testseq update (6/13/17)
Adil Iqbal <[email protected]> Tue, 13 Jun 2017 02:30:28 -0500
| Newsgroups | gmane.comp.python.bio.devel |
|---|---|
| Message-ID | <CABJ4PdJqC5RjeBCRafR-q6rGsXWBHhvpxEUBDNHoBwXdRNpgmQ@mail.gmail.com> |
*TL:DR - Importing issue solved by 'manually_import' function. It can be used to solve similar problems in the future. Decided to remove non-Bio doctest for problematic versions of python. Open to input/suggestions/criticisms. Thank you.* Hello all, I have solved the 'testseq' importing issue. Since I could not import 'testseq' directly, I wrote a function that could manually import 'testseq' into the 'test_testseq' unit test using the built-in module 'importlib'. The function, named 'manually_import,' is generalized to work for any future unit tests for modules outside the 'Bio' package. You can see the code in isolation here: https://github.com/Adil-Iqbal/Personal-Projects/blob/master/Test%20Sequence/manually_import.py If ever such an issue should arise again, please direct the contributor to "Tests/test_testseq.py" They can import the 'manually_import' function directly from there. Than the issue arose that the 'run_tests.py' file could not import 'Scripts.testseq' prior to python 3.3. I decided to try using a permutation of the 'manually_import' code to solve the problem and it worked! With one caveat, the doctests within 'testseq.py' were subject to the same import restrictions and copying the 'manually_import' code again within the doctests seemed excessive. The solution that worked in the end was to remove doctests from outside of the 'Bio' package in python versions prior to 3.3. Some of you have noted that I am very 'commited' to finishing my work on this project. I've downloaded and am now running flake8 tests locally. I'm looking into integrating flake8 directly into my IDE. I've also downloaded virtualenv, and am looking into other solutions for local testing as well (though it's not currently set up). The problem will definitely be addressed before I begin work on reverting the seeding. Thank you for helping. It means a lot. Best, Adil _______________________________________________ Biopython-dev mailing list [email protected] http://mailman.open-bio.org/mailman/listinfo/biopython-dev