All tests must pass before a pull request can be merged into the
Run all tests
python3 -m unittest
Run a single test
r2dt.py test TestRibovisionLSU python3 -m unittest tests.tests.TestRibovisionLSU
When running tests with
r2dt.py testthe results and intermediate files are kept by default to facilitate debugging. If tests are launched with
python3 -m unittest, the results are deleted at the end of the tests. To keep the results, set the following environment variable:
R2DT_KEEP_TEST_RESULTS=1 python3 -m unittest tests.tests.TestRnasep
Updating example files
Sometimes a change in the algorithm results in a different secondary structure layout, and the tests are designed to alert the developers about any changes. However, sometimes changes are normal and expected, which means that precomputed examples need to be reviewed and updated, if needed.
When a test produces a structure that is not identical to the precomputed example, an HTML report including both structures is automatically generated and placed in the
tests folder. The HTML files are named according to the name of the test.
For example, a file
TestRnasep_2.html is generated when the second sequence in the
TestRnasep class in tests.py is different. These files are meant to be examined visually, and if the changes are acceptable, the examples can be updated with a helper command:
r2dt.py update-test-examples <test-name>
r2dt.py update-test-examples TestRfam
Once the precomputed examples are updated, it is recommended to check the output of
git diff for the SVGs before committing the new example files, in case some changes were not picked up by eye.