pyproject.toml, ruff, Python 3.10, update CI (#11)

* pyproject.toml, ruff, Python 3.10, update CI * Fix definition of Python version in tests * Fix ruff errors * Remove internal test * Add audmetric to depednencies * Fix linkcheck on PyPI
audeering · Aug 19, 2024 · e88e04f · e88e04f
1 parent ff7eb5a
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diff --git a/.github/workflows/linter.yml b/.github/workflows/linter.yml
@@ -0,0 +1,29 @@
+name: Linter
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.10'
+
+    - name: Install pre-commit hooks
+      run: |
+        pip install pre-commit
+        pre-commit install --install-hooks
+
+    - name: Code style check via pre-commit
+      run: |
+        pre-commit run --all-files
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -1,4 +1,4 @@
-name: Publish
+name: Publish Python Package
 
 on:
   push:
@@ -8,31 +8,36 @@ on:
 jobs:
   deploy:
     runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      contents: write
+      id-token: write
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}
+
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 2
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.10'
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install build virtualenv
 
     # PyPI package
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        python setup.py sdist bdist_wheel
-        python -m twine upload dist/*
+    - name: Build Python package
+      run: python -m build
 
-    # Docuemntation
+    - name: Publish Python package to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+    # Documentation
     - name: Install doc dependencies
       run: |
         pip install -r requirements.txt
@@ -43,7 +48,7 @@ jobs:
         python -m sphinx docs/ docs/_build/ -b html
 
     - name: Deploy documentation to Github pages
-      uses: peaceiris/actions-gh-pages@v3
+      uses: peaceiris/actions-gh-pages@v4
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: ./docs/_build
@@ -54,20 +59,21 @@ jobs:
       run: |
         # Get bullet points from last CHANGELOG entry
         CHANGELOG=$(git diff -U0 HEAD^ HEAD | grep '^[+][\* ]' | sed 's/\+//')
-        # Support for multiline, see
-        # https://github.com/actions/create-release/pull/11#issuecomment-640071918
-        CHANGELOG="${CHANGELOG//'%'/'%25'}"
-        CHANGELOG="${CHANGELOG//$'\n'/'%0A'}"
-        CHANGELOG="${CHANGELOG//$'\r'/'%0D'}"
         echo "Got changelog: $CHANGELOG"
-        echo "::set-output name=body::$CHANGELOG"
+        # Support for multiline, see
+        # https://docs.github.com/en/actions/using-workflows/workflow-commands-for-github-actions#multiline-strings
+        {
+          echo 'body<<EOF'
+          echo "$CHANGELOG"
+          echo EOF
+        } >> "$GITHUB_OUTPUT"
 
     - name: Create release on Github
       id: create_release
-      uses: actions/create-release@v1
+      uses: softprops/action-gh-release@v2
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       with:
         tag_name: ${{ github.ref }}
-        release_name: Release ${{ github.ref }}
+        name: Release ${{ github.ref_name }}
         body: ${{ steps.changelog.outputs.body }}
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -13,21 +13,24 @@ jobs:
     strategy:
       matrix:
         os: [ ubuntu-latest, macOS-latest, windows-latest ]
-        python-version: [ 3.8 ]
+        python-version: [ "3.10" ]
         tasks: [ tests ]
         include:
           - os: ubuntu-latest
-            python-version: 3.9
+            python-version: "3.8"
             tasks: tests
           - os: ubuntu-latest
-            python-version: 3.8
+            python-version: "3.9"
+            tasks: tests
+          - os: ubuntu-latest
+            python-version: "3.10"
             tasks: docs
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -45,7 +48,7 @@ jobs:
       if: matrix.tasks == 'tests'
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,26 @@
+# Configuration of checks run by pre-commit
+#
+# The tests are executed in the CI pipeline,
+# see CONTRIBUTING.rst for further instructions.
+# You can also run the checks directly at the terminal, e.g.
+#
+# $ pre-commit install
+# $ pre-commit run --all-files
+#
+#
+default_language_version:
+  python: python3.10
+
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.8
+    hooks:
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -1,83 +1,118 @@
 Contributing
 ============
 
-If you would like to add new functionality fell free to create a `pull
-request`_ . If you find errors, omissions, inconsistencies or other things
-that need improvement, please create an issue_.
-Contributions are always welcome!
+Everyone is invited to contribute to this project.
+Feel free to create a `pull request`_ .
+If you find errors,
+omissions,
+inconsistencies,
+or other things
+that need improvement,
+please create an issue_.
+
+.. _issue: https://github.com/audeering/audpsychometric/issues/new/
+.. _pull request: https://github.com/audeering/audpsychometric/compare/
 
-.. _issue:
-    https://github.com/audeering/audpsychometric/issues/new/
-.. _pull request:
-    https://github.com/audeering/audpsychometric/compare/
 
 Development Installation
 ------------------------
 
-Instead of pip-installing the latest release from PyPI, you should get the
-newest development version from Github_::
+Instead of pip-installing the latest release from PyPI_,
+you should get the newest development version from Github_::
+
+   git clone https://github.com/audeering/audpsychometric/
+   cd audpsychometric
+   # Create virtual environment for this project
+   # e.g.
+   # virtualenv --python="python3"  $HOME/.envs/audpsychometric
+   # source $HOME/.envs/audpsychometric/bin/activate
+   pip install -r requirements.txt
+
 
-    git clone https://github.com/audeering/audpsychometric/
-    cd audpsychometric
-    # Use virtual environment
-    pip install -r requirements.txt
+This way,
+your installation always stays up-to-date,
+even if you pull new changes from the Github repository.
 
+.. _PyPI: https://pypi.org/project/audpsychometric/
 .. _Github: https://github.com/audeering/audpsychometric/
 
-This way, your installation always stays up-to-date,
-even if you pull new changes
-from the repository.
 
-Building the Documentation
---------------------------
+Coding Convention
+-----------------
 
-If you make changes to the documentation, you can re-create the HTML pages
-using Sphinx_.
-You can install it and a few other necessary packages with::
+We follow the PEP8_ convention for Python code
+and use ruff_ as a linter and code formatter.
+In addition,
+we check for common spelling errors with codespell_.
+Both tools and possible exceptions
+are defined in :file:`pyproject.toml`.
 
-    pip install -r requirements.txt
-    pip install -r docs/requirements.txt
+The checks are executed in the CI using `pre-commit`_.
+You can enable those checks locally by executing::
 
-To create the HTML pages, use::
+    pip install pre-commit  # consider system wide installation
+    pre-commit install
+    pre-commit run --all-files
+
+Afterwards ruff_ and codespell_ are executed
+every time you create a commit.
 
-	python -m sphinx docs/ build/sphinx/html -b html
+You can also install ruff_ and codespell_
+and call it directly::
 
-The generated files will be available in the directory ``build/sphinx/html/``.
+    pip install ruff codespell  # consider system wide installation
+    ruff check --fix .  # lint all Python files, and fix any fixable errors
+    ruff format .  # format code of all Python files
+    codespell
 
-.. Note::
+It can be restricted to specific folders::
 
-    During the default building of the documentation
-    Jupyter notebooks are not executed to save time.
+    ruff check audfoo/ tests/
+    codespell audfoo/ tests/
 
-To execute the notebooks as well, copy and paste
-the following into your terminal and press the enter key::
 
-    python -m sphinx -W docs/ \
-        -D nbsphinx_execute='always' \
-        -d build/sphinx/doctrees \
-        build/sphinx/html \
-        -b html
+.. _codespell: https://github.com/codespell-project/codespell/
+.. _PEP8: http://www.python.org/dev/peps/pep-0008/
+.. _pre-commit: https://pre-commit.com
+.. _ruff: https://beta.ruff.rs
+
+
+Building the Documentation
+--------------------------
+
+If you make changes to the documentation,
+you can re-create the HTML pages using Sphinx_.
+You can install it and a few other necessary packages with::
+
+   pip install -r docs/requirements.txt
+
+To create the HTML pages, use::
+
+   python -m sphinx docs/ build/sphinx/html -b html
+
+The generated files will be available
+in the directory :file:`build/sphinx/html/`.
 
 It is also possible to automatically check if all links are still valid::
 
-    python -m sphinx docs/ build/sphinx/linkcheck -b linkcheck
+   python -m sphinx docs/ build/sphinx/html -b linkcheck
+
+.. _Sphinx: http://sphinx-doc.org
 
-.. _Sphinx: http://sphinx-doc.org/
 
 Running the Tests
 -----------------
 
 You'll need pytest_ for that.
 It can be installed with::
 
-    pip install -r tests/requirements.txt
+   pip install -r tests/requirements.txt
 
 To execute the tests, simply run::
 
-    python -m pytest
+   python -m pytest
 
-.. _pytest:
-    https://pytest.org/
+.. _pytest: https://pytest.org
 
 
 Creating a New Release
@@ -87,5 +122,5 @@ New releases are made using the following steps:
 
 #. Update ``CHANGELOG.rst``
 #. Commit those changes as "Release X.Y.Z"
-#. Create an (annotated) tag with ``git tag -a vX.Y.Z``
+#. Create an (annotated) tag with ``git tag -a X.Y.Z``
 #. Push the commit and the tag to Github
diff --git a/audpsychometric/__init__.py b/audpsychometric/__init__.py
@@ -16,24 +16,19 @@
 
 """
 import audpsychometric.core
-import audpsychometric.core.reliability
 from audpsychometric.core import datasets
-from audpsychometric.core.gold_standard import (
-    evaluator_weighted_estimator,
-    rater_confidence_pearson,
-    gold_standard_mean,
-    gold_standard_median,
-    gold_standard_mode,
-)
-from audpsychometric.core.reliability import (
-    congeneric_reliability,
-    cronbachs_alpha,
-    intra_class_correlation
-)
-
-from audpsychometric.core.datasets import (
-    list_datasets,
-    read_dataset)
+from audpsychometric.core.datasets import list_datasets
+from audpsychometric.core.datasets import read_dataset
+from audpsychometric.core.gold_standard import evaluator_weighted_estimator
+from audpsychometric.core.gold_standard import gold_standard_mean
+from audpsychometric.core.gold_standard import gold_standard_median
+from audpsychometric.core.gold_standard import gold_standard_mode
+from audpsychometric.core.gold_standard import rater_confidence_pearson
+import audpsychometric.core.reliability
+from audpsychometric.core.reliability import congeneric_reliability
+from audpsychometric.core.reliability import cronbachs_alpha
+from audpsychometric.core.reliability import intra_class_correlation
+
 
 # Disencourage from audpsychometric import *
 __all__ = []

diff --git a/audpsychometric/core/__init__.py b/audpsychometric/core/__init__.py
@@ -1,3 +0,0 @@
-"""
-The core module
-"""