[REVIEW]: xrdfit: A Python package for fitting synchrotron X-ray diffraction spectra

whedon commented 4 years ago

Submitting author: @merrygoat (Peter Crowther) Repository: https://github.com/LightForm-group/xrdfit Version: v1.1.2 Editor: @jgostick Reviewers: @KedoKudo, @mikapfl Archive: 10.5281/zenodo.3997251

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Review checklist for @KedoKudo

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 (@merrygoat) 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?
[ ] 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 @mikapfl

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 (@merrygoat) 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?

whedon commented 4 years ago

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

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.5281/ZENODO.11813 is OK
- 10.1016/j.msea.2008.05.017 is OK
- 10.3390/met5042252 is OK
- 10.1016/j.msea.2016.01.059 is OK
- 10.1016/j.actamat.2017.04.028 is OK
- 10.1107/s1600576717004708 is OK
- 10.1107/s1600576715004306 is OK
- 10.1107/s1600577515002283 is OK
- 10.1107/s1600576715010390 is OK
- 10.1080/08957959608201408 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 years ago

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

arfon commented 4 years ago

@jgostick - you can add a new reviewer here (when you've identified one) with @whedon add @reviewer2 as reviewer. Unfortunately you'll need to do a small amount of manual work to add a checklist for the second reviewer (Whedon doesn't know how to do this yet). Any issues, let me know :-)

jgostick commented 4 years ago

@whedon add @mikapfl as reviewer

whedon commented 4 years ago

OK, @mikapfl is now a reviewer

KedoKudo commented 4 years ago

@jgostick - I finished my review of xrdfit and submitted my feedbacks to the developers on the corresponding repo (https://github.com/LightForm-group/xrdfit/issues/39, https://github.com/LightForm-group/xrdfit/issues/38).

@merrygoat and @christopher-daniel - please feel free to ping me if you have any questions about the feedbacks.

merrygoat commented 4 years ago

@KedoKudo Thank you very much for your feedback. I will address the feedback items individually on the issues you have raised in the xrdfit repository.

jgostick commented 4 years ago

Thanks @KedoKudo! @merrygoat can you let me know in this issue when you've made the changes?

@mikapfl, how is your review coming along? It's only been 3 weeks, but things seem to move so fast at JOSS.

mikapfl commented 4 years ago

Hi,

I've been down with a cold the last week, but hope to do some progress with the review this weekend.

Cheers

Mika

merrygoat commented 4 years ago

Thanks @jgostick. Done the easy changes already. My colleague @christopher-daniel is on holiday this week but we will meet to resolve the outstanding issues next week.

mikapfl commented 4 years ago

Hi,

I've looked into the paper itself. I think it is a nice and short description of the the capabilities of xrdfit and motivates well what the purpose of xrdfit is. I found only a couple of minor things which could be clearer:

In the first paragraph, you write:

The experiment requires a beamline, such as Diamond Light Source […]

However, the Diamond Light Source is a synchrotron radiation facility comprising many beamlines, so this is not quite correct. Maybe something along the lines "The experiment requires a beamline at a synchrotron radiation facily such as […]" or such might be better.

A little later you write:

However, since many intensity profiles are collected during each experiment, with detectors recording at speeds of up to 250 Hz (Diamond Light Source Ltd, 2020b),

Here, I think the web page of the I12 beamline at Diamond might not be an ideal citation. Maybe https://doi.org/10.1109/NSSMIC.2012.6551180 would be the best citation for the recording speeds of PILATUS3 X CdTe detectors? This is the best description of the PILATUS3 ASIC I know of. They specify a maximum frame rate of 500 Hz, which is not realized in the commercial 2M detector, which is described in detail at the web page of dectris: https://www.dectris.com/products/pilatus3/pilatus3-x-cdte-for-synchrotron/pilatus3-x-cdte-2m/ .

In figure 2, your choice of the colours red and green for the two right axes and the lines for temperature and deformation is not optimal, because it is not colourblind-friendly. Consider using colours with different grey levels or something like dotted or dashed lines.

Best Regards,

Mika

jgostick commented 4 years ago

Hi @merrygoat, did you notice the comments from @mikapfl above? He has a few 'unchecked' boxes for you to address, but this is almost over the finish line!

merrygoat commented 4 years ago

Thank you yes - we have added those paper changes here and here.

We are just finishing up the last of the issues the reviewers raised, and adding a little more documentation for the data preparation step and we should be good.

merrygoat commented 4 years ago

That's it - I think we have addressed all of the outstanding issues. Let me know if I have missed anything!

jgostick commented 4 years ago

@merrygoat Here is a list of what to do next:

[ ] Double check authors and affiliations (including ORCIDs)
[ ] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[ ] Archive the release on Zenodo/figshare/etc and post the DOI here.
[ ] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.

merrygoat commented 4 years ago

@jgostick Thank you.

ORCIDs and Names checked
Release v1.1.1 - https://github.com/LightForm-group/xrdfit/releases/tag/v1.1.1
Zenodo DOI: 10.5281/zenodo.3991638
Names match between Zenodo and paper

jgostick commented 4 years ago

@whedon set 10.5281/zenodo.3991638 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3991638 is the archive.

jgostick 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

- 10.5281/ZENODO.11813 is OK
- 10.1016/j.msea.2008.05.017 is OK
- 10.3390/met5042252 is OK
- 10.1016/j.msea.2016.01.059 is OK
- 10.1016/j.actamat.2017.04.028 is OK
- 10.1107/s1600576717004708 is OK
- 10.1107/s1600576715004306 is OK
- 10.1107/s1600577515002283 is OK
- 10.1107/s1600576715010390 is OK
- 10.1080/08957959608201408 is OK
- 10.1107/S1600576716000455 is OK
- 10.1107/S0021889869006558 is OK
- 10.1017/S0885715613001346 is OK
- 10.1109/NSSMIC.2012.6551180 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/1663

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1663, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

jgostick commented 4 years ago

Hi @merrygoat this paper is now acceptable, and an Editor in Chief will come make the final acceptance. Thanks to the reviewers their for time!

mikapfl commented 4 years ago

In the generated pdf (https://github.com/openjournals/joss-papers/blob/5c52f575ebfaac4c6c44846620f181dd6859ae5a/joss.02381/10.21105.joss.02381.pdf) the formatting of the citations at the end of the first paragraph looks funny. It somehow uses [] instead of () and the Hammersley_2016 also doesn't look right.

merrygoat commented 4 years ago

@mikapfl Thank you - you are right, we had missed an @ symbol there. Corrected and released as version v1.1.2.

@jgostick Is it possible to tell whedon to use another version? The updated doi is: 10.5281/zenodo.3997251

We would also like to thank both reviewers - your comments were insightful and lead to significant improvements.

arfon commented 4 years ago

@whedon set v1.1.2 as version

whedon commented 4 years ago

OK. v1.1.2 is the version.

arfon commented 4 years ago

@whedon set 10.5281/zenodo.3997251 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3997251 is the archive.

arfon commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

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/1672

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1672, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.5281/ZENODO.11813 is OK
- 10.1016/j.msea.2008.05.017 is OK
- 10.3390/met5042252 is OK
- 10.1016/j.msea.2016.01.059 is OK
- 10.1016/j.actamat.2017.04.028 is OK
- 10.1107/s1600576717004708 is OK
- 10.1107/s1600576715004306 is OK
- 10.1107/s1600577515002283 is OK
- 10.1107/s1600576715010390 is OK
- 10.1080/08957959608201408 is OK
- 10.1107/S1600576716000455 is OK
- 10.1107/S0021889869006558 is OK
- 10.1017/S0885715613001346 is OK
- 10.1109/NSSMIC.2012.6551180 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Kevin-Mattheus-Moerman commented 4 years ago

@merrygoat These are some required steps before we proceed:

[x] Please amend the archive meta data, in terms of the title and authors (you can edit this on ZENODO) such that it matches your paper (@jgostick, thanks for handling this submission. For future reference this :point_up: is a check the handling editor should also do).
[x] I've checked your paper and it seems in order. This work is about to be processed for acceptance. If you haven't already re-read your paper now is the time to give it a final check (in particular author names, affiliations, and acknowledgements).

merrygoat commented 4 years ago

@Kevin-Mattheus-Moerman Ah yes - thank you. I forgot I would have to update the metadata again with the new version. I have done that now.

I am also happy with the proof.

Kevin-Mattheus-Moerman 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 (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.5281/ZENODO.11813 is OK
- 10.1016/j.msea.2008.05.017 is OK
- 10.3390/met5042252 is OK
- 10.1016/j.msea.2016.01.059 is OK
- 10.1016/j.actamat.2017.04.028 is OK
- 10.1107/s1600576717004708 is OK
- 10.1107/s1600576715004306 is OK
- 10.1107/s1600577515002283 is OK
- 10.1107/s1600576715010390 is OK
- 10.1080/08957959608201408 is OK
- 10.1107/S1600576716000455 is OK
- 10.1107/S0021889869006558 is OK
- 10.1017/S0885715613001346 is OK
- 10.1109/NSSMIC.2012.6551180 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/1687

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1687, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

Kevin-Mattheus-Moerman 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/1688
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02381
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

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:

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[![DOI](https://joss.theoj.org/papers/10.21105/joss.02381/status.svg)](https://doi.org/10.21105/joss.02381)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.02381/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02381/status.svg
   :target: https://doi.org/10.21105/joss.02381

This is how it will look in your documentation:

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Kevin-Mattheus-Moerman commented 4 years ago

Congratulations @merrygoat.

@KedoKudo, @mikapfl thanks for reviewing this work for JOSS!

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