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[REVIEW]: pycoQC, interactive quality control for Oxford Nanopore Sequencing #1236

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whedon opened this Issue Feb 5, 2019 · 8 comments

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whedon commented Feb 5, 2019

Submitting author: @a-slide (Adrien Leger)
Repository: https://github.com/a-slide/pycoQC
Version: v2.2.0
Editor: @pjotrp
Reviewer: @george-githinji
Archive: Pending

Status

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Status badge code:

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Markdown: [![status](http://joss.theoj.org/papers/ea8e08dc950622bdd5d16a65649954aa/status.svg)](http://joss.theoj.org/papers/ea8e08dc950622bdd5d16a65649954aa)

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

@george-githinji, 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 @george-githinji

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 (v2.2.0)?
  • Authorship: Has the submitting author (@a-slide) 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 Feb 5, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @george-githinji 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:

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

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

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whedon commented Feb 5, 2019

Attempting PDF compilation. Reticulating splines etc...
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pjotrp commented Feb 5, 2019

Dear @a-slide, 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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whedon commented Feb 5, 2019

@george-githinji george-githinji pinned this issue Feb 6, 2019

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a-slide commented Feb 6, 2019

Hi @pjotrp and @george-githinji,

I confirm that I can tick all the boxes, except automated tests. Indeed, there is no straightforward way to do it as the outputs of pycoQC methods are dynamic plots. One possibility is to inspect visually the outputs and compare it with other software which I have done. Reports generated from the same datasets with pycoQC, Nanoplot and MinIONQC are available online at https://www.ebi.ac.uk/~aleg/data/pycoQC_test/comparison/. Although the 3 programs have different implementation, the results are similar for all 3 summary files tested. If this is an acceptable solution to you, I am happy to upload the datasets on Zenodo to get a DOI.

In addition, I made a dew minor changes in pycoQC and updated the software version to 2.2.1.

Thanks

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pjotrp commented Feb 7, 2019

Thanks. I am fine with not having automated tests for visualisations. One improvement is to create regresssion tests (where you just compare the outputs). But I think that is for more complex systems.

@george-githinji you can start review.

@arfon arfon unpinned this issue Feb 7, 2019

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a-slide commented Feb 11, 2019

Hi @george-githinji
Let me know if there is anything I can do to help or if you need any extra test files.
Thanks

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george-githinji commented Feb 11, 2019

I am currently going through the package and the the paper submission. Should get back to you in 2 days. Thanks!

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