feat: add pre-commit setup with gitlint
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17 changed files with 1197 additions and 360 deletions
54
.pre-commit-config.yaml
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54
.pre-commit-config.yaml
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@ -0,0 +1,54 @@
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# Pre-commit configuration for doi2dataset
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# See https://pre-commit.com for more information
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# See https://pre-commit.com/hooks.html for more hooks
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repos:
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# Built-in pre-commit hooks
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.6.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-yaml
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- id: check-added-large-files
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- id: check-merge-conflict
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- id: check-json
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- id: check-toml
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- id: mixed-line-ending
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args: ['--fix=lf']
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# Python code formatting and linting
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.6.9
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hooks:
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- id: ruff
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args: [--fix, --exit-non-zero-on-fix]
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- id: ruff-format
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# Git commit message linting with gitlint
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- repo: https://github.com/jorisroovers/gitlint
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rev: v0.19.1
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hooks:
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- id: gitlint
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stages: [commit-msg]
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# Optional: Check for common security issues
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- repo: https://github.com/PyCQA/bandit
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rev: 1.7.10
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hooks:
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- id: bandit
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args: ["-c", "pyproject.toml"]
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additional_dependencies: ["bandit[toml]"]
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# Configuration for specific hooks
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ci:
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autofix_commit_msg: |
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[pre-commit.ci] auto fixes from pre-commit hooks
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for more information, see https://pre-commit.ci
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autofix_prs: true
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autoupdate_branch: ''
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autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
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autoupdate_schedule: weekly
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skip: []
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submodules: false
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94
README.md
94
README.md
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@ -152,6 +152,73 @@ Documentation is automatically built and deployed via GitLab CI/CD:
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- Deployed to GitLab Pages
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- Accessible at your project's Pages URL
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## Git Commit Message Linting
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This project uses [gitlint](https://jorisroovers.github.io/gitlint/) to enforce consistent commit message formatting. Commit messages should follow the [Conventional Commits](https://www.conventionalcommits.org/) specification.
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### Commit Message Format
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Commit messages must follow this format:
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```
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<type>(<scope>): <description>
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[optional body]
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[optional footer(s)]
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```
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**Types:**
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- `feat`: A new feature
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- `fix`: A bug fix
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- `docs`: Documentation only changes
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- `style`: Changes that do not affect the meaning of the code
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- `refactor`: A code change that neither fixes a bug nor adds a feature
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- `test`: Adding missing tests or correcting existing tests
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- `chore`: Changes to the build process or auxiliary tools
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- `ci`: Changes to CI configuration files and scripts
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- `build`: Changes that affect the build system or dependencies
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- `perf`: A code change that improves performance
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- `revert`: Reverts a previous commit
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**Examples:**
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```
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feat(api): add support for DOI batch processing
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fix(metadata): handle missing author information gracefully
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docs: update installation instructions
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test(citation): add tests for license processing
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```
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### Linting Commit Messages
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To lint commit messages, use the provided script:
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```bash
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# Lint the last commit
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python scripts/lint-commit.py
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# Lint a specific commit
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python scripts/lint-commit.py --hash <commit-hash>
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# Lint a range of commits
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python scripts/lint-commit.py --range HEAD~3..
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# Install as a git hook (optional)
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python scripts/lint-commit.py --install-hook
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```
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### Git Hook Installation
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You can optionally install a git hook that automatically checks commit messages:
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```bash
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python scripts/lint-commit.py --install-hook
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```
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This will create a `commit-msg` hook that runs automatically when you commit, ensuring all commit messages follow the required format.
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## Testing
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Tests are implemented with pytest. The test suite provides comprehensive coverage of core functionalities. To run the tests, execute:
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@ -270,6 +337,33 @@ This version has been updated to make the tool more generalized and suitable for
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Contributions are welcome! Please fork the repository and submit a pull request with your improvements.
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### Development Setup
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1. Install development dependencies:
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```bash
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pip install -r requirements-dev.txt
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```
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2. Run tests to ensure everything works:
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```bash
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pytest
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```
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3. Install the git commit message hook (recommended):
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```bash
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python scripts/lint-commit.py --install-hook
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```
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### Code Quality
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- Follow the existing code style and formatting
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- Write tests for new functionality
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- Ensure all tests pass before submitting
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- Use meaningful commit messages following the conventional commits format
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- Run `python scripts/lint-commit.py` to validate commit messages
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## License
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This project is licensed under the MIT License. See the [LICENSE.md](LICENSE.md) file for details.
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@ -1,47 +1,47 @@
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@ECHO OFF
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pushd %~dp0
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REM Command file for Sphinx documentation
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if "%SPHINXBUILD%" == "" (
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set SPHINXBUILD=sphinx-build
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)
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set SOURCEDIR=source
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set BUILDDIR=build
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%SPHINXBUILD% >NUL 2>NUL
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if errorlevel 9009 (
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echo.
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echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
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echo.installed, then set the SPHINXBUILD environment variable to point
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echo.to the full path of the 'sphinx-build' executable. Alternatively you
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echo.may add the Sphinx directory to PATH.
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echo.
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echo.If you don't have Sphinx installed, grab it from
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echo.https://www.sphinx-doc.org/
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exit /b 1
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)
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if "%1" == "" goto help
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if "%1" == "multiversion" goto multiversion
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if "%1" == "multiversion-clean" goto multiversion-clean
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%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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goto end
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:multiversion
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sphinx-multiversion %SOURCEDIR% %BUILDDIR%\multiversion\html %SPHINXOPTS% %O%
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goto end
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:multiversion-clean
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rmdir /s /q %BUILDDIR%\html 2>nul
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sphinx-multiversion %SOURCEDIR% %BUILDDIR%\multiversion\html %SPHINXOPTS% %O%
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goto end
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:help
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%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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:end
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popd
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@ECHO OFF
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pushd %~dp0
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REM Command file for Sphinx documentation
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if "%SPHINXBUILD%" == "" (
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set SPHINXBUILD=sphinx-build
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)
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set SOURCEDIR=source
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set BUILDDIR=build
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%SPHINXBUILD% >NUL 2>NUL
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if errorlevel 9009 (
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echo.
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echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
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echo.installed, then set the SPHINXBUILD environment variable to point
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echo.to the full path of the 'sphinx-build' executable. Alternatively you
|
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echo.may add the Sphinx directory to PATH.
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echo.
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echo.If you don't have Sphinx installed, grab it from
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echo.https://www.sphinx-doc.org/
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exit /b 1
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)
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if "%1" == "" goto help
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if "%1" == "multiversion" goto multiversion
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if "%1" == "multiversion-clean" goto multiversion-clean
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%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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goto end
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:multiversion
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sphinx-multiversion %SOURCEDIR% %BUILDDIR%\multiversion\html %SPHINXOPTS% %O%
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goto end
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:multiversion-clean
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rmdir /s /q %BUILDDIR%\html 2>nul
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sphinx-multiversion %SOURCEDIR% %BUILDDIR%\multiversion\html %SPHINXOPTS% %O%
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goto end
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:help
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%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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:end
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popd
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229
docs/source/commit-messages.rst
Normal file
229
docs/source/commit-messages.rst
Normal file
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@ -0,0 +1,229 @@
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Git Commit Message Linting
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===========================
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This project uses `gitlint <https://jorisroovers.github.io/gitlint/>`_ to enforce consistent commit message formatting. All commit messages must follow the `Conventional Commits <https://www.conventionalcommits.org/>`_ specification to ensure clear and standardized project history.
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|
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Why Commit Message Standards Matter
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-----------------------------------
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Standardized commit messages provide several benefits:
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* **Improved readability**: Clear, consistent format makes it easier to understand changes
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* **Automated changelog generation**: Tools can parse conventional commits to generate changelogs
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* **Better collaboration**: Team members can quickly understand the nature of changes
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* **Easier debugging**: Well-formatted commits help identify when bugs were introduced
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* **Semantic versioning**: Conventional commits can trigger automated version bumps
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Commit Message Format
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---------------------
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All commit messages must follow this format:
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.. code-block:: text
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<type>(<scope>): <description>
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[optional body]
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|
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[optional footer(s)]
|
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Components
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~~~~~~~~~~
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**Type (required)**
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The type of change being made. Must be one of:
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* ``feat``: A new feature
|
||||
* ``fix``: A bug fix
|
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* ``docs``: Documentation only changes
|
||||
* ``style``: Changes that do not affect the meaning of the code (white-space, formatting, etc.)
|
||||
* ``refactor``: A code change that neither fixes a bug nor adds a feature
|
||||
* ``test``: Adding missing tests or correcting existing tests
|
||||
* ``chore``: Changes to the build process or auxiliary tools and libraries
|
||||
* ``ci``: Changes to CI configuration files and scripts
|
||||
* ``build``: Changes that affect the build system or external dependencies
|
||||
* ``perf``: A code change that improves performance
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* ``revert``: Reverts a previous commit
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|
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**Scope (optional)**
|
||||
The scope of the change, enclosed in parentheses. Common scopes for this project:
|
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|
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* ``api``: Changes to API functionality
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* ``metadata``: Changes to metadata processing
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* ``citation``: Changes to citation building
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* ``config``: Changes to configuration handling
|
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* ``tests``: Changes to test files
|
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* ``docs``: Changes to documentation
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* ``deps``: Changes to dependencies
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**Description (required)**
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A short description of the change:
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* Use the imperative, present tense: "change" not "changed" nor "changes"
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* Don't capitalize the first letter
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* No period (.) at the end
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* Maximum 50 characters
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|
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**Body (optional)**
|
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A longer description of the change:
|
||||
|
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* Use the imperative, present tense
|
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* Wrap at 72 characters
|
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* Explain what and why vs. how
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|
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**Footer (optional)**
|
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One or more footers may be provided:
|
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|
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* ``BREAKING CHANGE:`` description of breaking changes
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* ``Closes #123``: reference to closed issues
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* ``Co-authored-by: Name <email@example.com>``: additional authors
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Examples
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--------
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**Simple feature addition:**
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.. code-block:: text
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|
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feat(api): add support for DOI batch processing
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|
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**Bug fix with scope:**
|
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|
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.. code-block:: text
|
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|
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fix(metadata): handle missing author information gracefully
|
||||
|
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**Documentation update:**
|
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|
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.. code-block:: text
|
||||
|
||||
docs: update installation instructions
|
||||
|
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**Breaking change:**
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.. code-block:: text
|
||||
|
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feat(api): change metadata output format
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BREAKING CHANGE: The metadata output format has changed from JSON
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to YAML. Users need to update their parsing code accordingly.
|
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|
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**Multi-line with body:**
|
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.. code-block:: text
|
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|
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refactor(citation): improve author name parsing
|
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|
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The author name parsing logic has been refactored to handle
|
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more edge cases, including names with multiple middle initials
|
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and international characters.
|
||||
|
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Closes #45
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|
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Configuration
|
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-------------
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|
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The project uses a ``.gitlint`` configuration file that enforces:
|
||||
|
||||
* Maximum title length of 50 characters
|
||||
* Conventional commit format validation
|
||||
* Maximum body line length of 72 characters
|
||||
* Exclusion of certain words like "WIP", "TODO", "FIXME" in titles
|
||||
* Automatic ignoring of merge commits and dependency updates
|
||||
|
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Linting Tools
|
||||
-------------
|
||||
|
||||
Manual Linting
|
||||
~~~~~~~~~~~~~~~
|
||||
|
||||
Use the provided script to lint commit messages:
|
||||
|
||||
.. code-block:: bash
|
||||
|
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# Lint the last commit
|
||||
python scripts/lint-commit.py
|
||||
|
||||
# Lint a specific commit by hash
|
||||
python scripts/lint-commit.py --hash <commit-hash>
|
||||
|
||||
# Lint a range of commits
|
||||
python scripts/lint-commit.py --range HEAD~3..
|
||||
|
||||
# Check staged commit message
|
||||
python scripts/lint-commit.py --staged
|
||||
|
||||
Git Hook Installation
|
||||
~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Install an automated git hook to check commit messages:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
python scripts/lint-commit.py --install-hook
|
||||
|
||||
This creates a ``commit-msg`` hook that automatically validates commit messages when you commit. The commit will be rejected if the message doesn't meet the requirements.
|
||||
|
||||
Direct Gitlint Usage
|
||||
~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
You can also use gitlint directly:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
# Lint last commit
|
||||
gitlint
|
||||
|
||||
# Lint specific commit
|
||||
gitlint --commit <commit-hash>
|
||||
|
||||
# Lint commit range
|
||||
gitlint --commits HEAD~3..
|
||||
|
||||
Common Validation Errors
|
||||
-------------------------
|
||||
|
||||
**Title too long**
|
||||
Keep titles under 50 characters. If you need more space, use the body.
|
||||
|
||||
**Invalid type**
|
||||
Use only the allowed types: ``feat``, ``fix``, ``docs``, ``style``, ``refactor``, ``test``, ``chore``, ``ci``, ``build``, ``perf``, ``revert``.
|
||||
|
||||
**Missing colon**
|
||||
Don't forget the colon after the type/scope: ``feat(api): add feature``
|
||||
|
||||
**Capitalized description**
|
||||
Don't capitalize the first letter of the description: ``feat: add feature`` not ``feat: Add feature``
|
||||
|
||||
**Trailing period**
|
||||
Don't add a period at the end of the title: ``feat: add feature`` not ``feat: add feature.``
|
||||
|
||||
**Body line too long**
|
||||
Keep body lines under 72 characters. Break long lines appropriately.
|
||||
|
||||
Troubleshooting
|
||||
---------------
|
||||
|
||||
**Gitlint not found**
|
||||
Install development dependencies:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
pip install -r requirements-dev.txt
|
||||
|
||||
**Hook not working**
|
||||
Ensure the hook is executable:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
chmod +x .git/hooks/commit-msg
|
||||
|
||||
**Existing commits don't follow format**
|
||||
The linting only applies to new commits. Existing commits can be left as-is or rebased if necessary.
|
||||
|
||||
Integration with CI/CD
|
||||
----------------------
|
||||
|
||||
The commit message linting can be integrated into CI/CD pipelines to ensure all commits in pull requests follow the standard format. This helps maintain consistency across all contributors.
|
||||
|
||||
For more information on gitlint configuration and advanced usage, see the `official gitlint documentation <https://jorisroovers.github.io/gitlint/>`_.
|
||||
|
|
@ -115,20 +115,47 @@ Development Setup
|
|||
|
||||
pip install -r requirements-dev.txt
|
||||
|
||||
4. Make your changes
|
||||
5. Run tests to ensure everything works
|
||||
6. Submit a pull request
|
||||
4. Install the git commit message hook (recommended):
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
python scripts/lint-commit.py --install-hook
|
||||
|
||||
5. Make your changes
|
||||
6. Run tests to ensure everything works
|
||||
7. Validate your commit messages follow the standards
|
||||
8. Submit a pull request
|
||||
|
||||
Code Style
|
||||
----------
|
||||
|
||||
Please follow the existing code style and conventions used in the project. Make sure to:
|
||||
|
||||
- Write clear, descriptive commit messages
|
||||
- Write clear, descriptive commit messages following the :doc:`commit-messages` standards
|
||||
- Add tests for new functionality
|
||||
- Update documentation as needed
|
||||
- Follow Python best practices
|
||||
|
||||
Commit Message Standards
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
All commit messages must follow the Conventional Commits specification. See the :doc:`commit-messages` documentation for detailed information on:
|
||||
|
||||
- Required message format
|
||||
- Available commit types
|
||||
- Examples of proper commit messages
|
||||
- How to use the linting tools
|
||||
|
||||
To validate your commit messages:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
# Lint the last commit
|
||||
python scripts/lint-commit.py
|
||||
|
||||
# Install automatic validation hook
|
||||
python scripts/lint-commit.py --install-hook
|
||||
|
||||
Submitting Changes
|
||||
------------------
|
||||
|
||||
|
|
@ -136,6 +163,7 @@ Submitting Changes
|
|||
2. Make your changes with appropriate tests
|
||||
3. Ensure all tests pass
|
||||
4. Update documentation if needed
|
||||
5. Submit a pull request with a clear description of your changes
|
||||
5. Ensure all commit messages follow the conventional commits format
|
||||
6. Submit a pull request with a clear description of your changes
|
||||
|
||||
Thank you for contributing to **doi2dataset**!
|
||||
|
|
|
|||
|
|
@ -39,4 +39,5 @@ Key Features:
|
|||
usage
|
||||
modules
|
||||
contributing
|
||||
commit-messages
|
||||
faq
|
||||
|
|
|
|||
679
doi2dataset.py
679
doi2dataset.py
File diff suppressed because it is too large
Load diff
|
|
@ -50,6 +50,7 @@ dev = [
|
|||
"pytest-mock>=3.14.0,<4.0",
|
||||
"pytest-cov>=6.0.0,<7.0",
|
||||
"ruff>=0.11.1,<0.20",
|
||||
"gitlint>=0.19.1,<0.20",
|
||||
]
|
||||
test = [
|
||||
"pytest>=8.3.5,<9.0",
|
||||
|
|
@ -132,3 +133,7 @@ ignore = [
|
|||
|
||||
[tool.ruff.lint.per-file-ignores]
|
||||
"tests/*" = ["E501"]
|
||||
|
||||
[tool.bandit]
|
||||
exclude_dirs = ["tests", "docs", ".venv", "build", "dist"]
|
||||
skips = ["B101", "B601", "B404", "B603"]
|
||||
|
|
|
|||
|
|
@ -2,3 +2,4 @@ pytest>=8.3.5,<9.0
|
|||
pytest-mock>=3.14.0,<4.0
|
||||
pytest-cov>=6.0.0,<7.0
|
||||
ruff>=0.11.1,<0.20
|
||||
gitlint>=0.19.1,<0.20
|
||||
|
|
|
|||
179
scripts/lint-commit.py
Normal file
179
scripts/lint-commit.py
Normal file
|
|
@ -0,0 +1,179 @@
|
|||
#!/usr/bin/env python3
|
||||
"""
|
||||
Simple script to lint git commit messages using gitlint.
|
||||
|
||||
This script can be used to:
|
||||
1. Lint the last commit message
|
||||
2. Lint a specific commit by hash
|
||||
3. Lint commit messages in a range
|
||||
4. Be used as a pre-commit hook
|
||||
|
||||
Usage:
|
||||
python scripts/lint-commit.py # Lint last commit
|
||||
python scripts/lint-commit.py --hash <hash> # Lint specific commit
|
||||
python scripts/lint-commit.py --range <range> # Lint commit range
|
||||
python scripts/lint-commit.py --staged # Lint staged commit message
|
||||
|
||||
This implementation enforces conventional commit message format.
|
||||
"""
|
||||
|
||||
import argparse
|
||||
import subprocess
|
||||
import sys
|
||||
from pathlib import Path
|
||||
|
||||
|
||||
def run_command(cmd, check=True):
|
||||
"""Run a shell command and return the result."""
|
||||
try:
|
||||
result = subprocess.run(cmd, capture_output=True, text=True, check=check)
|
||||
return result
|
||||
except subprocess.CalledProcessError as e:
|
||||
print(f"Error running command: {cmd}")
|
||||
print(f"Exit code: {e.returncode}")
|
||||
print(f"Output: {e.stdout}")
|
||||
print(f"Error: {e.stderr}")
|
||||
return e
|
||||
|
||||
|
||||
def check_gitlint_installed():
|
||||
"""Check if gitlint is installed."""
|
||||
result = run_command(["which", "gitlint"], check=False)
|
||||
if result.returncode != 0:
|
||||
print("Error: gitlint is not installed.")
|
||||
print("Please install it with: pip install gitlint")
|
||||
print("Or install dev dependencies: pip install -r requirements-dev.txt")
|
||||
sys.exit(1)
|
||||
|
||||
|
||||
def lint_commit(commit_hash=None, commit_range=None, staged=False):
|
||||
"""Lint commit message(s) using gitlint."""
|
||||
# Build gitlint command
|
||||
cmd = ["gitlint"]
|
||||
|
||||
if staged:
|
||||
# Lint staged commit message
|
||||
cmd.extend(["--staged"])
|
||||
elif commit_range:
|
||||
# Lint commit range
|
||||
cmd.extend(["--commits", commit_range])
|
||||
elif commit_hash:
|
||||
# Lint specific commit
|
||||
cmd.extend(["--commit", commit_hash])
|
||||
else:
|
||||
# Lint last commit (default)
|
||||
cmd.extend(["--commit", "HEAD"])
|
||||
|
||||
print(f"Running: {' '.join(cmd)}")
|
||||
print("-" * 50)
|
||||
|
||||
# Run gitlint
|
||||
result = run_command(cmd, check=False)
|
||||
|
||||
if result.returncode == 0:
|
||||
print("✅ All commit messages are valid!")
|
||||
return True
|
||||
else:
|
||||
print("❌ Commit message validation failed:")
|
||||
print(result.stdout)
|
||||
if result.stderr:
|
||||
print("Error output:")
|
||||
print(result.stderr)
|
||||
return False
|
||||
|
||||
|
||||
def main():
|
||||
"""Main entry point."""
|
||||
parser = argparse.ArgumentParser(
|
||||
description="Lint git commit messages using gitlint",
|
||||
formatter_class=argparse.RawDescriptionHelpFormatter,
|
||||
epilog="""
|
||||
Examples:
|
||||
%(prog)s # Lint last commit
|
||||
%(prog)s --hash abc123 # Lint specific commit
|
||||
%(prog)s --range HEAD~3.. # Lint last 3 commits
|
||||
%(prog)s --staged # Lint staged commit message
|
||||
""",
|
||||
)
|
||||
|
||||
parser.add_argument("--hash", help="Specific commit hash to lint")
|
||||
|
||||
parser.add_argument("--range", help="Commit range to lint (e.g., HEAD~3..)")
|
||||
|
||||
parser.add_argument(
|
||||
"--staged", action="store_true", help="Lint staged commit message"
|
||||
)
|
||||
|
||||
parser.add_argument(
|
||||
"--install-hook", action="store_true", help="Install as git commit-msg hook"
|
||||
)
|
||||
|
||||
args = parser.parse_args()
|
||||
|
||||
# Check if gitlint is installed
|
||||
check_gitlint_installed()
|
||||
|
||||
# Install hook if requested
|
||||
if args.install_hook:
|
||||
install_hook()
|
||||
return
|
||||
|
||||
# Validate arguments
|
||||
exclusive_args = [args.hash, args.range, args.staged]
|
||||
if sum(bool(arg) for arg in exclusive_args) > 1:
|
||||
print("Error: --hash, --range, and --staged are mutually exclusive")
|
||||
sys.exit(1)
|
||||
|
||||
# Lint commits
|
||||
success = lint_commit(
|
||||
commit_hash=args.hash, commit_range=args.range, staged=args.staged
|
||||
)
|
||||
|
||||
sys.exit(0 if success else 1)
|
||||
|
||||
|
||||
def install_hook():
|
||||
"""Install the script as a git commit-msg hook."""
|
||||
git_dir = Path(".git")
|
||||
if not git_dir.exists():
|
||||
print("Error: Not in a git repository")
|
||||
sys.exit(1)
|
||||
|
||||
hooks_dir = git_dir / "hooks"
|
||||
hooks_dir.mkdir(exist_ok=True)
|
||||
|
||||
hook_file = hooks_dir / "commit-msg"
|
||||
|
||||
hook_content = """#!/usr/bin/env python3
|
||||
# Git commit-msg hook for gitlint
|
||||
# Python-based commit message linting with gitlint
|
||||
import subprocess
|
||||
import sys
|
||||
|
||||
# Run gitlint on the commit message
|
||||
result = subprocess.run( # nosec B603
|
||||
["gitlint", "--msg-filename", sys.argv[1]],
|
||||
capture_output=True,
|
||||
text=True
|
||||
)
|
||||
|
||||
if result.returncode != 0:
|
||||
print("Commit message validation failed:")
|
||||
print(result.stdout)
|
||||
if result.stderr:
|
||||
print("Error output:")
|
||||
print(result.stderr)
|
||||
sys.exit(1)
|
||||
|
||||
print("✅ Commit message is valid!")
|
||||
"""
|
||||
|
||||
hook_file.write_text(hook_content)
|
||||
hook_file.chmod(0o755)
|
||||
|
||||
print(f"✅ Installed commit-msg hook at {hook_file}")
|
||||
print("The hook will automatically run when you commit.")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
|
|
@ -23,7 +23,7 @@ def test_pi():
|
|||
given_name="Author",
|
||||
orcid="0000-0000-0000-1234",
|
||||
email="test.author@example.org",
|
||||
affiliation="Test University"
|
||||
affiliation="Test University",
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -115,7 +115,9 @@ def test_build_authors_with_ror(openalex_data, pi_finder):
|
|||
pytest.skip("Test data doesn't contain any ROR identifiers")
|
||||
|
||||
# Create builder with ror=True to enable ROR identifiers
|
||||
builder = CitationBuilder(data=openalex_data, doi=doi, pi_finder=pi_finder, ror=True)
|
||||
builder = CitationBuilder(
|
||||
data=openalex_data, doi=doi, pi_finder=pi_finder, ror=True
|
||||
)
|
||||
|
||||
# Get authors
|
||||
authors, _ = builder.build_authors()
|
||||
|
|
@ -129,11 +131,11 @@ def test_build_authors_with_ror(openalex_data, pi_finder):
|
|||
|
||||
for author in authors:
|
||||
# Check if author has affiliation
|
||||
if not hasattr(author, 'affiliation') or not author.affiliation:
|
||||
if not hasattr(author, "affiliation") or not author.affiliation:
|
||||
continue
|
||||
|
||||
# Check if affiliation is an Institution with a ROR ID
|
||||
if not hasattr(author.affiliation, 'ror'):
|
||||
if not hasattr(author.affiliation, "ror"):
|
||||
continue
|
||||
|
||||
# Check if ROR ID is present and contains "ror.org"
|
||||
|
|
@ -154,7 +156,7 @@ def test_build_authors_with_ror(openalex_data, pi_finder):
|
|||
assert affiliation_field.value == institution_with_ror.ror
|
||||
|
||||
# Verify the expanded_value dictionary has the expected structure
|
||||
assert hasattr(affiliation_field, 'expanded_value')
|
||||
assert hasattr(affiliation_field, "expanded_value")
|
||||
assert isinstance(affiliation_field.expanded_value, dict)
|
||||
|
||||
# Check specific fields in the expanded_value
|
||||
|
|
|
|||
|
|
@ -13,6 +13,7 @@ def test_sanitize_filename():
|
|||
result = sanitize_filename(doi)
|
||||
assert result == expected
|
||||
|
||||
|
||||
def test_split_name_with_comma():
|
||||
"""Test splitting a full name that contains a comma."""
|
||||
full_name = "Doe, John"
|
||||
|
|
@ -20,6 +21,7 @@ def test_split_name_with_comma():
|
|||
assert given == "John"
|
||||
assert family == "Doe"
|
||||
|
||||
|
||||
def test_split_name_without_comma():
|
||||
"""Test splitting a full name that does not contain a comma."""
|
||||
full_name = "John Doe"
|
||||
|
|
@ -27,11 +29,13 @@ def test_split_name_without_comma():
|
|||
assert given == "John"
|
||||
assert family == "Doe"
|
||||
|
||||
|
||||
def test_validate_email_address_valid():
|
||||
"""Test that a valid email address is correctly recognized."""
|
||||
valid_email = "john.doe@iana.org"
|
||||
assert validate_email_address(valid_email) is True
|
||||
|
||||
|
||||
def test_validate_email_address_invalid():
|
||||
"""Test that an invalid email address is correctly rejected."""
|
||||
invalid_email = "john.doe@invalid_domain"
|
||||
|
|
|
|||
|
|
@ -20,6 +20,7 @@ class FakeResponse:
|
|||
"""
|
||||
A fake response object to simulate an API response.
|
||||
"""
|
||||
|
||||
def __init__(self, json_data, status_code=200):
|
||||
self._json = json_data
|
||||
self.status_code = status_code
|
||||
|
|
@ -30,6 +31,7 @@ class FakeResponse:
|
|||
def raise_for_status(self):
|
||||
pass
|
||||
|
||||
|
||||
@pytest.fixture(autouse=True)
|
||||
def load_config_test():
|
||||
"""
|
||||
|
|
@ -39,6 +41,7 @@ def load_config_test():
|
|||
config_path = os.path.join(os.path.dirname(__file__), "config_test.yaml")
|
||||
Config.load_config(config_path=config_path)
|
||||
|
||||
|
||||
@pytest.fixture
|
||||
def fake_openalex_response():
|
||||
"""
|
||||
|
|
@ -50,6 +53,7 @@ def fake_openalex_response():
|
|||
data = json.load(f)
|
||||
return data
|
||||
|
||||
|
||||
def test_fetch_doi_data_with_file(mocker, fake_openalex_response):
|
||||
"""
|
||||
Test fetching DOI metadata by simulating the API call with a locally saved JSON response.
|
||||
|
|
@ -88,7 +92,7 @@ def test_openalex_abstract_extraction(mocker, fake_openalex_response):
|
|||
assert abstract_text is not None
|
||||
|
||||
# If abstract exists in the response, it should be properly extracted
|
||||
if 'abstract_inverted_index' in fake_openalex_response:
|
||||
if "abstract_inverted_index" in fake_openalex_response:
|
||||
assert len(abstract_text) > 0
|
||||
|
||||
|
||||
|
|
@ -152,7 +156,7 @@ def test_pi_finder_find_by_orcid():
|
|||
given_name="Jon",
|
||||
orcid="0000-0000-0000-0000",
|
||||
email="jon.doe@iana.org",
|
||||
affiliation="Institute of Science, Some University"
|
||||
affiliation="Institute of Science, Some University",
|
||||
)
|
||||
|
||||
# Create PIFinder with our test PI
|
||||
|
|
@ -181,8 +185,10 @@ def test_metadata_processor_fetch_data(mocker, fake_openalex_response):
|
|||
doi = "10.1038/srep45389"
|
||||
|
||||
# Mock API response
|
||||
mocker.patch("doi2dataset.APIClient.make_request",
|
||||
return_value=FakeResponse(fake_openalex_response, 200))
|
||||
mocker.patch(
|
||||
"doi2dataset.APIClient.make_request",
|
||||
return_value=FakeResponse(fake_openalex_response, 200),
|
||||
)
|
||||
|
||||
# Create processor with upload disabled and progress disabled
|
||||
processor = MetadataProcessor(doi=doi, upload=False, progress=False)
|
||||
|
|
|
|||
|
|
@ -3,37 +3,27 @@ from doi2dataset import License, LicenseProcessor
|
|||
|
||||
def test_license_processor_cc_by():
|
||||
"""Test processing a CC BY license"""
|
||||
data = {
|
||||
"primary_location": {
|
||||
"license": "cc-by"
|
||||
}
|
||||
}
|
||||
data = {"primary_location": {"license": "cc-by"}}
|
||||
license_obj = LicenseProcessor.process_license(data)
|
||||
assert isinstance(license_obj, License)
|
||||
assert license_obj.short == "cc-by"
|
||||
assert license_obj.name == "CC BY 4.0"
|
||||
assert license_obj.uri == "https://creativecommons.org/licenses/by/4.0/"
|
||||
|
||||
|
||||
def test_license_processor_cc0():
|
||||
"""Test processing a CC0 license"""
|
||||
data = {
|
||||
"primary_location": {
|
||||
"license": "cc0"
|
||||
}
|
||||
}
|
||||
data = {"primary_location": {"license": "cc0"}}
|
||||
license_obj = LicenseProcessor.process_license(data)
|
||||
assert isinstance(license_obj, License)
|
||||
assert license_obj.short == "cc0"
|
||||
assert license_obj.name == "CC0 1.0"
|
||||
assert license_obj.uri == "https://creativecommons.org/publicdomain/zero/1.0/"
|
||||
|
||||
|
||||
def test_license_processor_unknown_license():
|
||||
"""Test processing an unknown license"""
|
||||
data = {
|
||||
"primary_location": {
|
||||
"license": "unknown-license"
|
||||
}
|
||||
}
|
||||
data = {"primary_location": {"license": "unknown-license"}}
|
||||
license_obj = LicenseProcessor.process_license(data)
|
||||
assert isinstance(license_obj, License)
|
||||
assert license_obj.short == "unknown-license"
|
||||
|
|
@ -41,17 +31,17 @@ def test_license_processor_unknown_license():
|
|||
assert license_obj.name == "unknown-license" or license_obj.name == ""
|
||||
assert hasattr(license_obj, "uri")
|
||||
|
||||
|
||||
def test_license_processor_no_license():
|
||||
"""Test processing with no license information"""
|
||||
data = {
|
||||
"primary_location": {}
|
||||
}
|
||||
data = {"primary_location": {}}
|
||||
license_obj = LicenseProcessor.process_license(data)
|
||||
assert isinstance(license_obj, License)
|
||||
assert license_obj.short == "unknown"
|
||||
assert license_obj.name == ""
|
||||
assert license_obj.uri == ""
|
||||
|
||||
|
||||
def test_license_processor_no_primary_location():
|
||||
"""Test processing with no primary location"""
|
||||
data = {}
|
||||
|
|
|
|||
|
|
@ -33,7 +33,10 @@ def test_build_metadata_basic_fields(metadata_processor, openalex_data, monkeypa
|
|||
abstract_mock = MagicMock()
|
||||
abstract_mock.text = "This is a sample abstract"
|
||||
abstract_mock.source = "openalex"
|
||||
monkeypatch.setattr("doi2dataset.AbstractProcessor.get_abstract", lambda *args, **kwargs: abstract_mock)
|
||||
monkeypatch.setattr(
|
||||
"doi2dataset.AbstractProcessor.get_abstract",
|
||||
lambda *args, **kwargs: abstract_mock,
|
||||
)
|
||||
|
||||
# Mock the _fetch_data method to return our test data
|
||||
metadata_processor._fetch_data = MagicMock(return_value=openalex_data)
|
||||
|
|
@ -47,21 +50,23 @@ def test_build_metadata_basic_fields(metadata_processor, openalex_data, monkeypa
|
|||
|
||||
# Verify the basic metadata fields were extracted correctly
|
||||
assert metadata is not None
|
||||
assert 'datasetVersion' in metadata
|
||||
assert "datasetVersion" in metadata
|
||||
|
||||
# Examine the fields inside datasetVersion.metadataBlocks
|
||||
assert 'metadataBlocks' in metadata['datasetVersion']
|
||||
citation = metadata['datasetVersion']['metadataBlocks'].get('citation', {})
|
||||
assert "metadataBlocks" in metadata["datasetVersion"]
|
||||
citation = metadata["datasetVersion"]["metadataBlocks"].get("citation", {})
|
||||
|
||||
# Check fields in citation section
|
||||
assert 'fields' in citation
|
||||
fields = citation['fields']
|
||||
assert "fields" in citation
|
||||
fields = citation["fields"]
|
||||
|
||||
# Check for basic metadata fields in a more flexible way
|
||||
field_names = [field.get('typeName') for field in fields]
|
||||
assert 'title' in field_names
|
||||
assert 'subject' in field_names
|
||||
assert 'dsDescription' in field_names # Description is named 'dsDescription' in the schema
|
||||
field_names = [field.get("typeName") for field in fields]
|
||||
assert "title" in field_names
|
||||
assert "subject" in field_names
|
||||
assert (
|
||||
"dsDescription" in field_names
|
||||
) # Description is named 'dsDescription' in the schema
|
||||
|
||||
|
||||
def test_build_metadata_authors(metadata_processor, openalex_data, monkeypatch):
|
||||
|
|
@ -73,7 +78,10 @@ def test_build_metadata_authors(metadata_processor, openalex_data, monkeypatch):
|
|||
abstract_mock = MagicMock()
|
||||
abstract_mock.text = "This is a sample abstract"
|
||||
abstract_mock.source = "openalex"
|
||||
monkeypatch.setattr("doi2dataset.AbstractProcessor.get_abstract", lambda *args, **kwargs: abstract_mock)
|
||||
monkeypatch.setattr(
|
||||
"doi2dataset.AbstractProcessor.get_abstract",
|
||||
lambda *args, **kwargs: abstract_mock,
|
||||
)
|
||||
|
||||
# Mock the _fetch_data method to return our test data
|
||||
metadata_processor._fetch_data = MagicMock(return_value=openalex_data)
|
||||
|
|
@ -86,33 +94,35 @@ def test_build_metadata_authors(metadata_processor, openalex_data, monkeypatch):
|
|||
metadata = metadata_processor._build_metadata(openalex_data)
|
||||
|
||||
# Examine the fields inside datasetVersion.metadataBlocks
|
||||
assert 'metadataBlocks' in metadata['datasetVersion']
|
||||
citation = metadata['datasetVersion']['metadataBlocks'].get('citation', {})
|
||||
assert "metadataBlocks" in metadata["datasetVersion"]
|
||||
citation = metadata["datasetVersion"]["metadataBlocks"].get("citation", {})
|
||||
|
||||
# Check fields in citation section
|
||||
assert 'fields' in citation
|
||||
fields = citation['fields']
|
||||
assert "fields" in citation
|
||||
fields = citation["fields"]
|
||||
|
||||
# Check for author and datasetContact fields
|
||||
field_names = [field.get('typeName') for field in fields]
|
||||
assert 'author' in field_names
|
||||
assert 'datasetContact' in field_names
|
||||
field_names = [field.get("typeName") for field in fields]
|
||||
assert "author" in field_names
|
||||
assert "datasetContact" in field_names
|
||||
|
||||
# Verify these are compound fields with actual entries
|
||||
for field in fields:
|
||||
if field.get('typeName') == 'author':
|
||||
assert 'value' in field
|
||||
assert isinstance(field['value'], list)
|
||||
assert len(field['value']) > 0
|
||||
if field.get("typeName") == "author":
|
||||
assert "value" in field
|
||||
assert isinstance(field["value"], list)
|
||||
assert len(field["value"]) > 0
|
||||
|
||||
if field.get('typeName') == 'datasetContact':
|
||||
assert 'value' in field
|
||||
assert isinstance(field['value'], list)
|
||||
if field.get("typeName") == "datasetContact":
|
||||
assert "value" in field
|
||||
assert isinstance(field["value"], list)
|
||||
# The datasetContact might be empty in test environment
|
||||
# Just check it exists rather than asserting length
|
||||
|
||||
|
||||
def test_build_metadata_keywords_and_topics(metadata_processor, openalex_data, monkeypatch):
|
||||
def test_build_metadata_keywords_and_topics(
|
||||
metadata_processor, openalex_data, monkeypatch
|
||||
):
|
||||
"""Test that _build_metadata correctly extracts keywords and topics"""
|
||||
# Mock the console to avoid print errors
|
||||
metadata_processor.console = MagicMock()
|
||||
|
|
@ -121,7 +131,10 @@ def test_build_metadata_keywords_and_topics(metadata_processor, openalex_data, m
|
|||
abstract_mock = MagicMock()
|
||||
abstract_mock.text = "This is a sample abstract"
|
||||
abstract_mock.source = "openalex"
|
||||
monkeypatch.setattr("doi2dataset.AbstractProcessor.get_abstract", lambda *args, **kwargs: abstract_mock)
|
||||
monkeypatch.setattr(
|
||||
"doi2dataset.AbstractProcessor.get_abstract",
|
||||
lambda *args, **kwargs: abstract_mock,
|
||||
)
|
||||
|
||||
# Mock the _fetch_data method to return our test data
|
||||
metadata_processor._fetch_data = MagicMock(return_value=openalex_data)
|
||||
|
|
@ -134,27 +147,27 @@ def test_build_metadata_keywords_and_topics(metadata_processor, openalex_data, m
|
|||
metadata = metadata_processor._build_metadata(openalex_data)
|
||||
|
||||
# Examine the fields inside datasetVersion.metadataBlocks
|
||||
assert 'metadataBlocks' in metadata['datasetVersion']
|
||||
citation = metadata['datasetVersion']['metadataBlocks'].get('citation', {})
|
||||
assert "metadataBlocks" in metadata["datasetVersion"]
|
||||
citation = metadata["datasetVersion"]["metadataBlocks"].get("citation", {})
|
||||
|
||||
# Check fields in citation section
|
||||
assert 'fields' in citation
|
||||
fields = citation['fields']
|
||||
assert "fields" in citation
|
||||
fields = citation["fields"]
|
||||
|
||||
# Check for keyword and subject fields
|
||||
field_names = [field.get('typeName') for field in fields]
|
||||
field_names = [field.get("typeName") for field in fields]
|
||||
|
||||
# If keywords exist, verify structure
|
||||
if 'keyword' in field_names:
|
||||
if "keyword" in field_names:
|
||||
for field in fields:
|
||||
if field.get('typeName') == 'keyword':
|
||||
assert 'value' in field
|
||||
assert isinstance(field['value'], list)
|
||||
if field.get("typeName") == "keyword":
|
||||
assert "value" in field
|
||||
assert isinstance(field["value"], list)
|
||||
|
||||
# Check for subject field which should definitely exist
|
||||
assert 'subject' in field_names
|
||||
assert "subject" in field_names
|
||||
for field in fields:
|
||||
if field.get('typeName') == 'subject':
|
||||
assert 'value' in field
|
||||
assert isinstance(field['value'], list)
|
||||
assert len(field['value']) > 0
|
||||
if field.get("typeName") == "subject":
|
||||
assert "value" in field
|
||||
assert isinstance(field["value"], list)
|
||||
assert len(field["value"]) > 0
|
||||
|
|
|
|||
|
|
@ -8,7 +8,7 @@ def test_person_to_dict_with_string_affiliation():
|
|||
given_name="John",
|
||||
orcid="0000-0001-2345-6789",
|
||||
email="john.doe@example.org",
|
||||
affiliation="Test University"
|
||||
affiliation="Test University",
|
||||
)
|
||||
|
||||
result = person.to_dict()
|
||||
|
|
@ -29,7 +29,7 @@ def test_person_to_dict_with_institution_ror():
|
|||
given_name="John",
|
||||
orcid="0000-0001-2345-6789",
|
||||
email="john.doe@example.org",
|
||||
affiliation=inst
|
||||
affiliation=inst,
|
||||
)
|
||||
|
||||
result = person.to_dict()
|
||||
|
|
@ -48,7 +48,7 @@ def test_person_to_dict_with_institution_display_name_only():
|
|||
family_name="Smith",
|
||||
given_name="Jane",
|
||||
orcid="0000-0001-9876-5432",
|
||||
affiliation=inst
|
||||
affiliation=inst,
|
||||
)
|
||||
|
||||
result = person.to_dict()
|
||||
|
|
@ -63,11 +63,7 @@ def test_person_to_dict_with_empty_institution():
|
|||
# Create an Institution with empty values
|
||||
inst = Institution("")
|
||||
|
||||
person = Person(
|
||||
family_name="Brown",
|
||||
given_name="Robert",
|
||||
affiliation=inst
|
||||
)
|
||||
person = Person(family_name="Brown", given_name="Robert", affiliation=inst)
|
||||
|
||||
result = person.to_dict()
|
||||
|
||||
|
|
@ -79,9 +75,7 @@ def test_person_to_dict_with_empty_institution():
|
|||
def test_person_to_dict_with_no_affiliation():
|
||||
"""Test Person.to_dict() with no affiliation."""
|
||||
person = Person(
|
||||
family_name="Green",
|
||||
given_name="Alice",
|
||||
orcid="0000-0002-1111-2222"
|
||||
family_name="Green", given_name="Alice", orcid="0000-0002-1111-2222"
|
||||
)
|
||||
|
||||
result = person.to_dict()
|
||||
|
|
|
|||
|
|
@ -14,44 +14,44 @@ def metadata_processor():
|
|||
processor.console = MagicMock()
|
||||
return processor
|
||||
|
||||
|
||||
def test_get_publication_year_with_publication_year(metadata_processor):
|
||||
"""Test that _get_publication_year extracts year from publication_year field"""
|
||||
data = {"publication_year": 2020}
|
||||
year = metadata_processor._get_publication_year(data)
|
||||
assert year == 2020
|
||||
|
||||
|
||||
def test_get_publication_year_with_date(metadata_processor):
|
||||
"""Test that _get_publication_year returns empty string when publication_year is missing"""
|
||||
data = {"publication_date": "2019-05-15"}
|
||||
year = metadata_processor._get_publication_year(data)
|
||||
assert year == ""
|
||||
|
||||
|
||||
def test_get_publication_year_with_both_fields(metadata_processor):
|
||||
"""Test that _get_publication_year prioritizes publication_year over date"""
|
||||
data = {
|
||||
"publication_year": 2020,
|
||||
"publication_date": "2019-05-15"
|
||||
}
|
||||
data = {"publication_year": 2020, "publication_date": "2019-05-15"}
|
||||
year = metadata_processor._get_publication_year(data)
|
||||
assert year == 2020
|
||||
|
||||
|
||||
def test_get_publication_year_with_partial_date(metadata_processor):
|
||||
"""Test that _get_publication_year returns empty string when only publication_date is present"""
|
||||
data = {"publication_date": "2018"}
|
||||
year = metadata_processor._get_publication_year(data)
|
||||
assert year == ""
|
||||
|
||||
|
||||
def test_get_publication_year_with_missing_data(metadata_processor):
|
||||
"""Test that _get_publication_year handles missing data"""
|
||||
data = {"other_field": "value"}
|
||||
year = metadata_processor._get_publication_year(data)
|
||||
assert year == ""
|
||||
|
||||
|
||||
def test_get_publication_year_with_invalid_data(metadata_processor):
|
||||
"""Test that _get_publication_year returns whatever is in publication_year field"""
|
||||
data = {
|
||||
"publication_year": "not-a-year",
|
||||
"publication_date": "invalid-date"
|
||||
}
|
||||
data = {"publication_year": "not-a-year", "publication_date": "invalid-date"}
|
||||
year = metadata_processor._get_publication_year(data)
|
||||
assert year == "not-a-year"
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue