run-tests
+        name: Run Tests
+        entry: pytest
+        language: system
+        types: [python]

MANIFEST.in

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+# Include essential files
+include README.md
+include LICENSE
+
+# Include all .yml files in the utils directory
+recursive-include bioneuralnet/utils *.yml
+
+# Include shell scripts in the scripts directory
+recursive-include bioneuralnet/scripts *.sh
+
+# Include all requirements files
+include requirements.txt
+include requirements-cpu.txt
+include requirements-cuda.txt
+include requirements-dev.txt
+
+# Include documentation source files
+recursive-include docs/source *.rst
+recursive-include docs *.md
+
+# Include examples
+recursive-include examples *
+