Beta Release Clean Up

.github/workflows/docs.yml

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+name: Build and Deploy Documentation
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  build-deploy-docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          check-latest: true
+
+      - name: Install Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install -r requirements-dev.txt
+          pip install torch
+          pip install torch_geometric
+        shell: bash
+
+      - name: Verify Documentation Directory
+        run: test -d docs/source/ || { echo "Docs source directory missing"; exit 1; }
+
+      - name: Build Documentation
+        run: |
+          mkdir -p docs/build/html
+          sphinx-build -b html docs/source/ docs/build/html/
+        shell: bash
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/build/html

.github/workflows/pre-commit.yml

@@ -0,0 +1,35 @@
+name: Pre-Commit Checks
+
+on:
+  push:
+    branches:
+      - "**"
+  pull_request:
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Cache pip dependencies
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt', '**/requirements-dev.txt') }}
+          restore-keys: ${{ runner.os }}-pip-
+
+      - name: Install Pre-Commit and Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install pre-commit
+
+      - name: Run Pre-Commit Checks
+        run: pre-commit run --all-files --show-diff-on-failure

.github/workflows/python-app.yml

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+name: BioNeuralNet CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.10", "3.11"]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          check-latest: true
+
+      - name: Cache pip dependencies
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt', '**/requirements-dev.txt') }}
+          restore-keys: ${{ runner.os }}-pip-
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install -r requirements-dev.txt
+          pip install torch
+          pip install torch_geometric
+        shell: bash
+
+      - name: Install R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: "latest"
+
+      - name: Install R packages
+        run: |
+          Rscript -e "if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager', repos='https://cran.r-project.org')"
+          Rscript -e "install.packages(c('dplyr', 'jsonlite'), repos='https://cran.r-project.org')"
+          Rscript -e "BiocManager::install(c('impute', 'preprocessCore', 'GO.db', 'AnnotationDbi'), update=FALSE, ask=FALSE)"
+          Rscript -e "install.packages('SmCCNet', repos='https://cran.r-project.org')"
+          Rscript -e "install.packages('WGCNA', repos='https://cran.r-project.org')"
+        shell: bash
+
+      - name: Run tests with pytest
+        run: |
+          find . -name ".coverage*" -delete
+          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

@@ -1,2 +1,69 @@
+# Python
+*.pyc
 __pycache__/
-.venv/
+*.pyo
+*.pyd
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+.pytest_cache
+release.md
+bioneuralnet.egg-info
+/dist/
+/build/
+/docker_files/
+.mypy_cache
+
+# Block sensitive file types globally
+*.csv
+*.RData
+
+
+# Sphinx documentation build
+docs/build/
+
+# Virtual environment
+venv/
+ENV/
+env/
+env.bak/
+venv.bak/
+.venv/
+bioneuralnet-env/
+
+# 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
+test_output/
+dpmon_output_*
+lib/
+.DS_Store

.pre-commit-config.yaml

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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: 24.10.0
+    hooks:
+      - id: black
+        name: Format Python code with Black
+        language_version: python3
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.14.1
+    hooks:
+      - id: mypy
+        name: Static type checking with MyPy
+        args: [--ignore-missing-imports]
+
+  - repo: local
+    hooks:
+      - id: remove-pyc-and-pycache
+        name: Remove .pyc files and __pycache__ directories
+        entry: bash -c "find . \( -path './.venv' -o -path './docs' -o -path './node_modules' \) -prune -o -type f -name '*.pyc' -exec rm -f {} + -o -type d -name '__pycache__' -exec rm -rf {} +"
+        language: system
+        stages: [pre-commit]
+
+      - id: clean-coverage-files
+        name: Remove stale .coverage files
+        entry: bash -c "find . -name '.coverage*' -delete"
+        language: system
+        stages: [pre-commit]
+
+      - id: check-forbidden-files
+        name: Prevent adding forbidden file types
+        entry: bash -c "if git diff --cached --name-only | grep -E '\\.csv$|\\.RData$'; then echo 'Forbidden file types detected!'; exit 1; fi"
+        language: system
+        types: [file]
+
+      - id: run-tests
+        name: Run Tests with Pytest
+        entry: pytest --cov=bioneuralnet --cov-report=term-missing
+        language: system
+        types: [python]