pha4ge / hAMRonization

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
GNU Lesser General Public License v3.0
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Add sanity testing for hAMRonization #40

Closed cimendes closed 3 years ago

cimendes commented 3 years ago

This PR adds, through the pytest package, sanity testing for the parsers implemented so far. This adressed issues #18 and #19.

To run the sanity tests, simple invoke pytest in the test directory. The sanity tests are implemented in the test_sanity.py file, which are automatically detected by pytest. More information is available in the README.md file inside the test directory. The single-entry files used in the sanity testing are stored in test/dummy. I'm not sure if this is the most appropriate name/location. Raw outputs are available at test/data and contain real reports.

Main issues to be discussed:

This still to be adressed:

Additionally, unit tests to each of the parsers functions could be implemented.