[REVIEW]: Lexicon-Mono-Seq, DOM Text Based Async MSA Viewer

whedon commented 5 years ago

Submitting author: @IbrahimTanyalcin (Ibrahim Tanyalcin) Repository: https://github.com/IbrahimTanyalcin/lexicon-mono-seq Version: v0.19.0 Editor: @csoneson Reviewer: @hrhotz, @jkanche, @imallona Archive: 10.5281/zenodo.3273310

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Markdown: [![status](http://joss.theoj.org/papers/9fbf126b501ad921825f755732450278/status.svg)](http://joss.theoj.org/papers/9fbf126b501ad921825f755732450278)

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

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

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

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

Review checklist for @hrhotz

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: v0.19.0
[x] Authorship: Has the submitting author (@IbrahimTanyalcin) 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
[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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @jkanche

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: v0.19.0
[x] Authorship: Has the submitting author (@IbrahimTanyalcin) 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
[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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @imallona

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: v0.19.0
[x] Authorship: Has the submitting author (@IbrahimTanyalcin) 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
[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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

csoneson commented 5 years ago

Thanks @imallona - could you please tick the last box in the checklist above too? Thanks!

csoneson commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

csoneson commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


OK DOIs

- 10.1109/MCSE.2018.011111125 is OK
- 10.1155/2018/1718046 is OK
- 10.1093/bioinformatics/btm404 is OK
- 10.1186/1756-0500-7-468 is OK
- 10.1093/bioinformatics/btw474 is OK
- 10.1038/nbt.1754 is OK
- 10.1093/nar/gkx273 is OK
- 10.1093/bioinformatics/btx007 is OK

MISSING DOIs

- None

INVALID DOIs

- None

hrhotz commented 5 years ago

I have just ticked the last box and I am happy to recommend the current version for acceptance. @IbrahimTanyalcin it was a pleasure to work with you @imallona and @jkanche thanks for the collaboration @csoneson thank you very much for the excellent guidance

IbrahimTanyalcin commented 5 years ago

@hrhotz , thank you for the great input for the color schemes and url fetching idea. The pleasure is mine. Also, @imanolla thank you for pointing out very important points including w3c recommendation for animation fps, which I had no idea about. I don't know if @jkanche is here, but I also thank him for performance related issues. @csoneson, thank you for checking if all is on the track. I'm sorry to bother all of you during summer time for the review. I really appreciate that.

csoneson commented 5 years ago

👋 @jkanche - could you let us know whether you have additional comments for @IbrahimTanyalcin or if you are happy with the current state of the submission? Thanks!

jkanche commented 5 years ago

@csoneson No, I am good with the current state of the submission. Thank you @IbrahimTanyalcin for your work on this!

csoneson commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


OK DOIs

- 10.1109/MCSE.2018.011111125 is OK
- 10.1155/2018/1718046 is OK
- 10.1093/bioinformatics/btm404 is OK
- 10.1186/1756-0500-7-468 is OK
- 10.1093/bioinformatics/btw474 is OK
- 10.1038/nbt.1754 is OK
- 10.1093/nar/gkx273 is OK
- 10.1093/bioinformatics/btx007 is OK

MISSING DOIs

- None

INVALID DOIs

- None

csoneson commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

csoneson commented 5 years ago

@IbrahimTanyalcin - we're almost there! I have sent a PR with some small edits to the paper, could you please take a look and merge this if you agree. Also, I noticed that for the Rauscher et al. and Wilm et al. references, the author list in the bibliography does not agree with the one on the journal website - can you fix this?

IbrahimTanyalcin commented 5 years ago

:wave: @csoneson , thank you! I'll take a look now.

IbrahimTanyalcin commented 5 years ago

:wave: @csoneson I rewrote the author fields, I've no idea why they were wrong in the first place. Thank you for pointing in out. I also merged your PR. Thank you.

csoneson commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


OK DOIs

- 10.1109/MCSE.2018.011111125 is OK
- 10.1155/2018/1718046 is OK
- 10.1093/bioinformatics/btm404 is OK
- 10.1186/1756-0500-7-468 is OK
- 10.1093/bioinformatics/btw474 is OK
- 10.1038/nbt.1754 is OK
- 10.1093/nar/gkx273 is OK
- 10.1093/bioinformatics/btx007 is OK

MISSING DOIs

- None

INVALID DOIs

- None

csoneson commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

csoneson commented 5 years ago

@IbrahimTanyalcin - great! I think this looks good. To finalize, could you create a Zenodo archive and post the resulting DOI here? Please make sure that the authors and title are exactly the same for the Zenodo archive and the manuscript, and that the version is consistent everywhere.

IbrahimTanyalcin commented 5 years ago

@csoneson , before I even submitted for JOSS, I went ahead and created one: https://zenodo.org/record/3272107#.XSOFeOszapo

I just released a new release now (ARIES), so the badge does not work yet, I guess it will work in a couple of hours. But it seems like it has tracked all the versions correctly. Is that ok?

csoneson commented 5 years ago

Yes, the DOI of the latest release should be fine. However, the title and author list of the Zenodo archive must be the same as in your paper.

IbrahimTanyalcin commented 5 years ago

@csoneson ok, I added .zenodo.json, hopefully the webhook will work and it'll be picked up.

csoneson commented 5 years ago

@IbrahimTanyalcin Just checked, and the Zenodo record still looks the same to me.

IbrahimTanyalcin commented 5 years ago

:wave: @csoneson the webhooks for zenodo works in a weird unpredictable way. I waited about half a day for things to be refreshed however I realized that won't happen. So I went ahead and registered a new DOI manually. Is it better now?

csoneson commented 5 years ago

Ok, great. Yes, 10.5281/zenodo.3273310 looks fine.

csoneson commented 5 years ago

@whedon set 10.5281/zenodo.3273310 as archive

whedon commented 5 years ago

OK. 10.5281/zenodo.3273310 is the archive.

csoneson commented 5 years ago

@whedon set v0.19.0 as version

whedon commented 5 years ago

OK. v0.19.0 is the version.

csoneson commented 5 years ago

Ok @IbrahimTanyalcin - I'll send this off to the editor-in-chief on duty for the formal acceptance!

csoneson commented 5 years ago

@openjournals/joss-eics - we're ready to accept this paper!

arfon commented 5 years ago

@whedon accept

whedon commented 5 years ago

Attempting dry run of processing paper acceptance...

whedon commented 5 years ago


OK DOIs

- 10.1109/MCSE.2018.011111125 is OK
- 10.1155/2018/1718046 is OK
- 10.1093/bioinformatics/btm404 is OK
- 10.1186/1756-0500-7-468 is OK
- 10.1093/bioinformatics/btw474 is OK
- 10.1038/nbt.1754 is OK
- 10.1093/nar/gkx273 is OK
- 10.1093/bioinformatics/btx007 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 5 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/828

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/828, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

arfon commented 5 years ago

@whedon accept deposit=true

whedon commented 5 years ago

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

whedon commented 5 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 5 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/829
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01407
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

arfon commented 5 years ago

@hrhotz, @jkanche, @imallona - many thanks for your reviews and to @csoneson for editing this submission ✨

@IbrahimTanyalcin - your paper is now accepted into JOSS :zap::rocket::boom:

whedon commented 5 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:
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HTML:
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  <img src="http://joss.theoj.org/papers/10.21105/joss.01407/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01407/status.svg
   :target: https://doi.org/10.21105/joss.01407

This is how it will look in your documentation:

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