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Test ppanggolin outputs consistency

Open JeanMainguy opened this issue 10 months ago • 0 comments

PPanGGOLiN has a CI that tests most of its commands and parameters to make sure that none are broken. However, it does not test the content of the file created by the command. This means that if a change in the code affects the content of an output, we may not see it.

To mitigate this risk, this PR introduces a minimal check on the output files produced by the `ppanggolin info' command to ensure that no changes have been made to the contents of the pangenome.

  • The CI pipeline now includes a call to a Python script named compare_results.py, located within the testingDataset directory. This script compares the content of the files produced by the CI with the expected files stored in the testingDataset/expected_info_files directory.
  • A companion script named launch_test_locally.py has also been added to the testingDataset directory. This script reads the CI pipeline file and creates a bash script to launch the contents of the pipeline locally. This is useful to not only rely on the github action to test changes made to the code. Documentation has been updated to include how to use this script.

JeanMainguy avatar Apr 22 '24 16:04 JeanMainguy