test.assessr

Overview

test.assessr helps in the assessment of a package’s test reliability and validity.

It calculates unit test coverage for packages with standard testing frameworks and non-standard testing frameworks, including Bioconductor packages.

Description

This package executes the following tasks:

1. upload the source package(tar.gz file)

2. Unpack the tar.gz file

3. Install the package locally

4. Run code coverage

Package Installation

from Github

• Create a Personal Access Token (PAT) on github

  • Log into your github account
  • Go to the token settings URL using the Token Settings URL
    • (do not forget to add the SSH Sanofi-Public authorization)

• Create a .Renviron file with your GITHUBTOKEN as:

# .Renviron
GITHUBTOKEN=dfdxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxfdf

• restart R session
• You can install the package with:

auth_token = Sys.getenv("GITHUBTOKEN")
devtools::install_github("Sanofi-Public/test.assessr", ref = "main", auth_token = auth_token)

Usage

Assessing your own package for test coverage

To assess your package’s test coverage, do the following steps:

1 - save your package as a tar.gz file

• This can be done in RStudio -> Build Tab -> More -> Build Source Package

2 - Run the following code sample by loading or add path parameter to your tar.gz package source code

# for local tar.gz R package
dp <- (path/to/your/package)

test_package_coverage <- get_package_coverage(dp)

generate_test_report(test_package_coverage)

test.assessr results

For a package with a standard testing framework such as testthat or testit or non-standard testing frameworks such as BiocGenerics and RUnit, test_assessr can provide data on which tests are passing and which tests are skipped.

The standard testing framework test report tells you which tests have passed:

The report provides information on which test blocks have passed and the start line of each test block.

The standard testing framework test report tells you which tests have been skipped:

The report provides information on which test blocks have passed, expectation type, and the start line of each test block.

The non-standard testing framework test report tells you which functions have no tests:

The report tells you which tests have passed:

The test report tells you which tests have been skipped:

Current/Future directions

• to develop methods for checking the validity of test data
• to develop methods of checking mocks

Acknowledgements

The project is inspired by the covrpage and mpn.scorecard packages and draws on some of their ideas and functions.