[REVIEW]: SODAR Core #1584

whedon · 2019-07-19T14:46:44Z

Submitting author: @mikkonie (Mikko Nieminen)
Repository: https://github.com/bihealth/sodar_core
Version: v0.6.2
Editor: @lpantano
Reviewer: @rbatorsky, @olgabot
Archive: Pending

Status

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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) by leaving comments 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

@rbatorsky & @olgabot, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @lpantano know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @rbatorsky

Conflict of interest

As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

I confirm that I read and will adhere to the JOSS 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 (v0.6.2)?
Authorship: Has the submitting author (@mikkonie) 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)?

Review checklist for @olgabot

Conflict of interest

As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

I confirm that I read and will adhere to the JOSS 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 (v0.6.2)?
Authorship: Has the submitting author (@mikkonie) 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)?

whedon · 2019-07-19T14:46:48Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @rbatorsky, @olgabot it looks like you're currently assigned to review this paper 🎉.

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whedon · 2019-07-19T14:46:49Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-07-19T14:47:11Z

👉 Check article proof 📄 👈

olgabot · 2019-07-22T14:36:58Z

Hello, it seems that I am not able to edit the first comment to complete the checklist. Could you add me as an editor for this PR?

@whedon commands

danielskatz · 2019-07-22T14:38:10Z

Please see the first comment in this issue - you need to accept the invitation...

olgabot · 2019-07-22T14:46:13Z

Ah sorry! I skipped that section somehow. Thank you!

lpantano · 2019-08-12T13:59:25Z

Hi @mikkonie, wanted to check if everything is ok, and you are not waiting for us but trying to address the issues opened by the reviewers.

Hi @olgabot, any chance you could update the checklist above for the items that are ok?

Thank you all!

lpantano · 2019-09-02T16:56:45Z

👋 @mikkonie, any update on this? if you are not able to work on this right now, we can pause this review until you can work again. Thanks.

lpantano · 2019-10-03T13:23:05Z

@mikkonie, I am going to pause this for now. Let me know when you have time to continue.

mikkonie · 2019-10-08T11:38:02Z

Hello,

Apologies for the radio silence @lpantano. I have actually made changes as suggested by your comments into the master branch of the project and commented on these changes in the issue tickets raised in our project. I missed the updates here and didn't realize I also had to respond in this issue.

Again, sorry about this. Please let me know if you have further comments regarding the issues as they've currently been handled.

lpantano · 2019-10-08T13:19:02Z

Thanks! @olgabot , @rbatorsky, let me know if you can continue with the review.

rbatorsky · 2019-10-08T13:25:10Z

Hi all,
Sorry, I missed the update.
I'll be able to review the changes and hopefully complete the review this week.
Thanks,
Rebecca

olgabot · 2019-10-10T21:15:02Z

Sorry, I missed the update as well. I'll take a look this week. Thank you for the ping!

rbatorsky · 2019-10-16T16:50:09Z

Hello,
I've gone through and read the updates. I submitted one issue about installation bihealth/sodar_core#6 but other than that I think I've completed my review.
Best,
Rebecca

lpantano · 2019-10-18T11:46:38Z

Thank you @rbatorsky, @olgabot remember to check the boxes when you are finishing each point. Thanks!

mikkonie · 2019-10-28T09:57:20Z

Hello,

FYI, I made changes according to @rbatorsky's new issue and detailed them in the issue comments.

-Mikko

lpantano · 2019-10-30T13:44:54Z

Thank you. I will wait for @olgabot to finish the review. Thanks.

olgabot · 2019-11-02T02:10:40Z

Took a look at this, and have some questions/concerns:

The release version is now 0.7.0, but this issue refers to 0.6.2 -- should this get updated in the issue?
I've never used Django before, and I can't seem to get my mind around what this package does and how to use it, and thus cannot evaluate the functionality or performance. Continued the discussion here: bihealth/sodar_core#4
"Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems)." (emphasis mine) -- It's not clear to me how this solves analysis problems. So far, I can tell that there is a web server but I don't understand how to set it up or how it can help solve analysis problems

kthyng · 2019-11-19T18:42:23Z

hi @mikkonie! Have you had a chance to address comments from @olgabot?

danielskatz · 2019-12-05T10:38:59Z

👋 @mikkonie - it looks like this review is waiting on you...

whedon assigned lpantano Jul 19, 2019

whedon added the review label Jul 19, 2019

whedon mentioned this issue Jul 19, 2019

[PRE REVIEW]: SODAR Core #1547

Closed

whedon assigned rbatorsky Jul 20, 2019

olgabot mentioned this issue Jul 22, 2019

Add installation instructions in README and docs #3

Open

olgabot mentioned this issue Jul 22, 2019

Add example workflow or use case #4

Open

rbatorsky mentioned this issue Jul 22, 2019

Instructions for use within Docker container #5

Closed

whedon assigned olgabot Jul 23, 2019

lpantano mentioned this issue Jul 23, 2019

[PRE REVIEW]: ivis: dimensionality reduction in very large datasets using Siamese Networks #1583

Closed

lpantano added the paused label Oct 3, 2019

lpantano removed the paused label Oct 8, 2019

olgabot mentioned this issue Nov 2, 2019

Add community guidelines for getting help and contributing #8

Open

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[REVIEW]: SODAR Core #1584

Comments

whedon commented Jul 19, 2019 • edited by olgabot

Status

Reviewer instructions & questions

Review checklist for @rbatorsky

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @olgabot

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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whedon commented Jul 19, 2019 •

edited by olgabot

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