[REVIEW]: CollatriX: A GUI to collate MorphoMetriX outputs

whedon commented 4 years ago

Submitting author: @cbirdferrer (Clara Bird) Repository: https://github.com/cbirdferrer/collatrix Version: v1.0.5 Editor: @KristinaRiemer Reviewer: @evaristor, @katmratliff Archive: 10.5281/zenodo.3937611

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Markdown: [![status](https://joss.theoj.org/papers/b8a3517580cb619a25a2932b08006639/status.svg)](https://joss.theoj.org/papers/b8a3517580cb619a25a2932b08006639)

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

@evaristor & @katmratliff, 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 @KristinaRiemer know.

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

Review checklist for @evaristor

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 (@cbirdferrer) 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?

Review checklist for @katmratliff

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 (@cbirdferrer) 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. @evaristor, @katmratliff it looks like you're currently assigned to review this paper :tada:.

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whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.21105/joss.01825 is OK
- 10.1002/ecs2.1468 is OK
- 10.3389/fmars.2017.00366 is OK
- 10.3354/meps12522 is OK
- 10.1111/mms.12527 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 years ago

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

KristinaRiemer commented 4 years ago

@arfon is whedon supposed to auto-assign both reviewers as assignees to the Review issue? It looks like it missed @katmratliff here.

arfon commented 4 years ago

@KristinaRiemer - Whedon can only do this once the reviewer has accepted the invite (which it looks like they now have). Whedon then updates assignments nightly so by tomorrow the assignments should look correct.

devarops commented 4 years ago

This software will be very useful to the users of MorphoMetriX since it automates the collation of the MorphoMetriX outputs with the aid of a friendly GUI. I suggest the authors make the following Minor Revisions before acceptance.

From the checklist

[x] Automated tests: There are no automated tests. I suggest using pytest-qt (or Qt Test) in conjunction with GitHub Actions or Travis. You can find more information here:
PyQt: GUI Testing
Test PyQt GUIs with QTest and unittest
[x] Community guidelines: Please add a section in the README with guidelines for third parties wishing to 1) contribute to the software, 2) report issues or problems with the software, and 3) seek support.

Additional suggestions

[x] Help messages: The messages in the dialog boxes (titles and names of fields) are too brief. On the other hand, the description in the README (and even the comments in the code) are satisfactorily detailed. I suggest adding text boxes to the GUI with more detailed information.
[x] Commented-out code: Please remove the commented-out code. Lines 2 and 19 of setup.py and lines 6, 12, 16, and 17 of meta.yaml are commented out. You can find more information about why that is considered a bad idea here:
Please, don’t commit commented-out code
Don’t share commented-out code
[x] Build: Please show how to build the package. You could add a shell script, a Makefile, or a GitHub Actions (or Travis) configuration file that includes the command used to build the conda package.
[x] Output: The header in column 1 of the output CSV file is blank. Please add a header to the first column of the output to ensure that it is a valid CSV file.

I added these suggestions as issues on the CollatriX repo.

KristinaRiemer commented 4 years ago

Hi @katmratliff, have you had a chance to look at this submission yet?

katmratliff commented 4 years ago

Hi @KristinaRiemer I am planning to complete my review this week.

KristinaRiemer commented 4 years ago

Great, thanks so much @katmratliff!

katmratliff commented 4 years ago

Hi @KristinaRiemer, I have completed my review and have submitted the following suggestions via issues in the repository:

Under the Documentation checklist, I have currently left Functionality documentation unchecked because additional information is needed in the input dialog boxes (or a link to the documentation). I have also left Automated tests unchecked because there is currently no documentation on how to run the tests manually.

UPDATE: these suggestions have now been addressed.

devarops commented 4 years ago

@KristinaRiemer: I recommend accepting this paper in its current form

KristinaRiemer commented 4 years ago

@evaristor thank you for confirming your acceptance! @katmratliff if you are also satisfied with this at this point, could you please confirm that?

katmratliff commented 4 years ago

@KristinaRiemer yes I recommend accepting as well

KristinaRiemer commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

KristinaRiemer commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.21105/joss.01825 is OK
- 10.1002/ecs2.1468 is OK
- 10.3389/fmars.2017.00366 is OK
- 10.3354/meps12522 is OK
- 10.1111/mms.12527 is OK

MISSING DOIs

- None

INVALID DOIs

- None

KristinaRiemer commented 4 years ago

Thank you for your reviews @evaristor and @katmratliff!

@cbirdferrer, I'm just going through the article proof linked above for correct DOIs, typos, etc., which you should do also to make sure it looks good to you.

I only found a couple minors things that you can fix when you get a chance:

Dawson (2017) reference is missing some authors
There is inconsistency between whether or not a comma follows "i.e."; I've been taught that it should always be "i.e.,"?

cbirdferrer commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

cbirdferrer commented 4 years ago

Thanks @KristinaRiemer! Fixed both!

cbirdferrer commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

cbirdferrer commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.21105/joss.01825 is OK
- 10.1002/ecs2.1468 is OK
- 10.3389/fmars.2017.00366 is OK
- 10.3354/meps12522 is OK
- 10.1111/mms.12527 is OK

MISSING DOIs

- None

INVALID DOIs

- None

KristinaRiemer commented 4 years ago

That looks great @cbirdferrer!

The next steps are to: 1) create a tagged release on GitHub and 2) archive the code (on Zenodo, figshare, institutional repository, etc.) to generate a DOI. If you can post a link to the DOI here when you're done please.

cbirdferrer commented 4 years ago

@KristinaRiemer here's the link to the DOI https://zenodo.org/record/3937611#.XwdcpZNKhTY
DOI: 10.5281/zenodo.3937611

KristinaRiemer commented 4 years ago

@whedon set v1.0.5 as version

whedon commented 4 years ago

OK. v1.0.5 is the version.

KristinaRiemer commented 4 years ago

@whedon set 10.5281/zenodo.3937611 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3937611 is the archive.

KristinaRiemer 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

- 10.21105/joss.01825 is OK
- 10.1002/ecs2.1468 is OK
- 10.3389/fmars.2017.00366 is OK
- 10.3354/meps12522 is OK
- 10.1111/mms.12527 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/1555

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1555, 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

All looks good here, thanks!

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/1556
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02328
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

Congratulations @cbirdferrer on your article's publication in JOSS!

Many thanks to @evaristor and @katmratliff for reviewing this, and @KristinaRiemer 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:

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</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02328/status.svg
   :target: https://doi.org/10.21105/joss.02328

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