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[REVIEW]: Chromatiblock: scalable whole-genome visualization of structural differences in prokaryotes #2451

Closed whedon closed 3 years ago

whedon commented 4 years ago

Submitting author: @mjsull (Mitchell) Repository: https://github.com/mjsull/chromatiblock/ Version: v1.0.0 Editor: @will-rowe Reviewers: @telatin, @rpetit3 Archive: 10.5281/zenodo.4034604

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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

@telatin & @rpetit3, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. 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 @will-rowe know.

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

Review checklist for @telatin

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @rpetit3

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @telatin, @rpetit3 it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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whedon commented 4 years ago

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

will-rowe commented 4 years ago

Hi all. I'm about to go on annual leave for a week. Please let me know if you need anything before I go - I'll pick things up when I get back otherwise.

I see @telatin has already done his review - thank you very much.

rpetit3 commented 4 years ago

@will-rowe Can the invitation link be resent, seems I was too slow to respond and it has expired. Can't edit the first comment at the moment. (Apologies!)

will-rowe commented 4 years ago

Hi @rpetit3 - that seems odd! I'll try reassigning you but I've not had this before. It does say that you are already assigned but let's try again

will-rowe commented 4 years ago

@whedon add @rpetit3 as reviewer

whedon commented 4 years ago

OK, @rpetit3 is now a reviewer

rpetit3 commented 4 years ago

That did it thank you!

will-rowe commented 4 years ago

Hi @mjsull. Just want to check back in with this. Looks like we now have 2 excellent reviews completed for you. Please let us know when you have had chance to address these comments and we can take another look over the submission.

will-rowe commented 4 years ago

Hey @mjsull. Just checking in to see how you are doing with this submission? Cheers.

mjsull commented 4 years ago

Hi Will,

Sorry about missing your earlier email. Definitely very helpful, working through the comments now. Will finish over the weekend.

Best,

Mitch

On Thu, 6 Aug 2020 at 22:16, Will Rowe notifications@github.com wrote:

Hey @mjsull https://github.com/mjsull. Just checking in to see how you are doing with this submission? Cheers.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2451#issuecomment-669891414, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAYTVBMZOLIQBKXVROAWNDDR7KNIRANCNFSM4OU5Y7MA .

will-rowe commented 4 years ago

Hi @mjsull - just checking in to see how things are going with your submission?

will-rowe commented 4 years ago

Hi again @mjsull. Just want to see how you are getting on? Let me know if you need anything or if want to pause your submission?

mjsull commented 4 years ago

Hi Will,

Apologies, I was waiting to get feedback from my co-author (who has been a bit snowed under by sars-cov-2 related work). He said he'd get back to me later today.

Thanks again,

Mitch

On Mon, 31 Aug 2020 at 04:41, Will Rowe notifications@github.com wrote:

Hi again @mjsull https://github.com/mjsull. Just want to see how you are getting on? Let me know if you need anything or if want to pause your submission?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2451#issuecomment-683455168, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAYTVBISD7AUALZEBDVQVR3SDKMMFANCNFSM4OU5Y7MA .

will-rowe commented 4 years ago

No problem at all!

mjsull commented 3 years ago

Hi @will-rowe

I think I've addressed everything. Please find my comments for each reviewer in their issue threads.

https://github.com/mjsull/chromatiblock/issues/10 https://github.com/mjsull/chromatiblock/issues/12

Best,

Mitch

rpetit3 commented 3 years ago

@mjsull everything looks great! I have merged your latest release into Bioconda (https://github.com/bioconda/bioconda-recipes/pull/24287). Once its synced to Anaconda's CDN, I'll give it a test run and report back (hopefully today).

rpetit3 commented 3 years ago

Hi @will-rowe

I have tested @mjsull's latest release of Chromatiblock (v0.5.1) and everything looks good. The only major hold up on my end was the SVG, PNG, PDF output, which is now fixed in the latest version. I think @mjsull really went above and beyond responding to the rest of my comments.

I am happy to recommend this manuscript for publication!

Thank you for your time! Robert

will-rowe commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

will-rowe commented 3 years ago

@whedon check references

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1186/1471-2164-12-402 is OK
- 10.1093/bioinformatics/btq665 is OK
- 10.1101/gr.2289704 is OK
- 10.1186/1471-2164-13-202 is OK
- 10.1093/bioinformatics/btq413 is OK
- 10.1093/bioinformatics/bts217 is OK
- 10.1101/gr.092759.109 is OK
- 10.1101/548123 is OK
- 10.1093/bioinformatics/btr039 is OK

MISSING DOIs

- 10.1007/978-3-642-40453-5_17 may be a valid DOI for title: Sibelia: A Scalable and Comprehensive Synteny Block Generation Tool for Closely Related Microbial Genomes

INVALID DOIs

- None
will-rowe commented 3 years ago

Hi @mjsull - this is looking really nice. Just playing with the software now and am having no difficulties. The paper is also reading nicely. The only thing needing changing from my point of view is a fix for the Sibelia reference.

Thank you again @telatin and @rpetit3 - your reviews were excellent and this submission is looking great. Well done @mjsull with the responses.

@telatin has offered to take a look at your responses by end of the week - so we will wait on him to have a final look. Once has gives his approval - I'm happy for this to proceed to publication.

telatin commented 3 years ago

Hello @will-rowe! @mjsull answered my comments and I have been happy with the improvements. I am happy to recommend this manuscript for publication!

Thank you all, Andrea

will-rowe commented 3 years ago

perfect, thanks @telatin!

@mjsull - we can flag this for acceptance once you have done the following:

mjsull commented 3 years ago

Hi Will,

chromaitblock DOI has been added.

v1.0.0 released, the DOI: 10.5281/zenodo.4034604

will-rowe commented 3 years ago

@whedon check references

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1186/1471-2164-12-402 is OK
- 10.1093/bioinformatics/btq665 is OK
- 10.1101/gr.2289704 is OK
- 10.1186/1471-2164-13-202 is OK
- 10.1093/bioinformatics/btq413 is OK
- 10.1093/bioinformatics/bts217 is OK
- 10.1101/gr.092759.109 is OK
- 10.1101/548123 is OK
- 10.1007/978-3-642-40453-5_17 is OK
- 10.1093/bioinformatics/btr039 is OK

MISSING DOIs

- None

INVALID DOIs

- None
will-rowe commented 3 years ago

perfect - thanks @mjsull

will-rowe commented 3 years ago

@whedon set 10.5281/zenodo.4034604 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4034604 is the archive.

will-rowe commented 3 years ago

@whedon set v1.0.0 as version

whedon commented 3 years ago

OK. v1.0.0 is the version.

will-rowe commented 3 years ago

@whedon accept

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1186/1471-2164-12-402 is OK
- 10.1093/bioinformatics/btq665 is OK
- 10.1101/gr.2289704 is OK
- 10.1186/1471-2164-13-202 is OK
- 10.1093/bioinformatics/btq413 is OK
- 10.1093/bioinformatics/bts217 is OK
- 10.1101/gr.092759.109 is OK
- 10.1101/548123 is OK
- 10.1007/978-3-642-40453-5_17 is OK
- 10.1093/bioinformatics/btr039 is OK

MISSING DOIs

- None

INVALID DOIs

- None
will-rowe commented 3 years ago

This is with the EICs now. Thank you for a nice submission @mjsull and thank you very much @rpetit3 and @telatin for your reviews!

whedon commented 3 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/1739

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1739, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
mjsull commented 3 years ago

Awesome, thanks everyone.

kyleniemeyer commented 3 years ago

Hi @mjsull, I'm the EIC on duty this week, and doing some final checks before publishing. Could you address these issues?

mjsull commented 3 years ago

Hi @kyleniemeyer,

All fixed.

Cheers,

Mitch

kyleniemeyer commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

kyleniemeyer commented 3 years ago

@whedon accept

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1186/1471-2164-12-402 is OK
- 10.1093/bioinformatics/btq665 is OK
- 10.1101/gr.2289704 is OK
- 10.1186/1471-2164-13-202 is OK
- 10.1093/bioinformatics/btq413 is OK
- 10.1093/bioinformatics/bts217 is OK
- 10.1101/gr.092759.109 is OK
- 10.1101/548123 is OK
- 10.1007/978-3-642-40453-5_17 is OK
- 10.1093/bioinformatics/btr039 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 3 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/1749

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1749, 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 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦