Many of the Python files in Biopython still have self-tests at the end which are executed if the file is run directly via the idiom:
if __name__ == "__main__":
print("Running a quick self-test")
...This is bad for several reasons - these tests are not being run routinely via our buildbot [Update: We stopped using buildbot, but now have AppVeyor instead] or TravisCI (and therefore if the test breaks, we don't know about it), they are not counted on the coverage report https://codecov.io/github/biopython/biopython/ (and in fact actively reduce the coverage score [Update: We configured codecov to ignore the self tests]), and moreover with Python 3 making subtle changes to imports, some of these self tests have accidentally become Python 2 only.
This is a tracking issue to encourage more commits like these which move these self-tests under Tests/test_XXX.py using the unittest framework instead:
Or, in some cases using a doctest instead makes sense:
In those cases, we're left with a stub like this which is useful when working directly on a file's doctests:
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest(verbose=0)
Many of the Python files in Biopython still have self-tests at the end which are executed if the file is run directly via the idiom:
This is bad for several reasons - these tests are not being run routinely via our buildbot [Update: We stopped using buildbot, but now have AppVeyor instead] or TravisCI (and therefore if the test breaks, we don't know about it), they are not counted on the coverage report https://codecov.io/github/biopython/biopython/ (and in fact actively reduce the coverage score [Update: We configured codecov to ignore the self tests]), and moreover with Python 3 making subtle changes to imports, some of these self tests have accidentally become Python 2 only.
This is a tracking issue to encourage more commits like these which move these self-tests under
Tests/test_XXX.pyusing the unittest framework instead:Or, in some cases using a doctest instead makes sense:
In those cases, we're left with a stub like this which is useful when working directly on a file's doctests: