'testseq' update (6/10/17)
Adil Iqbal <[email protected]> Sat, 10 Jun 2017 23:40:53 -0500
| Newsgroups | gmane.comp.python.bio.devel |
|---|---|
| Message-ID | <CABJ4PdJctaP5JnFWXpcDEO2HWYYegg6jhCmr5d7rChn29wCUxw@mail.gmail.com> |
*TL:DR - Game plan: (1) Resolve unittest importing issue. (2) Revert testseq seeding. (3) Revisit testseq doctests. (4) Update unittest for reverted seeding. (2) Thank you for your patience.* Hello all, I'd like to let everyone know where 'testseq' is in development. You can find the code for it here: https://github.com/Adil-Iqbal/Personal-Projects/tree/master/Test%20Sequence The biggest issue (unexpectedly) was importing the 'testseq' module into the 'test_testseq' unit test. Absolute and relative importing did not work since the 'Scripts' folder is not a part of the 'Bio' package. After trying out several solutions, the one that looks the most promising is using the "importlib" module. The issue is not yet resolved but I am confident that it is just a matter of working out the details. I've gotten the chance to tackle part of another big issue, which is python version and operating system compatibility. Since the 'testseq' function uses randomization, its output can be different across versions and platforms. This poses a problem for code testing. Luckily there are a few work-arounds that I've implemented in the unit test which should work fine. I will also be revisiting the 'testseq' doctests to ensure they are also compatible, though I have not yet run into any issues with that on Travis CI. (Peter warned me about this. ^_^) Today, an argument was presented for reverting the seeding implementation, which was that user intuition should preferably be developed with respect to best practices. Unless anyone has a reasonable rebuttal, I will probably revert the seeding to an earlier state. Though, that will have to wait until after I've resolved the importing issue. Also, I'd like to thank you for being patient with me. I would've completed this sooner, but I have other obligations as well. Warmest regards, Adil _______________________________________________ Biopython-dev mailing list [email protected] http://mailman.open-bio.org/mailman/listinfo/biopython-dev