Merge branch 'main' into some-devops

Author: drbenvincent

.github/workflows/ci.yml

@@ -7,31 +7,16 @@ on:
     branches: [main]
 
 jobs:
-  lint:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.8", "3.9", "3.10"]
-
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Run lint
-        uses: pre-commit/action@v3.0.0
-
   test:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v3
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
       - name: Run doctests

.github/workflows/release.yml

@@ -12,12 +12,12 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.11
       - name: Build the sdist and the wheel
         run: |
           pip install build
@@ -27,7 +27,7 @@ jobs:
           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__)"
           cd ..
@@ -40,7 +40,7 @@ jobs:
           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__)"
           cd ..
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v3
         with:
           name: artifact
           path: dist/*
@@ -60,9 +60,9 @@ jobs:
           user: __token__
           password: ${{ secrets.TEST_PYPI_API_TOKEN }}
           repository_url: https://test.pypi.org/legacy/
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v4
         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,

.pre-commit-config.yaml

@@ -1,23 +1,36 @@
+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/lucianopaz/head_of_apache
+    rev: "0.0.3"
+    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: v4.4.0
+    rev: v4.6.0
     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
-        args: ['--maxkb=1500']
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.1.4
+        args: ["--maxkb=1500"]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.3
     hooks:
       - id: ruff
+        args: ["--fix", "--output-format=full"]
       - id: ruff-format
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.0
+    rev: 1.8.5
     hooks:
       - id: nbqa-ruff
   - repo: https://github.com/econchick/interrogate

causalpy/__init__.py

@@ -1,3 +1,16 @@
+#   Copyright 2024 The PyMC Labs Developers
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
 import arviz as az
 
 from causalpy import pymc_experiments, pymc_models, skl_experiments, skl_models

causalpy/custom_exceptions.py

@@ -1,3 +1,16 @@
+#   Copyright 2024 The PyMC Labs Developers
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
 """
 Custom Exceptions for CausalPy.
 """

causalpy/data/__init__.py

@@ -1,4 +1,18 @@
+#   Copyright 2024 The PyMC Labs Developers
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
 """Code for loading datasets."""
+
 from .datasets import load_data
 
 __all__ = ["load_data"]

causalpy/data/datasets.py

@@ -1,6 +1,20 @@
+#   Copyright 2024 The PyMC Labs Developers
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
 """
 Functions to load example datasets
 """
+
 import pathlib
 
 import pandas as pd

causalpy/data/simulate_data.py

@@ -1,6 +1,20 @@
+#   Copyright 2024 The PyMC Labs Developers
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
 """
 Functions that generate data sets used in examples
 """
+
 import numpy as np
 import pandas as pd
 from scipy.stats import dirichlet, gamma, norm, uniform

causalpy/data_validation.py

@@ -1,3 +1,16 @@
+#   Copyright 2024 The PyMC Labs Developers
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
 import warnings  # noqa: I001
 
 import pandas as pd

causalpy/plot_utils.py

@@ -1,3 +1,16 @@
+#   Copyright 2024 The PyMC Labs Developers
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
 """
 Plotting utility functions.
 """