[REVIEW]: papaya2 & Morphometer: 2D Irreducible Minkowski Tensor computation

whedon commented 4 years ago

Submitting author: @skapfer (Sebastian Kapfer) Repository: https://github.com/morphometry/papaya2 Version: v1.0.0 Editor: @hugoledoux Reviewers: @kenohori, @rmjarvis Archive: 10.5281/zenodo.4071543

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Review checklist for @kenohori

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 (@skapfer) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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?

Review checklist for @rmjarvis

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 (@skapfer) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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.
[ ] 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?

skapfer commented 4 years ago

Slight adjustment to the acknowledgments since we're postponing Morphometer to a separate paper. Proof looks good :-)

hugoledoux commented 4 years ago

We're thinking of 'Irreducible Minkowski Tensors' (IMTs for short) as a proper name, which is why we titlecased it. If that is not possible for some reason, we prefer titlecasing the whole title, i.e. "papaya2: 2D Irreducible Minkowski Tensor Computation".

If IMT is in the paper also then of course it's fine. Now "irreducible" is not capitalised in the paper! I'm good with anything, as long as consistent.

hugoledoux commented 4 years ago

@whedon check references

skapfer commented 4 years ago

@hugoledoux Good point. I've fixed capitalization the paper!

@whedon generate pdf from branch joss

skapfer commented 4 years ago

@whedon generate pdf from branch joss

whedon commented 4 years ago

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

whedon commented 4 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

arfon commented 4 years ago

@whedon check references from branch joss

whedon commented 4 years ago

Attempting to check references... from custom branch joss

arfon commented 4 years ago

@whedon check references from branch joss

whedon commented 4 years ago

Attempting to check references... from custom branch joss

arfon commented 4 years ago

@whedon check references from branch joss

whedon commented 4 years ago

Attempting to check references... from custom branch joss

whedon commented 4 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1088/1742-5468/2008/12/P12015 is OK
- 10.1088/1742-5468/2010/11/p11010 is OK
- 10.1063/1.4774084 is OK
- 10.1007/978-3-319-51951-7_13 is OK
- 10.1002/adma.201100562 is OK
- 10.1111/j.1365-2818.2009.03331.x is OK
- 10.1209/0295-5075/90/34001 is OK
- 10.1209/0295-5075/111/24002 is OK
- 10.1051/0004-6361:20010604 is OK
- 10.1140/epjb/e2006-00328-1 is OK
- 10.1016/j.actamat.2012.02.029 is OK
- 10.1209/0295-5075/128/60001 is OK
- 10.1088/1361-648x/aa57c7 is OK
- 10.1088/1475-7516/2019/01/009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

arfon commented 4 years ago

@hugoledoux - looks to be fixed now. Sorry for the noise debugging this.

hugoledoux commented 4 years ago

@arfon cheers. All were good!

hugoledoux commented 4 years ago

@skapfer one last thing needs to be done, you have a release but no version , since there is none so far I propose naming the release v1.0.0?

I guess it means updating the zenodo too, so please send me back the DOI if modified. Once this is done, we will formally accept it and your paper should be publish within a few days.

skapfer commented 4 years ago

Good point, the publication is a good point to start semantic versioning. I've tagged v1.0.0 and updated the Zenodo record. The DOI didn't change.

hugoledoux commented 4 years ago

@whedon set 10.5281/zenodo.4071543 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.4071543 is the archive.

hugoledoux commented 4 years ago

@whedon set v1.0.0 as version

whedon commented 4 years ago

OK. v1.0.0 is the version.

hugoledoux commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

PDF failed to compile for issue #2538 with the following error:

Can't find any papers to compile :-(

hugoledoux commented 4 years ago

@skapfer the editor-in-chief will now process/finalise the paper. And it should be published pretty soon.

arfon commented 4 years ago

@whedon accept from branch joss

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1088/1742-5468/2008/12/P12015 is OK
- 10.1088/1742-5468/2010/11/p11010 is OK
- 10.1063/1.4774084 is OK
- 10.1007/978-3-319-51951-7_13 is OK
- 10.1002/adma.201100562 is OK
- 10.1111/j.1365-2818.2009.03331.x is OK
- 10.1209/0295-5075/90/34001 is OK
- 10.1209/0295-5075/111/24002 is OK
- 10.1051/0004-6361:20010604 is OK
- 10.1140/epjb/e2006-00328-1 is OK
- 10.1016/j.actamat.2012.02.029 is OK
- 10.1209/0295-5075/128/60001 is OK
- 10.1088/1361-648x/aa57c7 is OK
- 10.1088/1475-7516/2019/01/009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1802

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1802, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch joss

danielskatz commented 4 years ago

@skapfer - please spell out A&A in the references

danielskatz commented 4 years ago

@arfon - is this waiting for anything else?

skapfer commented 4 years ago

@whedon check references from branch joss

whedon commented 4 years ago

Attempting to check references... from custom branch joss

whedon commented 4 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1088/1742-5468/2008/12/P12015 is OK
- 10.1088/1742-5468/2010/11/p11010 is OK
- 10.1063/1.4774084 is OK
- 10.1007/978-3-319-51951-7_13 is OK
- 10.1002/adma.201100562 is OK
- 10.1111/j.1365-2818.2009.03331.x is OK
- 10.1209/0295-5075/90/34001 is OK
- 10.1209/0295-5075/111/24002 is OK
- 10.1051/0004-6361:20010604 is OK
- 10.1140/epjb/e2006-00328-1 is OK
- 10.1016/j.actamat.2012.02.029 is OK
- 10.1209/0295-5075/128/60001 is OK
- 10.1088/1361-648x/aa57c7 is OK
- 10.1088/1475-7516/2019/01/009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

skapfer commented 4 years ago

@whedon generate pdf from branch joss

whedon commented 4 years ago

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

whedon commented 4 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

skapfer commented 4 years ago

@danielskatz Fixed!

arfon commented 4 years ago

@arfon - is this waiting for anything else?

Nope, good to go as far as I'm concerned.

danielskatz commented 4 years ago

@whedon accept deposit=true from branch joss

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/1804
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02538
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz commented 4 years ago

Congratulations to @skapfer (Sebastian Kapfer) and co-authors!!

Thanks to @kenohori and @rmjarvis for reviewing! And @hugoledoux for editing!

whedon commented 4 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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