Feature/add precommit hooks

.github/workflows/codeql-analysis.yml

@@ -2,10 +2,10 @@ name: "CodeQL"
 
 on:
   push:
-    branches: [ main, develop ]
+    branches: [main, develop]
   pull_request:
     # The branches below must be a subset of the branches above
-    branches: [ main, develop ]
+    branches: [main, develop]
   schedule:
     - cron: '34 21 * * 1'
 
@@ -17,40 +17,40 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        language: [ 'python' ]
+        language: ['python']
         # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python' ]
         # Learn more:
         # https://docs.github.com/en/free-pro-team@latest/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#changing-the-languages-that-are-analyzed
 
     steps:
-    - name: Checkout repository
-      uses: actions/checkout@v2
-
-    # Initializes the CodeQL tools for scanning.
-    - name: Initialize CodeQL
-      uses: github/codeql-action/init@v1
-      with:
-        languages: ${{ matrix.language }}
-        # If you wish to specify custom queries, you can do so here or in a config file.
-        # By default, queries listed here will override any specified in a config file.
-        # Prefix the list here with "+" to use these queries and those in the config file.
-        # queries: ./path/to/local/query, your-org/your-repo/queries@main
-
-    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
-    # If this step fails, then you should remove it and run the build manually (see below)
-    - name: Autobuild
-      uses: github/codeql-action/autobuild@v1
-
-    # ℹ️ Command-line programs to run using the OS shell.
-    # 📚 https://git.io/JvXDl
-
-    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
-    #    and modify them (or add more) to build your code if your project
-    #    uses a compiled language
-
-    #- run: |
-    #   make bootstrap
-    #   make release
-
-    - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v1
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      # Initializes the CodeQL tools for scanning.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v1
+        with:
+          languages: ${{ matrix.language }}
+          # If you wish to specify custom queries, you can do so here or in a config file.
+          # By default, queries listed here will override any specified in a config file.
+          # Prefix the list here with "+" to use these queries and those in the config file.
+          # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+      # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+      # If this step fails, then you should remove it and run the build manually (see below)
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v1
+
+      # ℹ️ Command-line programs to run using the OS shell.
+      # 📚 https://git.io/JvXDl
+
+      # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+      #    and modify them (or add more) to build your code if your project
+      #    uses a compiled language
+
+      #- run: |
+      #   make bootstrap
+      #   make release
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v1

.github/workflows/python-publish.yml

@@ -12,9 +12,6 @@ on:
   # normal behavior: run when a new release is created
   release:
     types: [published]
-  # allow running manually on main
-  workflow_dispatch:
-    branches: [main]
 
 permissions:
   contents: read
@@ -27,19 +24,19 @@ jobs:
       name: pypi
       url: https://pypi.org/project/viapy/
     permissions:
-      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.11'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install build
-    - name: Build package
-      run: python -m build
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@release/v1
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build package
+        run: python -m build
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/unit_tests.yml

@@ -3,7 +3,7 @@ name: unit tests
 on:
   push: # run on all branches
   pull_request:
-    - branches: [develop, main]
+    branches: [develop, main]
   schedule: # run automatically on main branch each Tuesday at 11am
     - cron: "0 16 * * 2"
 
@@ -20,25 +20,23 @@ jobs:
         uses: actions/checkout@v6
 
       - name: Install uv and Python version
-        uses: astral-sh/setup@v7
+        uses: astral-sh/setup-uv@v7
         with:
           python-version: ${{ matrix.python }}
 
       - name: Install package dependencies
-        run: |
-          {
-            if [ "${{ matrix.django }}" -gt "0" ]
-            then
-              uv add django==${{ matrix.django }}
-              uv sync --extra test --extra django_test
-            else
-              uv sync --extra test
-          }
+        run: >-
+          if [ "${{ matrix.django }}" -gt "0" ]; then
+            uv add django=="${{ matrix.django }}";
+            uv sync --extra test --extra django_test;
+          else
+            uv sync --extra test;
+          fi
 
       - name: Setup test settings
         run: |
           cp ci/testsettings.py testsettings.py
-          python -c "import uuid; print('SECRET_KEY = \'%s\'' % uuid.uuid4())" >> testsettings.py
+          uv run python -c "import uuid; print('SECRET_KEY = \'%s\'' % uuid.uuid4())" >> testsettings.py
 
       - name: Run pytest
         run: uv run pytest --cov=viapy --cov=tests --cov-report=xml --cov-report=term

.pre-commit-config.yaml

@@ -0,0 +1,55 @@
+# This config file specifies which pre-commit hooks to run.
+#
+# To set up, run `pre-commit install`
+# To run all hooks manually, run `pre-commit run --all-files`
+repos:
+  # Ruff Python linter and formatter (configs in pyproject.toml)
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.12.7
+    hooks:
+      # Run the linter
+      - id: ruff-check
+        args: [--fix, --show-fixes] # enable lint fixes
+      # Run the formatter
+      - id: ruff-format
+  # yamlfmt for formatting YAML files
+  - repo: https://github.com/google/yamlfmt
+    rev: v0.17.2
+    hooks:
+      - id: yamlfmt
+  # Codespell for spell checking
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.4.1
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli
+        exclude_types: ["css", "html", "javascript", "json"]
+  # Some out-of-the-box file checks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      # Check for files with merge conflict strings
+      - id: check-merge-conflict
+      # Verify syntax of TOML files
+      - id: check-toml
+      # Verify syntax of YAML files
+      - id: check-yaml
+        args: [--unsafe]
+      # Verifies that test files begin with test_
+      - id: name-tests-test
+        args: [--pytest-test-first]
+      # Removes trailing whitespace from all files
+      - id: trailing-whitespace
+        exclude: "docs/"
+  # Check uv.lock file is up to date
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    # uv version.
+    rev: 0.8.6
+    hooks:
+      - id: uv-lock
+  # Validate GitHub Actions workflow files
+  - repo: https://github.com/mpalmer/action-validator
+    rev: v0.8.0
+    hooks:
+      - id: action-validator

CHANGELOG.rst

@@ -15,7 +15,7 @@ CHANGELOG
 * Handle negative years when parsing birth and death dates
 * Now tested on python 3.9 through 3.12
 * Now tested against Django 3.2 through 5.0
-* Migrate continous integration to GitHub Actions
+* Migrate continuous integration to GitHub Actions
 
 0.2
 ---

README.rst

@@ -19,15 +19,15 @@ django-autocomplete-light lookup view and a VIAF url widget.
 
 .. image:: https://codecov.io/gh/Princeton-CDH/viapy/branch/master/graph/badge.svg
     :target: https://codecov.io/gh/Princeton-CDH/viapy/branch/master
-    :alt: Code coverage  
+    :alt: Code coverage
 
 .. image:: https://www.codefactor.io/repository/github/princeton-cdh/viapy/badge
    :target: https://www.codefactor.io/repository/github/princeton-cdh/viapy
    :alt: CodeFactor
 
 .. image:: https://img.shields.io/pypi/pyversions/viapy
    :alt: PyPI - Python Version
-   
+
 .. image:: https://img.shields.io/pypi/djversions/viapy
    :alt: PyPI - Django Version
 
@@ -80,7 +80,7 @@ and a tool of your choice for creating python virtual environments
 
 Initial setup and installation:
 
-* Install ``uv`` if it's not installed. 
+* Install ``uv`` if it's not installed.
   It can be installed via PyPi, Homebrew, or a standalone installer.
   See uv's `installation documentation <https://docs.astral.sh/uv/getting-started/installation>`_
   for more details.

ci/testsettings.py

@@ -8,15 +8,14 @@
 
 INSTALLED_APPS = (
     # 'django.contrib.contenttypes',
-    'dal',
-    'dal_select2',
-    'viapy',
+    "dal",
+    "dal_select2",
+    "viapy",
 )
 
-ROOT_URLCONF = 'viapy.test_urls'
+ROOT_URLCONF = "viapy.test_urls"
 
-LANGUAGE_CODE = 'en-us'
+LANGUAGE_CODE = "en-us"
 
 # must be added
 # SECRET_KEY = ''
-

pyproject.toml

@@ -57,12 +57,19 @@ django = ["django>=3.2", "django-autocomplete-light"]
 django_test = ["pytest-django", "viapy[django]"]
 docs = ["sphinx"]
 test_all = ["viapy[test]", "viapy[django_test]"]
-dev = ["pre-commit", "viapy[django]", "viapy[test_all]", "viapy[docs]"]
+dev = [
+  "ruff",
+  "pre-commit",
+  "viapy[django]",
+  "viapy[test_all]",
+  "viapy[docs]"
+]
 
 [dependency-groups]
 dev = ["viapy[dev]"]
 
-[tool.pytest]
+[tool.pytest.ini_options]
+# Need to use ini_options for Python 3.9
 testpaths = ["tests"]
 pythonpath = ["."]
 DJANGO_SETTINGS_MODULE = "testsettings"
@@ -80,3 +87,19 @@ exclude_lines = [
 
 [tool.coverage.html]
 directory = "coverage_html_report"
+
+[tool.ruff.lint]
+# Include these rules in addition to ruff's defaults
+extend-select = [
+  "B",    # flake8-bugbear
+  "C4",   # flake8-comprehensions
+  "I",    #isort
+  "NPY",  # numpy-specific rules
+  "PERF", # perflint
+  "PTH",  # flake8-use-pathlib
+  "RUF",  # ruff-specific rules
+  "SIM",  # flake8-simplify
+  "UP",   # pyupgrade
+]
+# Can use to ignore specific rules within above selection
+ignore = []

sphinx-docs/conf.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 #
 # viapy documentation build configuration file, created by
 # sphinx-quickstart on Thu Oct 12 17:06:23 2017.
@@ -15,23 +14,25 @@
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
+# documentation root, use pathlib.Path.resolve to make it absolute, like shown here.
 #
-# import os
+# import pathlib
 # import sys
-# sys.path.insert(0, os.path.abspath('.'))
+# sys.path.insert(0, pathlib.Path().resolve())
 
 import os
+import pathlib
 import sys
+
 import django
 
-sys.path.insert(0, os.path.abspath("."))
+from viapy import __version__
+
+sys.path.insert(0, pathlib.Path().resolve())
 
 os.environ["DJANGO_SETTINGS_MODULE"] = "docsettings"
 django.setup()
 
-from viapy import __version__
-
 
 # -- General configuration ------------------------------------------------
 

sphinx-docs/docsettings.py

@@ -8,14 +8,13 @@
 
 INSTALLED_APPS = (
     # 'django.contrib.contenttypes',
-    'dal',
-    'dal_select2',
-    'viapy',
+    "dal",
+    "dal_select2",
+    "viapy",
 )
 
-ROOT_URLCONF = 'viapy.test_urls'
+ROOT_URLCONF = "viapy.test_urls"
 
-LANGUAGE_CODE = 'en-us'
-
-SECRET_KEY = 'f$J4FB3B=}1bFtJ$}b9s28Vsf?&otV}o0*V)g;#OD5%20uksel'
+LANGUAGE_CODE = "en-us"
 
+SECRET_KEY = "f$J4FB3B=}1bFtJ$}b9s28Vsf?&otV}o0*V)g;#OD5%20uksel"