Research Software FAIRness Checks (RSFC)

A command line interface to automatically evaluate the fairness of a Github or Gitlab repository.

Authors: Daniel Garijo, Andrés Montero

Features

Given a repository URL, RSFC will perform a series of checks based on a list of research software quality indicators (RSQI). The RSQIs currently covered by the package are:

• software_has_license
• software_has_citation
• has_releases
• repository_workflows
• version_control_use
• requirements_specified
• software_documentation
• persistent_and_unique_identifier
• descriptive_metadata
• software_tests
• archived_in_software_heritage
• versioning_standards_use
• support_issue_tracking
• has_contribution_guidelines
• software_is_containerized

For more information about these RSQIs, you can check https://github.com/EVERSE-ResearchSoftware/indicators. We have plans to implement all of the RSQIs available in that repository.

Execution modes

RSFC offers the ability to run itself both in remote and local modes. Remote mode was the only execution mode available prior to version 0.1.8 and Local mode is an offline execution mode that uses the local path to your cloned repository instead of its Git URL.

Available tests

RSFC offers a catalogue of its tests that you can check here

Note: The short names stated in the catalogue will be the identifiers needed to run single-test assessments. More information later in the README

Differences between execution modes

Remote and Local execution modes have different test lists due to ability/inability to perform HTTP requests. The differences are presented in the following table:

Requirements

Python 3.10.8 or higher

Dependencies are available in the requirements.txt or pyproject.toml file located in the root of the repository

Install from PyPI

Just run in your terminal the following command:

pip install rsfc

Install from Github with Poetry

To install the package, first clone the repository in your machine. This project uses Poetry for dependency and environment management.

git clone https://github.com/oeg-upm/rsfc.git

Go to the project's root directory

cd rsfc

Install Poetry (if you haven’t already)

curl -sSL https://install.python-poetry.org | python3 -

Make sure Poetry is available in your PATH

poetry --version

Create the virtual environment and install dependencies

poetry install

Activate the virtual environment (Optional)

source $(poetry env info --path)/bin/activate

Your terminal prompt should now show something like:

(rsfc-py3.11) your-user@your-machine rsfc %

With virtual environment activated you can tried like this:

rsfc --help

Without poetry virtual environment activated you need to use the poetry run:

poetry run rsfc --help

Usage

Before anything, RSFC uses SOMEF internally. If this is your first time working with somef, you should run the following command in the root directory of the project:

somef configure -a

Now, you can use the package by running if you activated the poetry env

rsfc --repo <repo_url>

or like this without the poetry env

poetry run rsfc --repo <repo_url>

If you want the output in OSTrails format, you can use the following flag

rsfc --repo <repo_url> --ftr

And additionally, if you want to run only one test, you can indicate the test identifier when running RSFC like this

rsfc --repo <repo_url> --id <test_id>

RSFC also offers the possibility of using a personal Github token to avoid a rate limit issue with the Github API

rsfc --repo <repo_url> -t <token>

Parameter overview

Here is an overview of the available parameters supported by RSFC

Usage: rsfc [OPTIONS]

  RSFC - EVERSE Research Software Fairness Checks

Options:
  --repo TEXT        URL of the Github/Gitlab repository to be analyzed
  --local DIRECTORY  Local path of the repository to be analyzed
  -b TEXT            Name of the repo branch to analyze. By default
                     main/master
  -v TEXT            Tag of the release to analyze. By default latest release.
  --ftr              Flag to indicate if JSON-LD in FTR format is desired
  --id TEXT          Identifier of a specific test. Only that test will be ran
  --metadata FILE    SOMEF metadata file in case you already have one
  -t TEXT            Authorization Github token
  --help             Show this message and exit.

RSFC Badge

Below the output table you will find a README badge that states what the total FAIR coverage you got in your assessment. It is already adapted to Markdown so you will just need to copy it.

How is the coverage calculated?

The coverage is simply the rounded average percentage of the total tests passed. For example, if you passed 20 tests, the coverage will be (20/33)*100 = 61%

Docker installation

RSFC also offers a Dockerfile which you can build using the following commmand:

docker build -t --no-cache -t rsfc-docker .

For comodity, we provide a bash script that runs the container along with the necessary configurations. To execute it just run

./run_rsfc.sh --repo <repo_url> [--ftr] [--id <test_id>] [-t <token>]

The parameters used for the script are the same as if you executed RSFC normally

RSFC GitHub Action

This repository provides a reusable GitHub Action to run RSFC on a given repository.

Workflows

There are two key workflows:

• run-rsfc.yml:
  Defines the main RSFC execution logic.
  Note: This workflow cannot be triggered directly because it uses on: workflow_call.
  It is designed to be reusable and must be invoked from another workflow.

• use-rsfc.yml:
  A workflow file that triggers run-rsfc.yml. It must be placed in each repository that you want to analyze, since the repository where use-rsfc.yml is hosted is the one that will be processed.
  No additional inputs are required because the repository context is automatically passed by the call. This workflow can be triggered manually (workflow_dispatch) or automatically (e.g., on push events).

  • Secrets:
  • RSFC_TOKEN is optional but recommended if you plan to run multiple analyses or expect heavy usage. It allows RSFC to access private repositories and avoid rate limits.

Usage

To use RSFC in a repository:

1. Copy use-rsfc.yml into .github/workflows/ of the repository you want to analyze.
2. Ensure that the required secrets are defined (see below).
3. No inputs are needed — the workflow automatically uses the repository it resides in.

Viewing RSFC Results in a Pull Request

When a Pull Request is opened or updated, the RSFC workflow runs automatically and adds a neutral check named RSFC Results Summary.

This check displays:

• the formatted RSFC console output, including the full assessment table
• a link to the workflow job that executed the analysis

Accessing the JSON report

The workflow also generates an artifact named rsfc_assessment.json.

To download it:

1. Open the Checks tab of the Pull Request
2. Select the job Run RSFC Analysis
3. Download the artifact from the Artifacts section

Example:

name: Run RSFC analysis

on:
  workflow_dispatch: 
  pull_request: 
    types: [opened, synchronize, reopened]         

jobs:
  run-rsfc-checks:
    uses: oeg-upm/rsfc/.github/workflows/run-rsfc.yml@main
    with:
      repo_url: https://github.com/${{ github.repository }}
      is_fork: ${{ github.event.pull_request.head.repo.full_name != github.repository }}
      pr_sha: ${{ github.event.pull_request.head.sha }}
    secrets:
      RSFC_TOKEN: ${{ secrets.RSFC_TOKEN }}