Adding continuous integration.

.github/dependabot.yml

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+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+
+  # Maintain dependencies for Composer
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "monthly"

.github/workflows/build_docs.yml

@@ -0,0 +1,78 @@
+name: Build Sphinx Documentation
+
+on:
+    push:
+        branches:
+        - main
+    pull_request:
+        branches:
+        - 2-add-continuous-integration
+
+jobs:
+  build:
+    runs-on: ubuntu-latest  # You can also use `windows-latest` or `macos-latest` if needed
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'  # Set your preferred Python version
+
+    - name: Add src to PYTHONPATH
+      run: echo "PYTHONPATH=$PYTHONPATH:$(pwd)/contourusv" >> $GITHUB_ENV
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install sphinx
+        pip install sphinx_rtd_theme
+        # Install missing dependencies
+        pip install opencv-python numpy pandas
+        pip install tqdm scipy
+        pip install matplotlib
+        pip install codecarbon
+    - name: Build the documentation
+      run: |
+        # Generate reStructuredText files from the source code
+        sphinx-apidoc -o sphinx/ contourusv/ -f
+        rm -rf docs/
+
+        # Ensure the docs directory exists
+        mkdir -p docs
+        # Build the HTML documentation
+        sphinx-build -b html sphinx/ docs/
+        pwd
+        ls
+        # Add a .nojekyll file to bypass Jekyll processing on GitHub Pages
+        touch ./docs/.nojekyll
+        git config --global user.email "[email protected]"
+        git config --global user.name "Dallas Wade"
+        git add *
+        git commit -m "Adding docs"
+        git push origin main
+
+    - name: Commit and push generated docs
+      run: |
+          ls
+          git config --global user.email "[email protected]"
+          git config --global user.name "Dallas Wade"
+          git config --global pull.rebase false  # Or true, or --ff-only based on your preference
+          # Ensure gh-pages branch exists and switch to it
+          git fetch origin gh-pages || git checkout --orphan gh-pages
+          git checkout gh-pages
+          git pull origin gh-pages --rebase  # Or --no-rebase based on your configuration
+          git checkout main -- docs/
+          git clean -fdx
+          # Commit and push only docs to gh-pages
+          git add docs/
+          git commit -m "Update Sphinx documentation"
+          git push origin gh-pages
+          # Switch back to main and remove docs from the main branch
+          git checkout main
+          rm -rf docs/
+          git add -A
+          git commit -m "Remove docs folder from main branch"
+          git push origin main

.github/workflows/check_linting.yml

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+name: Style, Spellcheck, & Docstring
+
+on: pull_request
+
+jobs:
+  style:
+    name: Style
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          python-version: "3.11"
+      - uses: pre-commit/[email protected]
+      - name: Install dependencies
+        run: pip install .
+      # Run Ruff
+      - name: Install Ruff
+        run: pip install ruff      
+      - name: Run Ruff
+        run: ruff check contourusv
+      # Run Codespell
+      - name: Install Codespell
+        run: pip install codespell      
+      - name: Run Codespell
+        run: codespell contourusv

.github/workflows/pypi.yml

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+# release workflow
+name: Release workflow
+on:
+  release:
+    types:
+      - published
+
+jobs:
+  pypi-publish:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/contourusv
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      # retrieve your distributions here
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - name: Install pypa/build
+        run: >-
+          python -m
+          pip install
+          build
+          --user
+      - name: Build a binary wheel and a source tarball
+        run: >-
+          python -m
+          build
+          --sdist
+          --wheel
+          --outdir dist/
+          .
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1   

.github/workflows/test.yml

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+name: Test
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os:
+          - ubuntu-latest
+          - macos-latest # arm64 (Apple Silicon)
+          - macos-13  # latest Intel release
+          - windows-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.9"
+      - name: Force numpy < 2 on MacOS Intel
+        if: matrix.os == 'macos-13'
+        run: pip install 'numpy<2'
+      - name: Install ContourUSV
+        run: pip install -e .
+      - name: Test import
+        run: |
+          python -c "import contourusv"
+      #- name: Install testing dependencies
+      #  run: pip install -r requirements_testing.txt
+      #- name: Install QC depedencies
+      #  run: pip install -r requirements_qc.txt
+      - name: Install coverage & pytest
+        run: pip install coverage pytest
+      - name: Test
+        run: |
+          coverage run -m pytest
+      - name: Upload coverage to codecov (Only do this for the ubuntu-latest job)
+        if: matrix.os == 'ubuntu-latest'
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{secrets.CODECOV_TOKEN}}

.gitignore

@@ -1 +1,9 @@
-src/__pycache__
+src/__pycache__
+venv
+src/output
+src/tests
+contourusv/__pycache__
+contourusv/Experiments
+contourusv/output
+venv
+.gitignore

.pre-commit-config.yaml

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+repos:
+  # Ruff linter
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.286
+    hooks:
+      - id: ruff
+        name: ruff
+        files: ^contourusv/
+
+  # Codespell
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.5
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli
+        files: ^contourusv/|^docs/
+        types_or: [python, bib, rst, inc]