[REVIEW]: VIEWpoly: a visualization tool to integrate and explore results of polyploid genetic analysis

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@cristianetaniguti@mikldk<!--end-editor-- Reviewers: @cpalmer718, @jkanche, @raivivek Archive: 10.5281/zenodo.6621089

Status

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Markdown: [![status](https://joss.theoj.org/papers/26675494658140006640d0771a539697/status.svg)](https://joss.theoj.org/papers/26675494658140006640d0771a539697)

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

@cpalmer718 & @jkanche & @raivivek, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @jkanche

📝 Checklist for @raivivek

📝 Checklist for @cpalmer718

editorialbot commented 2 years ago

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editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (486.5 files/s, 106485.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               18            407            889           3874
Markdown                         5            174              0            625
TeX                              1             29              0            159
YAML                             3             18              2             87
Rmd                              1             30             48              4
HTML                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            29            658            939           4750
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

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

OK DOIs

- 10.1093/genetics/iyab124 is OK
- 10.1093/bioinformatics/bty371 is OK
- 10.1093/bioinformatics/btab574 is OK
- 10.1093/jhered/esx022 is OK
- 10.1093/bioinformatics/btab459 is OK
- 10.1534/g3.119.400378 is OK
- 10.1534/g3.119.400620 is OK
- 10.1534/genetics.120.303080 is OK
- 10.3835/plantgenome2015.08.0073 is OK
- 10.1534/genetics.115.185579 is OK
- 10.1093/genetics/iyab106 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

Wordcount for paper.md is 1372

editorialbot commented 2 years ago

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

raivivek commented 2 years ago

Review checklist for @raivivek

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 https://github.com/mmollina/viewpoly?
[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 (@cristianetaniguti) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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?

mikldk commented 2 years ago

@cpalmer718, @jkanche, @raivivek: Thanks for agreeing to review. Please carry out your review in this issue by first creating a checklist (@editorialbot generate my checklist) and then updating it as the review proceeds. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If possible create issues (and cross-reference) in the submission's repository to avoid too specific discussions in this review thread.

If you have any questions or concerns please let me know.

jkanche commented 2 years ago

Review checklist for @jkanche

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 https://github.com/mmollina/viewpoly?
[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 (@cristianetaniguti) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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?

mikldk commented 2 years ago

@cpalmer718, @jkanche, @raivivek, can you please give a brief status of your review? This is not to rush you, merely to give me an impression of the progress and time-frame.

raivivek commented 2 years ago

Hi @mikldk! I am hoping to complete my review by next week, if not earlier.

lightning-auriga commented 2 years ago

Hi @mikldk I'm maybe halfway through, aiming for finishing it this weekend.

lightning-auriga commented 2 years ago

Review checklist for @cpalmer718

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 https://github.com/mmollina/viewpoly?
[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 (@cristianetaniguti) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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?

lightning-auriga commented 2 years ago

Slightly more specific comments:

Most seriously: there are very few tests, and they really only seem to test that the app launches, not its functionality. This is obviously a challenge in GUI situations. @mikldk I think your guidance may be needed here. For a CL tool I'd say the test setup would need to be reworked from scratch, but I'm not sure that's a reasonable thing to ask here.

Assorted other comments and links:

installation was really smooth, though I was only able to test on Windows
broken links at various places make it hard to get example sets to use/evaluate; I've opened an issue here
image creation and download was a bit bumpy (though when it worked it was very cool): issue
I can't tell you how much I like the video tutorial; I wish more people would do that. I know this might be a pain, but it would be really helpful to have the screen in the video be a bit bigger; some parts were hard to see zooming by.
very minor issue about seemingly misleading error message here
functionality documentation is inconsistent here
there were comments about how to submit issues and get guidance, but I didn't find any guidelines for contribution.
fairly minor comments about paper here; I really appreciate how much information the authors provide. The only possible issue is that the Summary section may not be most appropriate for a general audience; I am very familiar with QTLs and linkage and ploidy, but the generalist audience may not be
this may just be my system, but I got a ton of warnings in the R instance I used to launch this; I'll post some in an issue here

mikldk commented 2 years ago

@cpalmer718 @Cristianetaniguti

Most seriously: there are very few tests, and they really only seem to test that the app launches, not its functionality. This is obviously a challenge in GUI situations. @mikldk I think your guidance may be needed here. For a CL tool I'd say the test setup would need to be reworked from scratch, but I'm not sure that's a reasonable thing to ask here.

Our guidelines states "In particular, your software should be full-featured, well-documented, and contain procedures (such as automated tests) for checking correctness.".

So we do not have a strong requirement for automated tests, but there should be some procedures for checking correctness. One way is to supply screendumps in the help files such that the user can compare her output with those.

...

jkanche commented 2 years ago

@mikldk @cpalmer718 I also made similar comments in my review.

It would be great to add functional testing not necessarily UI testing. UI testing is always hard for shiny applications.

mikldk commented 2 years ago

@Cristianetaniguti are you able to add functional testing as suggested by @cpalmer718 @jkanche?

raivivek commented 2 years ago

@Cristianetaniguti I'm reviewing the R package right now and noticing many minor issues. I see that early reviewers have highlighted them already, so perhaps I should pull the development branch for testing to make sure I have all the latest changes. Please let me know if/when I should install the latest version in case you are in the middle of any changes. Thanks!

Cristianetaniguti commented 2 years ago

Hello! Thank you all for the comments. Yes, @raivivek , please install the main branch (devtools::install_github("https://github.com/mmollina/viewpoly"). I have already pushed some modifications according to @cpalmer718 comments. Among them are more stable links for the example files. @mikldk I thought about using testthat functions to check the data used in ggplot to build the graphics.

raivivek commented 2 years ago

Hi @Cristianetaniguti Apologies for delay on my end — I was able to pull in the latest version and revise my comments. Will try to complete everything by this weekend. Cheers!

Cristianetaniguti commented 2 years ago

Hello @raivivek . No worries. I kept changing things these past few days, mostly about the tests. Then, I think you will not need to revise your comments again. I also just submitted answers to @jkanche review. Thanks!

Cristianetaniguti commented 2 years ago

Hello, I just pushed a simple Contributing Guidelines (mmollina/viewpoly@18ed13912d75f75882c8c9c6358a6f09954866f8) and with this, I think I cover all comments and suggestions made by @jkanche and @cpalmer718.

mikldk commented 2 years ago

@cpalmer718, @jkanche, @raivivek: Please have a look at your checklists again and let @Cristianetaniguti know if there is anything that needs to be done.

raivivek commented 2 years ago

Hi @Cristianetaniguti! I added a few comments to your repository based on my review! Let me know if you have any questions, but other than that, it's looks be in a very good shape.

jkanche commented 2 years ago

Thanks to @Cristianetaniguti for making all the changes, looks good to me

Cristianetaniguti commented 2 years ago

Hello, I also finished the modifications according to @raivivek suggestions. I am about to submit this new version to CRAN. Let me know if you have more suggestions. Thanks!

mikldk commented 2 years ago

@raivivek and @cpalmer718: I still see missing checks in your checklist. Can you please update us how far you are?

lightning-auriga commented 2 years ago

@mikldk apologies for the delay, I've been having some technical problems on the system I was using to evaluate this. I am hopeful that I'll be able to update this review in about 12 hours. sorry again for the trouble.

mikldk commented 2 years ago

@mikldk apologies for the delay, I've been having some technical problems on the system I was using to evaluate this. I am hopeful that I'll be able to update this review in about 12 hours. sorry again for the trouble.

@cpalmer718 No worries, thanks for the update :+1:

lightning-auriga commented 2 years ago

@mikldk @Cristianetaniguti So things look much improved, and I think most everything I mentioned was meaningfully addressed. I think the hosting site links are a really good solution in particular. I guess my last thought, and I'm open to being argued out of this, is that a lot of the interactions I can have with the interface (to be clear, deliberately silly interactions, like just clicking some text elements) cause a hard crash, or in the case of the hosted version a "disconnected from server" error. Issue is here.

That being said, there isn't an expectation for a bioinformatics tool of this sort to be bulletproof, so I'm fine with just passing on this one. I think the target functionality is really cool, and I've enjoyed interacting with the package for the little slice of its dev process that I've seen.

Cristianetaniguti commented 2 years ago

Hello @cpalmer718 , thanks again for your comments. And yes, it is difficult to make the app bulletproof, but I will try to fix these types of errors as I become aware of them. I just fixed the one that you pointed out, thanks for that too!

mikldk commented 2 years ago

Thanks.

Now, @raivivek and @cpalmer718 each only misses one checkbox. I hope you are able to state what is missing for those boxes to be checked?

lightning-auriga commented 2 years ago

@mikldk yes, dev has indicated that https://github.com/mmollina/viewpoly/issues/35 is resolvable, so I'll install the update, flag any remaining crashes I can find, and then I'll be content. I'll check the update later today.

lightning-auriga commented 2 years ago

@mikldk I've added the last checkbox. My issues have all been meaningfully addressed; thanks to @Cristianetaniguti for the excellent package and edits, and for following up on all my weird UI attempts.

raivivek commented 2 years ago

@mikldk I have completed the review as @Cristianetaniguti did an excellent job of addressing my comments!

mikldk commented 2 years ago

@cpalmer718, @jkanche, @raivivek: Thank you for your reviews.

@Cristianetaniguti :

Please have a final read though of the paper, checking language etc.
Have a final check of the proofs with @editorialbot generate pdf
In general, be sure that all versions are correct and that the repo is in the state that should be published.
Please make a tagged release and archive (e.g. with Zenodo) as described here, and report the version number and archive DOI in this thread. Please verify that the archive deposit has the correct metadata (title and author list), or edit these if that is not the case.

Cristianetaniguti commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

Cristianetaniguti commented 2 years ago

Package version: 0.2.0
DOI: 10.5281/zenodo.6621089

mikldk commented 2 years ago

@editorialbot set 10.5281/zenodo.6621089 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6621089

mikldk commented 2 years ago

@editorialbot set v0.2.0 as version

editorialbot commented 2 years ago

Done! version is now v0.2.0

mikldk commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

mikldk commented 2 years ago

@Cristianetaniguti

Author names do not match between archive and paper as requested:

Cristiane Hayumi Taniguti; Gabriel de Siqueira Gesteira; Jeekin Lau; Guilherme da Silva Pereira; Zhao-Bang Zeng; David Byrne; Oscar Riera-Lizarazu; Marcelo Mollinari
Cristiane Hayumi Taniguti; Gabriel Gesteira;             Jeekin Lau; Guilherme da Silva Pereira; Zhao-Bang Zeng; David Byrne; Oscar Riera-Lizarazu; Marcelo Mollinari

Please let me known once you have read through the paper a final time.

Cristianetaniguti commented 2 years ago

Hello @mikldk ,

I just went through the paper once more and I am confused about where should I change the co-author name, both places seem to be already matching.

mikldk commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.1093/genetics/iyab124 is OK
- 10.1093/bioinformatics/bty371 is OK
- 10.1093/bioinformatics/btab574 is OK
- 10.1093/jhered/esx022 is OK
- 10.1093/bioinformatics/btab459 is OK
- 10.1534/g3.119.400378 is OK
- 10.1534/g3.119.400620 is OK
- 10.1534/genetics.120.303080 is OK
- 10.3835/plantgenome2015.08.0073 is OK
- 10.1534/genetics.115.185579 is OK
- 10.1093/genetics/iyab106 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 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/3272

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3272, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

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