Review

.github/workflows/ci.yml

@@ -0,0 +1,52 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  build:
+    runs-on: windows-latest
+
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install Miniconda on Windows
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: true
+
+    - name: Create Conda environment
+      run: |
+        conda env create -f environment.yaml
+
+    - name: Activate Conda environment and run tests
+      run: |
+        conda activate MED3pa
+        python -m unittest discover -s tests
+      shell: cmd
+
+    - name: Install dependencies for documentation
+      run: |
+        conda activate MED3pa
+        conda install sphinx sphinx_rtd_theme
+      shell: cmd
+
+    - name: Build documentation
+      run: |
+        conda activate MED3pa
+        cd docs
+        make html
+      shell: cmd

.github/workflows/publish.yml

@@ -0,0 +1,63 @@
+name: Upload Python Package to PyPI and Deploy Documentation to Read the Docs
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  pypi-publish:
+    name: Publish release to PyPI and Deploy Documentation
+    runs-on: ubuntu-latest
+
+    permissions:
+      id-token: write
+      contents: read
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.12"
+
+      - name: Install Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+
+      - name: Initialize Conda
+        run: |
+          conda init bash
+        shell: bash
+
+      - name: Create Conda environment
+        run: |
+          conda env create -f environment.yaml
+
+      - name: Activate Conda environment
+        run: |
+          source ~/.bashrc
+          conda activate MED3pa
+        shell: bash
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools wheel setuptools-scm sphinx sphinx_rtd_theme
+
+      - name: Clean dist directory
+        run: |
+          rm -rf dist/
+
+      - name: Build package
+        run: |
+          python setup.py sdist bdist_wheel  # Could also be python -m build
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://upload.pypi.org/legacy/
+          skip-existing: true
+

.gitignore

@@ -0,0 +1,34 @@
+# Ignore Python bytecode files
+*.pyc
+*.pyo
+__pycache__/
+
+# Ignore Jupyter Notebook checkpoints
+.ipynb_checkpoints/
+
+# Ignore virtual environment directories
+venv/
+env/
+.venv/
+.env/
+
+# Ignore OS-specific files
+.DS_Store
+Thumbs.db
+
+# Ignore IDE-specific files
+.vscode/
+.idea/
+
+# Ignore log files
+*.log
+
+# Ignore specific directories or files
+node_modules/
+dist/
+build/
+
+experiments/
+
+*.MED3paResults
+*.csv