Closed editorialbot closed 2 years ago
Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.
For a list of things I can do to help you, just type:
@editorialbot commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@editorialbot generate pdf
Software report:
github.com/AlDanial/cloc v 1.88 T=0.10 s (558.2 files/s, 85401.7 lines/s)
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Language files blank comment code
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HTML 5 551 0 3284
Python 36 602 517 2555
Markdown 6 140 0 471
YAML 6 12 27 198
TeX 1 7 0 103
TOML 1 5 0 50
JavaScript 1 3 3 40
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SUM: 56 1320 547 6701
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 989
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1007/s11263-015-0816-y is OK
- 10.1007/978-3-030-32245-8_4 is OK
- 10.3390/info11020125 is OK
- 10.1002/essoar.10506807.2 is OK
- 10.1098/rsif.2021.0140 is OK
- 10.3389/fcell.2022.842342 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
👋 @jingpengw, @estenhl, could you please update us on how it's going with your reviews?
👋 @jingpengw, @estenhl, could you please update us on how it's going with your reviews?
Will finish it sometime next week
@osorensen
@OllyK
It seems that the State of the field
is missing. It would be better to compare with existing tools including my own:
https://github.com/flatironinstitute/neutorch
I have also listed some others in the README of my repo. DeepEM DataProvider3 PyTorchUtils pytorch_connectomics
As such, the reference list is not complete from this perspective.
Hi @jingpengw Thank you for taking the time to look at this. Sure, good point, I'll add this section next week and let you know when it's ready.
Hi @jingpengw I've made some changes to the paper now as requested. I'll ask editorialbot to regenerate the PDF and check references again, just in case. Best wishes OllyK
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot check repository
Software report:
github.com/AlDanial/cloc v 1.88 T=0.10 s (562.2 files/s, 87155.5 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
HTML 5 551 0 3284
Python 36 602 517 2555
Markdown 6 145 0 475
TeX 1 17 0 198
YAML 6 12 27 198
TOML 1 5 0 50
JavaScript 1 3 3 40
-------------------------------------------------------------------------------
SUM: 56 1335 547 6800
-------------------------------------------------------------------------------
gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 1216
Hi @osorensen , according to the docs, only editors can run the editorialbot check references
command. Would it be possible for you to run it? - I updated the references last week. Kind regards
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1007/s11263-015-0816-y is OK
- 10.1007/978-3-030-32245-8_4 is OK
- 10.3390/info11020125 is OK
- 10.1002/essoar.10506807.2 is OK
- 10.1098/rsif.2021.0140 is OK
- 10.3389/fcell.2022.842342 is OK
- 10.48550/arXiv.1706.05587 is OK
- 10.1038/s41598-019-55431-0 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@jingpengw, could you please let us now if the last edits by the authors address the remaining issues on your checklist?
@estenhl, thanks for your review!
Is the missing check in the Reproducibility section related to the results reported in this section of the paper?
thank you! I think it is good to go!
@estenhl Feel free to ask if there's anything that needs clarifying or updating. The paper doesn't contain any original results, it references studies where we've used earlier versions of the code to segment data. Best Wishes.
Sorry for the late reply @osorensen, the missing check was purely due to a mistake on my part. @OllyK, great work, and thanks for the detailed replies to @jinpengw's questions, both here and in the pre-review thread
@OllyK, I will now read through the manuscript a final time, and let you know if I have any suggested changes. Meanwhile, could you
Thanks very much @osorensen ! And once again many thanks to @jingpengw and @estenhl for taking the time to review
@OllyK, I will now read through the manuscript a final time, and let you know if I have any suggested changes. Meanwhile, could you
Please let me know if there's anything else you need. Best Wishes,
OllyK
@editorialbot generate pdf
@editorialbot check references
@editorialbot set 10.5281/zenodo.7143363 as archive
Done! Archive is now 10.5281/zenodo.7143363
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1007/s11263-015-0816-y is OK
- 10.1007/978-3-030-32245-8_4 is OK
- 10.3390/info11020125 is OK
- 10.1002/essoar.10506807.2 is OK
- 10.1098/rsif.2021.0140 is OK
- 10.3389/fcell.2022.842342 is OK
- 10.48550/arXiv.1706.05587 is OK
- 10.1038/s41598-019-55431-0 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@editorialbot v0.2.7 as version
I'm sorry human, I don't understand that. You can see what commands I support by typing:
@editorialbot commands
@editorialbot set v0.2.7 as version
Done! version is now v0.2.7
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@OllyK, I think the paper is clear and well written. As you see, I have opened some rather small issues in the source repository. Please let me know when they are fixed (or if you disagree with my suggestions, which is absolutely fine), and I can move forward with accepting the submission.
That's brilliant, thanks @osorensen ! I hope to resolve those issues today and will update you.
@osorensen Have updated the paper with the requested changes and closed the issues as you may have seen. Best wishes, OllyK
@editorialbot generate pdf
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1007/s11263-015-0816-y is OK
- 10.1007/978-3-030-32245-8_4 is OK
- 10.3390/info11020125 is OK
- 10.1002/essoar.10506807.2 is OK
- 10.1098/rsif.2021.0140 is OK
- 10.3389/fcell.2022.842342 is OK
- 10.48550/arXiv.1706.05587 is OK
- 10.48550/arXiv.2112.05754 is OK
- 10.1038/s41598-019-55431-0 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1007/s11263-015-0816-y is OK
- 10.1007/978-3-030-32245-8_4 is OK
- 10.3390/info11020125 is OK
- 10.1002/essoar.10506807.2 is OK
- 10.1098/rsif.2021.0140 is OK
- 10.3389/fcell.2022.842342 is OK
- 10.48550/arXiv.1706.05587 is OK
- 10.48550/arXiv.2112.05754 is OK
- 10.1038/s41598-019-55431-0 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::page_facing_up: Download article
If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3581, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
🎉 Thanks again @estenhl @jingpengw @osorensen . It's been a pleasure.
@editorialbot accept
Submitting author: !--author-handle-->@OllyK<!--end-author-handle-- (Oliver N. F. King) Repository: https://github.com/DiamondLightSource/volume-segmantics Branch with paper.md (empty if default branch): paper Version: v0.2.7 Editor: !--editor-->@osorensen<!--end-editor-- Reviewers: @jingpengw, @estenhl Archive: 10.5281/zenodo.7143363
Status
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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
@jingpengw & @estenhl, 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:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @osorensen 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 @estenhl
📝 Checklist for @jingpengw