Improve reqs, docs and CI

.gitattributes

@@ -1 +1 @@
-*.ipynb filter=strip-notebook-output  
+*.ipynb filter=strip-notebook-output

.github/actions/build-docs/action.yml

@@ -0,0 +1,40 @@
+name: "Build Documentation"
+description: "Build Sphinx documentation"
+inputs:
+  python-version:
+    description: "Python version to use"
+    required: false
+    default: "3.10"
+  treat-warnings-as-errors:
+    description: "Treat warnings as errors (-W flag)"
+    required: false
+    default: "false"
+runs:
+  using: "composite"
+  steps:
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - name: Install pandoc
+      shell: bash
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y pandoc
+
+    - name: Install Python dependencies
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        pip install ".[docs]"
+
+    - name: Build Sphinx docs
+      shell: bash
+      run: |
+        cd docs
+        if [ "${{ inputs.treat-warnings-as-errors }}" = "true" ]; then
+          sphinx-build -b html -W --keep-going source build/html
+        else
+          sphinx-build -b html source build/html
+        fi

.github/workflows/docs.yml → .github/workflows/publish_docs.yml

@@ -2,7 +2,7 @@ name: Deploy docs to GitHub Pages
 
 on:
   push:
-    branches: ["devel", "main"] # TODO: Set to main only after release
+    branches: ["devel"]
   workflow_dispatch:
 
 permissions:
@@ -25,20 +25,11 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Install pandoc
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y pandoc
-
-      - name: Install Python dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install ".[docs]"
-
-      - name: Build Sphinx docs
-        run: |
-          cd docs
-          make html
+      - name: Build documentation
+        uses: ./.github/actions/build-docs
+        with:
+          python-version: "3.10"
+          treat-warnings-as-errors: "false"
 
       - name: Setup Pages
         uses: actions/configure-pages@v5

.github/workflows/publish.yml → .github/workflows/publish_pypi.yml

@@ -8,6 +8,12 @@ on:
 jobs:
   build-and-publish:
     runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/template-python/
+    permissions:
+      id-token: write
+      contents: read
 
     steps:
       - name: Checkout repository
@@ -21,15 +27,10 @@ jobs:
       - name: Install build tools
         run: |
           python -m pip install --upgrade pip
-          pip install build twine
+          pip install build
 
       - name: Build the package
         run: python -m build
 
-      # Uncomment to publish on pypi
-      #- name: Publish to PyPI
-      #  env:
-      #    TWINE_USERNAME: __token__  # Use API token
-      #    TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
-      #  run: twine upload dist/*
-
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/static_analysis.yml

@@ -15,42 +15,32 @@ defaults:
     shell: bash
 
 jobs:
-  cloc:
+  pre-commit:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout the code
         uses: actions/checkout@v4
 
-      - name: Download and run cloc
-        run: |
-          curl -s https://raw.githubusercontent.com/AlDanial/cloc/master/cloc > cloc
-          chmod +x cloc
-          ./cloc --version
-          ./cloc $(git ls-files)
-
-  black:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout the code
-        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
 
-      - name: Code formatting with black
-        run: |
-          pip install black "black[jupyter]"
-          black --check src/
-          black --check tutorials/
+      - name: Run pre-commit
+        uses: pre-commit/action@v3.0.1
 
-  isort:
+  cloc:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout the code
         uses: actions/checkout@v4
 
-      - name: Code formatting with isort
+      - name: Download and run cloc
         run: |
-          pip install isort
-          isort --check src/
-          isort --check tutorials/
+          curl -s https://raw.githubusercontent.com/AlDanial/cloc/master/cloc > cloc
+          chmod +x cloc
+          ./cloc --version
+          ./cloc $(git ls-files)
 
   mypy:
     runs-on: ubuntu-latest
@@ -59,43 +49,12 @@ jobs:
       - name: Checkout the code
         uses: actions/checkout@v4
 
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
       - name: Type checking with mypy
         run: |
           pip install mypy
           mypy src/ || true
-
-  prospector:
-    runs-on: ubuntu-latest
-    continue-on-error: true
-    steps:
-      - name: Checkout the code
-        uses: actions/checkout@v4
-
-      - name: Code analysis with prospector
-        run: |
-          pip install prospector
-          prospector src/ || true
-
-  ruff:
-    runs-on: ubuntu-latest
-    continue-on-error: true
-    steps:
-      - name: Checkout the code
-        uses: actions/checkout@v4
-
-      - name: Linting with ruff
-        run: |
-          pip install ruff
-          ruff check src/ || true
-
-  pylint:
-    runs-on: ubuntu-latest
-    continue-on-error: true
-    steps:
-      - name: Checkout the code
-        uses: actions/checkout@v4
-
-      - name: Linting with pylint
-        run: |
-          pip install pylint
-          pylint src/ || true

.github/workflows/test_docs.yml

@@ -0,0 +1,36 @@
+name: Test Documentation Build
+
+on:
+  push:
+    branches:
+      - main
+      - devel
+  pull_request:
+    branches:
+      - main
+      - devel
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  test-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Build documentation
+        uses: ./.github/actions/build-docs
+        with:
+          python-version: "3.10"
+          treat-warnings-as-errors: "true"
+
+      - name: Upload docs artifact
+        uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: documentation
+          path: docs/build/html/
+          retention-days: 7

.github/workflows/test_pytest.yml

@@ -0,0 +1,41 @@
+name: Test Pytest
+
+on:
+  push:
+    branches:
+      - main
+      - devel
+  pull_request:
+    branches:
+      - main
+      - devel
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Cache pip
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install project
+        run: |
+          pip install --upgrade pip
+          pip install ".[test]"
+
+      - name: Run tests
+        run: |
+          pytest .

.github/workflows/test_setup_script.yml

@@ -0,0 +1,67 @@
+name: Test Setup Script
+
+on:
+  push:
+    branches:
+      - main
+      - devel
+  pull_request:
+    branches:
+      - main
+      - devel
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  test-setup-script:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Run setup script
+        run: |
+          bash setup_project.sh my-test-app
+
+      - name: Verify changes
+        run: |
+          # Check that src/app was moved to src/my_test_app
+          if [ ! -d "src/my_test_app" ]; then
+            echo "Error: src/my_test_app does not exist"
+            exit 1
+          fi
+
+          # Check that src/app no longer exists
+          if [ -d "src/app" ]; then
+            echo "Error: src/app still exists"
+            exit 1
+          fi
+
+          # Check that template-python was replaced in pyproject.toml
+          if grep -q "template-python" pyproject.toml; then
+            echo "Error: 'template-python' still found in pyproject.toml"
+            exit 1
+          fi
+
+          if ! grep -q "my-test-app" pyproject.toml; then
+            echo "Error: 'my-test-app' not found in pyproject.toml"
+            exit 1
+          fi
+
+          echo "✓ All checks passed!"
+
+      - name: Install project with new name
+        run: |
+          pip install --upgrade pip
+          pip install -e .
+
+      - name: Test renamed command works
+        run: |
+          my-test-app