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[REVIEW]: sierra-local: A lightweight standalone application for drug resistance prediction #1186

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whedon opened this Issue Jan 18, 2019 · 41 comments

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whedon commented Jan 18, 2019

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

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/c280ed01729b1e5a0631642a69d8e9cc"><img src="http://joss.theoj.org/papers/c280ed01729b1e5a0631642a69d8e9cc/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/c280ed01729b1e5a0631642a69d8e9cc/status.svg)](http://joss.theoj.org/papers/c280ed01729b1e5a0631642a69d8e9cc)

Reviewers and authors:

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:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @pjotrp know.

Please try and complete your review in the next two weeks

Review checklist for @azneto

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Version: Does the release version given match the GitHub release (v0.1.2)?
  • Authorship: Has the submitting author (@ArtPoon) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
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whedon commented Jan 18, 2019

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 🎉.

⭐️ Important ⭐️

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 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

For a list of things I can do to help you, just type:

@whedon commands
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whedon commented Jan 18, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Jan 18, 2019

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pjotrp commented Jan 18, 2019

@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.

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ArtPoon commented Jan 18, 2019

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?

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pjotrp commented Jan 19, 2019

Of course. '@whedon generate pdf' will do it.

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ArtPoon commented Jan 22, 2019

@whedon generate pdf

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whedon commented Jan 22, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Jan 22, 2019

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ArtPoon commented Jan 22, 2019

OK @pjotrp, I've checked the revised PDF output and it looks OK to me.

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pjotrp commented Jan 22, 2019

Thanks @ArtPoon. @azneto you can start review here. Please read the reviewer guidelines above.

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azneto commented Jan 22, 2019

@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:
PoonLab/sierra-local#52
PoonLab/sierra-local#53

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pjotrp commented Jan 22, 2019

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.

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pjotrp commented Jan 22, 2019

Also a good idea to add a few lines on community guidelines. How can people contribute. Sometimes it happens ;)

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azneto commented Jan 22, 2019

@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.

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ArtPoon commented Jan 22, 2019

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.

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ArtPoon commented Jan 23, 2019

Hi @azneto and @pjotrp, I've addressed and closed the issues.

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pjotrp commented Jan 24, 2019

@whedon generate pdf

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whedon commented Jan 24, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Jan 24, 2019

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pjotrp commented Jan 24, 2019

@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:

  1. Create a GitHub release of the
    current version of your software repository
  2. Deposit that release with Zenodo, figshare,
    or a similar DOI issuer.
  3. Post a comment here with the DOI for the release.
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ArtPoon commented Jan 24, 2019

DOI

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ArtPoon commented Jan 24, 2019

@whedon generate pdf

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whedon commented Jan 24, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Jan 24, 2019

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ArtPoon commented Jan 24, 2019

@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).

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pjotrp commented Jan 25, 2019

Hi @ArtPoon, can you post the zenodo or figshare doi of the software release here?

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ArtPoon commented Jan 25, 2019

I did post the Zenodo DOI in this issue.

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pjotrp commented Jan 25, 2019

Ah, sorry. Somehow it did not show.

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pjotrp commented Jan 25, 2019

@whedon set 10.5281/zenodo.2548745 as archive

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whedon commented Jan 25, 2019

OK. 10.5281/zenodo.2548745 is the archive.

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pjotrp commented Jan 25, 2019

@whedon accept

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whedon commented Jan 25, 2019

Attempting dry run of processing paper acceptance...
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whedon commented Jan 25, 2019

Check final proof 👉 openjournals/joss-papers#455

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#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
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pjotrp commented Jan 25, 2019

@arfon I think we are ready!

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arfon commented Jan 25, 2019

@whedon accept deposit=true

@whedon whedon added the accepted label Jan 25, 2019

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whedon commented Jan 25, 2019

Doing it live! Attempting automated processing of paper acceptance...
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whedon commented Jan 25, 2019

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#456
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01186
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

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arfon commented Jan 25, 2019

@azneto - many thanks for your review and to @pjotrp for editing this submission

@ArtPoon - your paper is now accepted into JOSS ⚡️🚀💥

@arfon arfon closed this Jan 25, 2019

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whedon commented Jan 25, 2019

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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:

DOI

We need your help!

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:

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ArtPoon commented Jan 25, 2019

Thanks @azneto for your review and @pjotrp for handling the process!
This has been a fascinating experience 😀

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