[REVIEW]: ASCENDS: Advanced data SCiENce toolkit for Non-Data Scientists

whedon commented 5 years ago

Submitting author: @ornlpmcp (Sangkeun Lee) Repository: https://github.com/ornlpmcp/ASCENDS Version: 0.4.1 Editor: @terrytangyuan Reviewer: @zhampel, @jrbourbeau Archive: 10.5281/zenodo.3635782

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

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

Make sure you're logged in to your GitHub account
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 @terrytangyuan know.

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

Review checklist for @zhampel

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Version: 0.4.1
[x] Authorship: Has the submitting author (@ornlpmcp) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

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

Review checklist for @jrbourbeau

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Version: 0.4.1
[x] Authorship: Has the submitting author (@ornlpmcp) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

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

zhampel commented 4 years ago

@terrytangyuan Yes, I'll chip away at this during this week, as NeurIPS is taking most of my time ;) I'll get back by the end of the week.

ornlpmcp commented 4 years ago

@zhampel @jrbourbeau this is a friendly reminder for reviewers :) happy holidays

ornlpmcp commented 4 years ago

@terrytangyuan Happy new year! Would you please help move this forward? Thanks a lot!

terrytangyuan commented 4 years ago

The reviewers probably already received enough notifications. I’d expect some delays due to the holidays so let us be patient.

labarba commented 4 years ago

👋 @terrytangyuan — would you like to reach out to the reviewers via email, at this point? It's been a long while...

terrytangyuan commented 4 years ago

Yes I’ve reached out by email.

ornlpmcp commented 4 years ago

@labarba @terrytangyuan @zhampel @jrbourbeau Thank you all for reviewing this submission. It has been 2 months since I updated my responses. I do understand you're all busy, but I would deeply appreciate if you could take a look at my responses and help us move forward. Big thanks,

jrbourbeau commented 4 years ago

I've done another review iteration and have no further review comments. Thanks for your hard work and patience @ornlpmcp

terrytangyuan commented 4 years ago

@labarba Any suggestions? Looks like we are only waiting for @zhampel now.

zhampel commented 4 years ago

@ornlpmcp thanks for addressing my previous comments, and indeed the install functions as advertised. I have completed my review and have no further comments. Apologies for the delays.

terrytangyuan commented 4 years ago

Thanks everyone!

terrytangyuan commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary:

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.actamat.2019.02.017 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1080/14686996.2017.1371559 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/adts.201800196 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1136/bmj.e4483 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1073/pnas.1309933111 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1109/ICCV.2003.1238308 is INVALID because of 'https://doi.org/' prefix

terrytangyuan commented 4 years ago

@ornlpmcp Could you fix the above issues with DOIs?

ornlpmcp commented 4 years ago

@terrytangyuan I made fixes and pushed it. Thanks a lot!

terrytangyuan commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1016/j.actamat.2019.02.017 is OK
- 10.1080/14686996.2017.1371559 is OK
- 10.1002/adts.201800196 is OK
- 10.1136/bmj.e4483 is OK
- 10.1073/pnas.1309933111 is OK
- 10.1109/ICCV.2003.1238308 is OK

MISSING DOIs

- None

INVALID DOIs

- None

terrytangyuan commented 4 years ago

@ornlpmcp Thanks! At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

The title of the archive is the same as the JOSS paper title
That the authors of the archive are the same as the JOSS paper authors I can then move forward with accepting the submission.

ornlpmcp commented 4 years ago

@terrytangyuan 0.4.1 release has been made. I created an archive of the software in Zenodo and here is the DOI on Zenodo: 10.5281/zenodo.3635782

ornlpmcp commented 4 years ago

https://zenodo.org/record/3635782#.Xjl2ZxNKjxg

terrytangyuan commented 4 years ago

@whedon set 10.5281/zenodo.3635782 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3635782 is the archive.

terrytangyuan commented 4 years ago

@whedon set 0.4.1 as version

whedon commented 4 years ago

OK. 0.4.1 is the version.

terrytangyuan commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1016/j.actamat.2019.02.017 is OK
- 10.1080/14686996.2017.1371559 is OK
- 10.1002/adts.201800196 is OK
- 10.1136/bmj.e4483 is OK
- 10.1073/pnas.1309933111 is OK
- 10.1109/ICCV.2003.1238308 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1266

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1266, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

terrytangyuan commented 4 years ago

@openjournals/joss-eics The paper looks good now. Could you take it from here?

whedon commented 4 years ago

I'm sorry @ornlpmcp, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

kthyng commented 4 years ago

I am taking over the submission from here. I've been looking through your paper and have found errors. Please consider the pull requests: #10 and #9.

I have some remaining concerns about the references:

MaTerialS: is this properly written with strange capitalization?
two of the references have "et al" — is there a reason you are not including the full author list?

ornlpmcp commented 4 years ago

@whedon generate pdf

ornlpmcp commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

PDF failed to compile for issue #1656 with the following error:

sh: 0: getcwd() failed: No such file or directory pandoc: 10.21105.joss.01656.pdf: openBinaryFile: does not exist (No such file or directory) Looks like we failed to compile the PDF

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

ornlpmcp commented 4 years ago

@kthyng I fixed capitalization, merged pull requests, and added full list of authors. Thanks a lot.

kthyng commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

kthyng commented 4 years ago

@ornlpmcp Have your changes been merged? I don't see updates in the latest proof.

ornlpmcp commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

ornlpmcp commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

ornlpmcp commented 4 years ago

@kthyng I see my changes in the latest proof. please let me know if there needs to be any updates. Thanks a lot for your support.

kthyng commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

kthyng commented 4 years ago

@ornlpmcp Sorry about the delay but I can't seem to get your changes to the bib file to come through to the generated file. I tried a different browser and had the same problem, though when I went to edit the bib files I then was able to see that you had updated them. I'm still seeing "et al"s in three entries, for example.

@openjournals/dev do you know of a way to force the new code to be used?

kthyng commented 4 years ago

Ok ok, I see — there was some delay at first, but I think what's happening now is our bib renderer converts the list of authors to "et al" after some number of authors.

kthyng commented 4 years ago

@ornlpmcp please check out this pull request to finish up your references.

ornlpmcp commented 4 years ago

@kthyng your latest pull request has been metged thanks again

openjournals / joss-reviews