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[REVIEW]: sierra-local: A lightweight standalone application for drug resistance prediction #1186
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Reviewer instructions & questions
@azneto , please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
Review checklist for @azneto
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referenced this issue
Jan 18, 2019
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To fix this do the following two things:
For a list of things I can do to help you, just type:
@ArtPoon, we are starting review in this issue tracker. To expedite the review process do you mind going through above list of check boxes and make sure they can be ticked (you can't tick them). Also check the PDF output carefully. Ping us here when you are done.
Thanks for your help @pjotrp. I confirm that I am unable to tick the checkboxes above.
I've read through the current article proof. The only issue I've noticed is that the capitalization of some article and journal titles was not properly protected in the
@ArtPoon, congratulations! This is a very useful tool to run the analyses on HIVdb. It considerably improves the user experience in every way by allowing to run analyses locally. I've ran the software a few times during the last days using Ubuntu. The software is well documented and runs really fast.
Though the documentation for the end users is really good and comprehensive, the code itself is not so inviting. It doesn't follow the PEP8 (Style Guide for Python Code) and the PEP20 (The Zen of Python). There are variables and libraries that were created/loaded and never used (eg. definitions, database, comments, pathlib.Path, requests, default_grange). The software flake8 can find those and also check if the code is compatible with the PEP8, in future releases. I also recommend using typing (https://docs.python.org/3/library/typing.html).
@ArtPoon The review process is now complete. To finalize your submission and
Second, we need you to deposit a copy of your software repository
To do so:
@pjotrp, I have deposited the current release of the repository to Zenodo, obtained and posted the DOI above. I also found and restored some missing DOIs for cited references in the paper. Unfortunately a couple of the journals we referenced do not provide DOIs (namely AIDS and Antiviral Therapy).
Further, I replaced a citation to a bioRxiv preprint with the recently published version of that manuscript (Rasmussen et al. 2018), and I removed a broken URL associated with Van Laethem et al. (2002).
Here's what you must now do:
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