Closed whedon closed 5 years ago
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @azneto it looks like you're currently assigned as the reviewer for this paper :tada:.
:star: Important :star:
If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews πΏ
To fix this do the following two things:
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@whedon commands
Attempting PDF compilation. Reticulating splines etc...
@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 .bib
file. I have made corrections - is it ok for me to re-render the proof?
Of course. '@whedon generate pdf' will do it.
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
OK @pjotrp, I've checked the revised PDF output and it looks OK to me.
Thanks @ArtPoon. @azneto you can start review here. Please read the reviewer guidelines above.
@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).
The software should be ACCEPTED with minor revisions: https://github.com/PoonLab/sierra-local/issues/52 https://github.com/PoonLab/sierra-local/issues/53
Thank you @azneto. @ArtPoon ping me when you are done. There are tools to automatically convert styles, btw. Also for PEP8. Good idea to try mentioned flake8.
Also a good idea to add a few lines on community guidelines. How can people contribute. Sometimes it happens ;)
@ArtPoon, the style is important but not required for this review. Just focus on the two pending issues and let the other improvements for the next releases.
Thanks @azneto for your review! As you suggest, I will address the issues you've opened for the paper, and then in the longer term work on improving the code style. I'll also add a CONTRIBUTING
file as suggested and report back here.
Hi @azneto and @pjotrp, I've addressed and closed the issues.
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
@ArtPoon The review process is now complete. To finalize your submission and accept your paper in JOSS, we need two things. First, can you confirm that all references in your bibliography have a DOI in the bibliography (if one exists).
Second, we need you to deposit a copy of your software repository (including any revisions made during the JOSS review process) with a data-archiving service.
To do so:
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
@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).
Hi @ArtPoon, can you post the zenodo or figshare doi of the software release here?
I did post the Zenodo DOI in this issue.
Ah, sorry. Somehow it did not show.
@whedon set 10.5281/zenodo.2548745 as archive
OK. 10.5281/zenodo.2548745 is the archive.
@whedon accept
Attempting dry run of processing paper acceptance...
Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/455
If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/455, then you can now move forward with accepting the submission by compiling again with the flag deposit=true
e.g.
@whedon accept deposit=true
@arfon I think we are ready!
@whedon accept deposit=true
Doing it live! Attempting automated processing of paper acceptance...
π¨π¨π¨ THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! π¨π¨π¨
Here's what you must now do:
Party like you just published a paper! πππ¦ππ»π€
Any issues? notify your editorial technical team...
@azneto - many thanks for your review and to @pjotrp for editing this submission β¨
@ArtPoon - your paper is now accepted into JOSS :zap::rocket::boom:
:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:
If you would like to include a link to your paper from your README use the following code snippets:
Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01186/status.svg)](https://doi.org/10.21105/joss.01186)
HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01186">
<img src="http://joss.theoj.org/papers/10.21105/joss.01186/status.svg" alt="DOI badge" >
</a>
reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01186/status.svg
:target: https://doi.org/10.21105/joss.01186
This is how it will look in your documentation:
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Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:
Thanks @azneto for your review and @pjotrp for handling the process! This has been a fascinating experience :grinning:
Submitting author: @ArtPoon (Art Poon) Repository: https://github.com/PoonLab/sierra-local Version: v0.1.2 Editor: @pjotrp Reviewer: @azneto Archive: 10.5281/zenodo.2548745
Status
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Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)
Reviewer instructions & questions
@azneto , please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @pjotrp know.
β¨ Please try and complete your review in the next two weeks β¨
Review checklist for @azneto
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
paper.md
file include a list of authors with their affiliations?