adding vs module

.github/workflows/ci.yml

@@ -7,39 +7,34 @@ on:
     branches: [main]
 
 jobs:
-  lint:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.8", "3.9", "3.10"]
-
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Run lint
-        uses: pre-commit/[email protected]
-
   test:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.11", "3.12", "3.13"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Update pip and setuptools
+        run: pip install --upgrade pip setuptools
+      - name: Setup environment
+        run: pip install -e .[test]
+      - name: Run doctests
+        run: pytest --doctest-modules --ignore=causalpy/tests/ causalpy/ --config-file=causalpy/tests/conftest.py
+      - name: Run extra tests
+        run: pytest docs/source/.codespell/test_notebook_to_markdown.py
       - name: Run tests
+        run: pytest --cov-report=xml --no-cov-on-fail
+      - name: Check codespell for notebooks
         run: |
-          pip install -e .[test]
-          pytest --cov-report=xml --no-cov-on-fail
+          python ./docs/source/.codespell/notebook_to_markdown.py --tempdir tmp_markdown
+          codespell
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
           name: ${{ matrix.python-version }}

.github/workflows/label-precommit-prs.yml

@@ -0,0 +1,18 @@
+name: Label Pre-Commit PRs
+
+on:
+  pull_request:
+    types: [opened, synchronize]
+
+jobs:
+  label:
+    if: github.actor == 'pre-commit-ci[bot]'
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
+    steps:
+      - name: Add "no releasenotes" label
+        uses: actions-ecosystem/action-add-labels@v1
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          labels: no releasenotes

.github/workflows/release.yml

@@ -1,5 +1,7 @@
 name: PyPI release
+
 on:
+  workflow_dispatch:
   pull_request:
     branches: [main]
   push:
@@ -12,57 +14,59 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.11
       - name: Build the sdist and the wheel
         run: |
           pip install build
           python -m build
+          ls dist  # List the contents of the dist directory
       - name: Check the sdist installs and imports
         run: |
           mkdir -p test-sdist
           cd test-sdist
           python -m venv venv-sdist
-          venv-sdist/bin/python -m pip install ../dist/CausalPy*.tar.gz
+          venv-sdist/bin/python -m pip install ../dist/causalpy*.tar.gz
           echo "Checking import and version number (on release)"
-          venv-sdist/bin/python -c "import causalpy; assert causalpy.__version__ == '${{  github.ref_name }}' if '${{ github.ref_type }}' == 'tag' else causalpy.__version__; print(causalpy.__version__)"
+          venv-sdist/bin/python -c "import causalpy; assert causalpy.__version__ == '${{ github.ref_name }}' if '${{ github.ref_type }}' == 'tag' else causalpy.__version__; print(causalpy.__version__)"
           cd ..
       - name: Check the bdist installs and imports
         run: |
           mkdir -p test-bdist
           cd test-bdist
           python -m venv venv-bdist
-          venv-bdist/bin/python -m pip install ../dist/CausalPy*.whl
+          venv-bdist/bin/python -m pip install ../dist/causalpy*.whl
           echo "Checking import and version number (on release)"
-          venv-bdist/bin/python -c "import causalpy; assert causalpy.__version__ == '${{  github.ref_name }}' if '${{ github.ref_type }}' == 'tag' else causalpy.__version__; print(causalpy.__version__)"
+          venv-bdist/bin/python -c "import causalpy; assert causalpy.__version__ == '${{ github.ref_name }}' if '${{ github.ref_type }}' == 'tag' else causalpy.__version__; print(causalpy.__version__)"
           cd ..
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: artifact
           path: dist/*
+
   test:
     name: Upload to Test PyPI
+    permissions:
+      id-token: write
     needs: [build]
     runs-on: ubuntu-latest
     if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: artifact
           path: dist
       - uses: pypa/gh-action-pypi-publish@release/v1
         with:
           skip_existing: true
-          user: __token__
-          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
           repository_url: https://test.pypi.org/legacy/
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.11
       - name: Test pip install from test.pypi
         run: |
           # Give time to test.pypi to update its index. If we don't wait,
@@ -71,19 +75,19 @@ jobs:
           python -m venv venv-test-pypi
           venv-test-pypi/bin/python -m pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple causalpy
           echo "Checking import and version number"
-          venv-test-pypi/bin/python -c "import causalpy; assert causalpy.__version__ == '${{  github.ref_name }}'"
+          venv-test-pypi/bin/python -c "import causalpy; assert causalpy.__version__ == '${{ github.ref_name }}'"
 
   publish:
+    environment: release
+    permissions:
+      id-token: write
     name: Upload release to PyPI
     needs: [build, test]
     runs-on: ubuntu-latest
     if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: artifact
           path: dist
       - uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/rtd-link-preview.yml

@@ -0,0 +1,16 @@
+name: Read the Docs Pull Request Preview
+on:
+  pull_request_target:
+    types:
+      - opened
+
+permissions:
+  pull-requests: write
+
+jobs:
+  documentation-links:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: readthedocs/actions/preview@v1
+        with:
+          project-slug: "causalpy"

.github/workflows/uml.yml

@@ -0,0 +1,73 @@
+name: Update the UML Diagrams
+on:
+  workflow_dispatch:
+  schedule:
+    - cron:  '0 12 * * 1'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions: write-all
+    steps:
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          ref: main
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install 'causalpy[docs]'
+          sudo apt-get update && sudo apt-get install -y graphviz
+
+      - name: Install pylint explicitly
+        run: python -m pip install pylint
+
+      - name: Verify pylint and pyreverse
+        run: |
+          python -m pip show pylint
+          which pyreverse
+          pyreverse --version
+
+      - name: Configure Git Identity
+        run: |
+          git config user.name 'github-actions[bot]'
+          git config user.email 'github-actions[bot]@users.noreply.github.com'
+
+      - name: Update the UML Diagrams
+        run: |
+          make uml
+
+      - name: Detect UML changes
+        id: changes
+        run: |
+          git add docs/source/_static/*.png
+          if git diff --staged --exit-code; then
+            echo "No changes to commit"
+            echo "changes_exist=false" >> $GITHUB_OUTPUT
+          else
+            echo "changes_exist=true" >> $GITHUB_OUTPUT
+          fi
+
+      - name: Create PR for changes
+        if: steps.changes.outputs.changes_exist == 'true'
+        run: |
+          git checkout -b update-uml-diagrams
+          git commit -m "Update UML Diagrams"
+          git push -u origin update-uml-diagrams
+          gh pr create \
+            --base main \
+            --title "Update UML Diagrams" \
+            --body "This PR updates the UML diagrams
+            This PR was created automatically by the [UML workflow](https://github.com/pymc-labs/CausalPy/blob/main/.github/workflows/uml.yml).
+            See the logs [here](https://github.com/pymc-labs/CausalPy/actions/workflows/uml.yml) for more details." \
+            --label "no releasenotes" \
+            --reviewer drbenvincent
+        env:
+          GH_TOKEN: ${{ github.token }}

.gitignore

@@ -6,6 +6,11 @@ _build
 *.egg-info
 build/
 dist/
-docs/_build/
 *.vscode
 .coverage
+*.jupyterlab-workspace
+
+# Sphinx documentation
+docs/build/
+docs/jupyter_execute/
+docs/source/api/generated/

.pre-commit-config.yaml

@@ -1,42 +1,57 @@
+ci:
+  autofix_prs: false
+
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
-    - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.4.0
-      hooks:
-          - id: trailing-whitespace
-            exclude_types: [svg]
-          - id: end-of-file-fixer
-            exclude_types: [svg]
-          - id: check-yaml
-          - id: check-added-large-files
-    - repo: https://github.com/pycqa/isort
-      rev: 5.12.0
-      hooks:
-          - id: isort
-            args: [--profile, black]
-            types: [python]
-    - repo: https://github.com/ambv/black
-      rev: 23.3.0
-      hooks:
-          - id: black
-    - repo: https://github.com/pycqa/flake8
-      rev: 6.0.0
-      hooks:
-          - id: flake8
-    - repo: https://github.com/nbQA-dev/nbQA
-      rev: 1.7.0
-      hooks:
-        - id: nbqa-black
-          # additional_dependencies: [jupytext]  # optional, only if you're using Jupytext
-        - id: nbqa-pyupgrade
-          args: ["--py37-plus"]
-        - id: nbqa-isort
-          args: ["--float-to-top"]
-    - repo: https://github.com/econchick/interrogate
-      rev: 1.5.0
-      hooks:
-          - id: interrogate
-            # needed to make excludes in pyproject.toml work
-            # see here https://github.com/econchick/interrogate/issues/60#issuecomment-735436566
-            pass_filenames: false
+  - repo: https://github.com/lucianopaz/head_of_apache
+    rev: "0.1.1"
+    hooks:
+      - id: head_of_apache
+        args:
+          - --author=The PyMC Labs Developers
+          - --exclude=docs/
+          - --exclude=scripts/
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: debug-statements
+      - id: trailing-whitespace
+        exclude_types: [svg]
+      - id: end-of-file-fixer
+        exclude_types: [svg]
+      - id: check-yaml
+      - id: check-added-large-files
+        exclude: &exclude_pattern '(iv_weak_instruments|its_lift_test)\.ipynb'
+        args: ["--maxkb=1500"]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.5
+    hooks:
+      # Run the linter
+      - id: ruff
+        types_or: [ python, pyi, jupyter ]
+        args: [ --fix ]
+      # Run the formatter
+      - id: ruff-format
+        types_or: [ python, pyi, jupyter ]
+  - repo: https://github.com/econchick/interrogate
+    rev: 1.7.0
+    hooks:
+      - id: interrogate
+        # needed to make excludes in pyproject.toml work
+        # see here https://github.com/econchick/interrogate/issues/60#issuecomment-735436566
+        pass_filenames: false
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.4.1
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          # Support pyproject.toml configuration
+          - tomli
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.18.2
+    hooks:
+      - id: mypy
+        args: [--ignore-missing-imports]
+        files: ^causalpy/
+        additional_dependencies: [numpy>=1.20, pandas-stubs]

.readthedocs.yaml

@@ -7,9 +7,9 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-lts-latest
   tools:
-    python: "3.10"
+    python: "3.11"
     # You can also specify other tool versions:
     # nodejs: "16"
     # rust: "1.55"