fix: Update CI workflow to use standard Python setup

- Remove ivpm bootstrap dependency (use actions/setup-python@v5)
- Update upload-artifact to v4 (v3 is deprecated)
- Add Python 3.10, 3.11, 3.12 test matrix
- Update codecov-action to v4
- Fix documentation publish branch (main not master)
- Simplify all jobs to use standard python commands

Author: mballance

.github/workflows/ci.yml

@@ -8,88 +8,100 @@ on:
 jobs:
   ci-linux:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
     steps:
     - uses: actions/checkout@v4
 
-    - name: Configure Python
-      run: |
-        # Install dependencies required to load ivpm.yaml file
-        ./bootstrap.sh
-        ./packages/python/bin/python3 -m pip install setuptools build --upgrade
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
 
     - name: Install Dependencies
       run: |
-        ./packages/python/bin/python3 -m pip install -e ".[dev]"
+        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install -e ".[dev]"
     
     - name: Run Linters
       run: |
-        # Run basic linting checks
-        ./packages/python/bin/python3 -m pip install ruff mypy
-        ./packages/python/bin/ruff check src/pywellen_mcp/ || true
-        ./packages/python/bin/mypy src/pywellen_mcp/ --ignore-missing-imports || true
+        python -m pip install ruff mypy
+        ruff check src/pywellen_mcp/ || true
+        mypy src/pywellen_mcp/ --ignore-missing-imports || true
     
     - name: Run Unit Tests
       run: |
-        export PYTHONPATH=$(pwd)/src:$(pwd)/tests
-        ./packages/python/bin/pytest tests/unit/ -v --cov=pywellen_mcp --cov-report=xml --cov-report=term
+        pytest tests/unit/ -v --cov=pywellen_mcp --cov-report=xml --cov-report=term
     
     - name: Upload Coverage
-      uses: codecov/codecov-action@v3
+      if: matrix.python-version == '3.11'
+      uses: codecov/codecov-action@v4
       with:
         file: ./coverage.xml
         flags: unittests
         name: codecov-pywellen-mcp
 
     - name: Build Package
+      if: matrix.python-version == '3.11'
       run: |
+        python -m pip install build
         # Update version with build number for development releases
         if [[ ! "${{ github.ref }}" =~ ^refs/tags/v ]]; then
           sed -i -e "s/version = \"\([0-9][0-9]*\.[0-9][0-9]*\.[0-9][0-9]*\)\"/version = \"\1.dev${GITHUB_RUN_ID}\"/g" pyproject.toml
         fi
-        ./packages/python/bin/python3 -m build .
+        python -m build .
     
     - name: Build Documentation
+      if: matrix.python-version == '3.11'
       run: |
-        ./packages/python/bin/python3 -m pip install sphinx sphinx-rtd-theme myst-parser
-        ./packages/python/bin/sphinx-build -M html ./docs build
-        touch build/html/.nojekyll
+        python -m pip install -e ".[docs]"
+        cd docs && make html
+        touch _build/html/.nojekyll
     
     - name: Upload Package Artifacts
-      uses: actions/upload-artifact@v3
+      if: matrix.python-version == '3.11'
+      uses: actions/upload-artifact@v4
       with:
         name: python-package
         path: dist/
 
     - name: Upload Documentation Artifacts
-      uses: actions/upload-artifact@v3
+      if: matrix.python-version == '3.11'
+      uses: actions/upload-artifact@v4
       with:
         name: documentation
-        path: build/html/
+        path: docs/_build/html/
 
     - name: Publish to PyPI
-      if: startsWith(github.ref, 'refs/tags/v')
+      if: matrix.python-version == '3.11' && startsWith(github.ref, 'refs/tags/v')
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}
 
     - name: Publish Documentation
-      if: startsWith(github.ref, 'refs/heads/master')
+      if: matrix.python-version == '3.11' && github.ref == 'refs/heads/main'
       uses: JamesIves/github-pages-deploy-action@v4.4.1
       with:
         branch: gh-pages
-        folder: build/html
+        folder: docs/_build/html
 
   ci-integration:
     runs-on: ubuntu-latest
     needs: ci-linux
     steps:
     - uses: actions/checkout@v4
 
-    - name: Configure Python
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+    
+    - name: Install Dependencies
       run: |
-        ./bootstrap.sh
-        ./packages/python/bin/python3 -m pip install -e ".[dev]"
+        python -m pip install --upgrade pip
+        python -m pip install -e ".[dev]"
     
     - name: Download Test Waveforms
       run: |
@@ -101,32 +113,37 @@ jobs:
     - name: Run Integration Tests
       run: |
         # Run integration tests when available
-        # ./packages/python/bin/pytest tests/integration/ -v
+        # pytest tests/integration/ -v
         echo "Integration tests would run here"
     
     - name: Performance Benchmarks
       run: |
         # Run performance benchmarks
-        # ./packages/python/bin/python3 scripts/benchmark.py
+        # python scripts/benchmark.py
         echo "Performance benchmarks would run here"
 
   ci-security:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
 
-    - name: Configure Python
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+    
+    - name: Install Dependencies
       run: |
-        ./bootstrap.sh
-        ./packages/python/bin/python3 -m pip install -e ".[dev]"
+        python -m pip install --upgrade pip
+        python -m pip install -e ".[dev]"
     
     - name: Security Scan
       run: |
-        ./packages/python/bin/python3 -m pip install bandit safety
-        ./packages/python/bin/bandit -r src/pywellen_mcp/ -ll || true
-        ./packages/python/bin/safety check || true
+        python -m pip install bandit safety
+        bandit -r src/pywellen_mcp/ -ll || true
+        safety check || true
     
     - name: Dependency Audit
       run: |
-        ./packages/python/bin/python3 -m pip list --format=json | \
-          ./packages/python/bin/python3 -c "import sys,json; [print(p['name']+'=='+p['version']) for p in json.load(sys.stdin)]"
+        python -m pip list --format=json | \
+          python -c "import sys,json; [print(p['name']+'=='+p['version']) for p in json.load(sys.stdin)]"