[REVIEW]: EspressoDB: A scientific database for managing high-performance computing workflows

whedon commented 4 years ago

Submitting author: @ckoerber (Christopher Körber) Repository: https://github.com/callat-qcd/espressodb Version: v1.1.0 Editor: @gkthiruvathukal Reviewer: @remram44, @ixjlyons Archive: 10.5281/zenodo.3677432

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

@remram44 & @ixjlyons, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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

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

Review checklist for @remram44

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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] Contribution and authorship: Has the submitting author (@ckoerber) 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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @ixjlyons

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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] Contribution and authorship: Has the submitting author (@ckoerber) 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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

kyleniemeyer commented 4 years ago

@ckoerber actually, it looks like one of your citations to an arXiv preprint (Berkowitz 2018) has since been published, can you update the info? https://doi.org/10.1109/sc.2018.00058

cchang5 commented 4 years ago

@kyleniemeyer Thank you for pointing this out. We have updated the citation.

kyleniemeyer commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

kyleniemeyer 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

- 10.1109/sc.2018.00054 is OK
- 10.1109/SC.2018.00060 is OK
- 10.1109/SC.2018.00058 is OK
- 10.1038/s41586-018-0161-8 is OK
- 10.1103/PhysRevLett.121.172501 is OK
- 10.1051/epjconf/201817509007 is OK
- 10.1103/PhysRevD.82.094502 is OK
- 10.1093/nar/gkt328 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/1333

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1333, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

cchang5 commented 4 years ago

Sorry... The new citation was referenced twice. I missed the second time.

kyleniemeyer commented 4 years ago

@cchang5 did you correct this? nothing has been finalized yet

ckoerber commented 4 years ago

Hello @kyleniemeyer,

Yes the second reference is now updated as well. The updates to the references (only changes) are on the master branch which is now ahead of the previous v1.1.0 tag. Do we have to move or create a new tag for the submission (if so, do we have to updated the Zenodo doi as well)?

kyleniemeyer commented 4 years ago

@ckoerber no, we aren't concerned with a minor update to the article—we archive that. I'll proceed with the existing Zenodo archive and version.

kyleniemeyer 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

- 10.1109/sc.2018.00054 is OK
- 10.1109/SC.2018.00060 is OK
- 10.1109/SC.2018.00058 is OK
- 10.1038/s41586-018-0161-8 is OK
- 10.1103/PhysRevLett.121.172501 is OK
- 10.1051/epjconf/201817509007 is OK
- 10.1103/PhysRevD.82.094502 is OK
- 10.1093/nar/gkt328 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/1334

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1334, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

kyleniemeyer commented 4 years ago

@whedon accept deposit=true

whedon commented 4 years ago

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

whedon commented 4 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 4 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/1335
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02007
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 4 years ago

Congrats @ckoerber & @cchang5 on your article's publication in JOSS!

Many thanks to @remram44 and @ixjlyons for reviewing this, and @gkthiruvathukal for editing.

whedon commented 4 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](https://joss.theoj.org/papers/10.21105/joss.02007/status.svg)](https://doi.org/10.21105/joss.02007)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02007">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02007/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02007/status.svg
   :target: https://doi.org/10.21105/joss.02007

This is how it will look in your documentation:

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