Closed whedon closed 3 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:.
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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.
@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!)
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
@whedon add @rpetit3 as reviewer
OK, @rpetit3 is now a reviewer
That did it thank you!
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.
Hey @mjsull. Just checking in to see how you are doing with this submission? Cheers.
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.
β 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 .
Hi @mjsull - just checking in to see how things are going with your submission?
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?
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?
β 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 .
No problem at all!
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
@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).
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
@whedon generate pdf
@whedon check references
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
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.
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
perfect, thanks @telatin!
@mjsull - we can flag this for acceptance once you have done the following:
Hi Will,
chromaitblock DOI has been added.
v1.0.0 released, the DOI: 10.5281/zenodo.4034604
@whedon check references
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
perfect - thanks @mjsull
@whedon set 10.5281/zenodo.4034604 as archive
OK. 10.5281/zenodo.4034604 is the archive.
@whedon set v1.0.0 as version
OK. v1.0.0 is the version.
@whedon accept
Attempting dry run of processing paper acceptance...
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
This is with the EICs now. Thank you for a nice submission @mjsull and thank you very much @rpetit3 and @telatin for your reviews!
: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
Awesome, thanks everyone.
Hi @mjsull, I'm the EIC on duty this week, and doing some final checks before publishing. Could you address these issues?
Hi @kyleniemeyer,
All fixed.
Cheers,
Mitch
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@whedon accept
Attempting dry run of processing paper acceptance...
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
: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
@whedon accept deposit=true
Doing it live! Attempting automated processing of paper acceptance...
π¦π¦π¦ π Tweet for this paper π π¦π¦π¦
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
: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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Review checklist for @rpetit3
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