retraction_check

A Python package to check whether papers in your .bib file or a specific bibtex entry have been listed on Retraction Watch.

Features

• Parse .bib files and extract paper information
• Query the Retraction Watch dataset for retracted papers
• Support both exact DOI matching and fuzzy title matching
• Robust error handling for various edge cases

Installation

```bash

Install from PyPI (when published)

pip install retraction-check

Or install from source

git clone https://github.com/codingfabi/retractioncheck.git cd retractioncheck pipenv install

Install development dependencies

pipenv install --dev ```

Usage

Command line

```bash

Using the installed command

retraction-check yourfile.bib

Or using the module

python -m retractioncheck.checkbib yourfile.bib ```

Development

Running tests

```bash

Run all tests

pipenv run test

Run tests with coverage

pipenv run test-cov

Run tests in watch mode

pipenv run test-watch

Run tests directly with Python

python tests/run_tests.py ```

Code quality

```bash

Format code

pipenv run format

Lint code

pipenv run lint

Type checking

pipenv run type-check

Run all checks

pipenv run check-all ```

Available test commands

• test - Run all tests with verbose output
• test-cov - Run tests with coverage report (HTML and terminal)
• test-watch - Run tests in watch mode with short traceback
• lint - Run flake8 linting
• format - Format code with black
• format-check - Check if code is properly formatted
• type-check - Run mypy type checking
• check-all - Run all quality checks (format, lint, type-check, test-cov)

Requirements

• Python 3.8+
• bibtexparser
• requests

Example: Automated Retraction Check with GitHub Actions

You can automate retraction checks for your bibliography file using GitHub Actions. The following workflow runs the check on demand, on a schedule, or on every commit to a specific branch. If any retractions are found, it will open a GitHub issue listing the findings.

```yaml name: Retraction Check

on: workflow_dispatch: # Allows manual trigger schedule: - cron: '0 8 * * 1' # Runs every Monday at 08:00 UTC push: paths: - yourfile.bib # Change this to your personal bib file to make sure the workflow runs every time the bibfile changes

jobs: retraction_check: runs-on: ubuntu-latest permissions: issues: write steps: - name: Checkout repository 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 .

  - name: Run retraction check
    id: retraction
    run: |
      python -m retraction_check.check_bib path/to/your/bibfileyourfile.bib > findings.txt
      grep -v "No retracted papers found." findings.txt > findings_only.txt || true

  - name: Create issue if retractions found
    if: success() && hashFiles('findings_only.txt') != ''
    uses: peter-evans/create-issue-from-file@v5
    with:
      title: "Retraction Watch: Retracted Papers Detected in Bibliography"
      content-filepath: findings_only.txt
      labels: retraction, automated-check

```

• Replace yourfile.bib with the path to your bibliography file.
• The workflow will create an issue only if retractions are found.
• You can trigger the workflow manually, on a schedule, or on every commit to the specified branch.

Example: Automated Retraction Check with GitLab CI

You can also automate retraction checks for your bibliography file using GitLab CI/CD. The following example runs the check on every push to the default branch and creates an issue if retractions are found (requires a GitLab personal access token with API scope stored as GITLAB_TOKEN).

yaml retraction_check: image: python:3.11 stage: test script: - pip install . - python -m retraction_check.check_bib path/to/yourfile.bib > findings.txt - grep -v "No retracted papers found." findings.txt > findings_only.txt || true # Only create an issue if findings_only.txt is not empty - | if [ -s findings_only.txt ]; then curl --header "PRIVATE-TOKEN: $GITLAB_TOKEN" \ --header "Content-Type: application/json" \ --data '{ "title": "Retraction Watch: Retracted Papers Detected in Bibliography", "description": "$(cat findings_only.txt)", "labels": "retraction, automated-check" }' \ --request POST "https://gitlab.com/api/v4/projects/$CI_PROJECT_ID/issues" fi only: - main # or your default branch rules: - changes: - path/to/yourfile.bib

• Replace path/to/yourfile.bib with the path to your bibliography file.
• Store a GitLab personal access token with API scope as a CI/CD variable named GITLAB_TOKEN.
• The job will create an issue only if retractions are found and the .bib file changes.