[REVIEW]: ACHR.cu: GPU sampling of metabolic networks.

whedon commented 5 years ago

Submitting author: @marouenbg (Marouen Ben Guebila) Repository: https://github.com/marouenbg/ACHR.cu Version: v0.2 Editor: @lpantano Reviewer: @wmegchel, @prasunanand Archive: 10.5281/zenodo.3233085

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/536aea75c0eadd41db178b1ca9604067"><img src="http://joss.theoj.org/papers/536aea75c0eadd41db178b1ca9604067/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/536aea75c0eadd41db178b1ca9604067/status.svg)](http://joss.theoj.org/papers/536aea75c0eadd41db178b1ca9604067)

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

@wmegchel & @prasunanand, 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @lpantano know.

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

Review checklist for @wmegchel

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: v0.2
[x] Authorship: Has the submitting author (@marouenbg) 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 @prasunanand

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: v0.2
[x] Authorship: Has the submitting author (@marouenbg) 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)?

marouenbg commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

marouenbg commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

lpantano commented 5 years ago

@whedon set 0.2 as version

whedon commented 5 years ago

OK. 0.2 is the version.

lpantano commented 5 years ago

@whedon set v0.2 as version

whedon commented 5 years ago

OK. v0.2 is the version.

lpantano commented 5 years ago

hi @marouenbg ,

thanks for the changes. Can you create now a zenodo archive and give me the DOI, after that we can proceed with the aceptance. Remember that the title and authors should match the paper information.

Thanks!

marouenbg commented 5 years ago

Hi @lpantano , here is the zenodo archive https://zenodo.org/record/3233085#.XO02GNNKii4 DOI/10.5281/zenodo.3233085

lpantano commented 5 years ago

@whedon set 10.5281/zenodo.3233085 as archive

whedon commented 5 years ago

OK. 10.5281/zenodo.3233085 is the archive.

lpantano commented 5 years ago

Hi @openjournals/joss-eics,

I think this is complete!

kyleniemeyer commented 5 years ago

Hi @marouenbg, I just submitted two minor PRs for the paper and references; could you merge those and then we can rebuild the PDF?

kyleniemeyer commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

marouenbg commented 5 years ago

Done! Thanks @kyleniemeyer for spotting them out.

whedon commented 5 years ago

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

kyleniemeyer commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


OK DOIs

- 10.1371/journal.pone.0086587 is OK
- 10.1101/440701 is OK
- 10.1145/1365490.1365500 is OK
- 10.1287/opre.46.1.84 is OK
- 10.1109/hpcsim.2014.6903792 is OK
- 10.1038/s41596-018-0098-2 is OK
- 10.1016/j.cell.2015.05.019 is OK
- 10.1016/j.ymben.2003.09.002 is OK
- 10.1109/99.660313 is OK
- 10.1007/bf02989823 is OK
- 10.1038/nbt.2488 is OK
- 10.1128/ecosalplus.10.2.1 is OK
- 10.1186/1752-0509-2-79 is OK
- 10.1007/978-3-642-22194-1_4 is OK
- 10.1145/3297663.3310308 is OK
- 10.1016/j.jpdc.2019.01.001 is OK

MISSING DOIs

- None

INVALID DOIs

- None

kyleniemeyer commented 5 years ago

@whedon accept

whedon commented 5 years ago

Attempting dry run of processing paper acceptance...

whedon commented 5 years ago


OK DOIs

- 10.1371/journal.pone.0086587 is OK
- 10.1101/440701 is OK
- 10.1145/1365490.1365500 is OK
- 10.1287/opre.46.1.84 is OK
- 10.1109/hpcsim.2014.6903792 is OK
- 10.1038/s41596-018-0098-2 is OK
- 10.1016/j.cell.2015.05.019 is OK
- 10.1016/j.ymben.2003.09.002 is OK
- 10.1109/99.660313 is OK
- 10.1007/bf02989823 is OK
- 10.1038/nbt.2488 is OK
- 10.1128/ecosalplus.10.2.1 is OK
- 10.1186/1752-0509-2-79 is OK
- 10.1007/978-3-642-22194-1_4 is OK
- 10.1145/3297663.3310308 is OK
- 10.1016/j.jpdc.2019.01.001 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 5 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/719

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/719, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

lpantano commented 5 years ago

Do the last changes change the Zenode DOI or/and version?

kyleniemeyer commented 5 years ago

@lpantano they were only minor changes to the paper, which we archive, so I wasn't worried about updating the Zenodo record

kyleniemeyer commented 5 years ago

@whedon accept deposit=true

whedon commented 5 years ago

Doing it live! Attempting automated processing of paper acceptance...

whedon commented 5 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 5 years ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/720
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01363
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

kyleniemeyer commented 5 years ago

Congrats @marouenbg on your paper's publication in JOSS! Thanks also to @wmegchel and @prasunanand for reviewing, and @lpantano for editing!

whedon commented 5 years ago

: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.01363/status.svg)](https://doi.org/10.21105/joss.01363)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01363">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01363/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01363/status.svg
   :target: https://doi.org/10.21105/joss.01363

This is how it will look in your documentation:

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marouenbg commented 4 years ago

@kyleniemeyer @arfon I just realized I had small typo in the title. First, a dash is missing in gpu accelerated. Second the title line ends with a full stop, which gives me references with two full stops. Is it possible to amend the title? Otherwise it is fine like it is.

arfon commented 4 years ago

@marouenbg - can you make your changes to the paper.md file and I can then update the paper.

marouenbg commented 4 years ago

@arfon I just corrected the title in paper.md. Thanks!

arfon commented 4 years ago

OK that's now updated. The changes might take a few hours to update as there's caching in place on the JOSS site.

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