Closed editorialbot closed 1 year 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=0.38 s (406.7 files/s, 78202.9 lines/s)
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Language files blank comment code
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Python 137 6080 8304 12596
HTML 2 36 4 274
TeX 1 20 0 255
YAML 5 1 4 171
Markdown 2 41 0 104
Jupyter Notebook 1 0 1386 92
IDL 1 12 4 32
SVG 4 0 0 4
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SUM: 153 6190 9702 13528
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gitinspector failed to run statistical information for the repository
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.7554/elife.61834 is OK
- 10.3389/fninf.2016.00006 is OK
- 10.1016/j.jneumeth.2009.06.031 is OK
- 10.1111/ejn.12558 is OK
- 10.1038/8144 is OK
- 10.1201/9781420039429.ch13 is OK
- 10.7554/elife.38173 is OK
- 10.1152/physiol.00032.2007 is OK
- 10.3389/fncel.2018.00128 is OK
- 10.1109/cvprw.2016.78 is OK
- 10.1038/srep21841 is OK
- 10.1007/s00359-017-1209-1 is OK
- 10.1007/s00441-020-03385-5 is OK
- 10.1016/j.conb.2018.11.004 is OK
- 10.1016/j.cmpb.2019.104991 is OK
- 10.1371/journal.pcbi.1005526 is OK
- 10.1046/j.1460-9568.1999.00826.x is OK
- 10.1038/nmeth.2019 is OK
- 10.1016/j.bpj.2017.09.040 is OK
- 10.1016/j.neuroimage.2014.04.041 is OK
- 10.1186/1471-2105-14-s18-s4 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Wordcount for paper.md
is 2603
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
šš¼ @ajkswamy, @adamltyson, @Yannan-Chen - this is the review thread for the submission. All our communications will happen here from now on.
Please check the post at the top of the issue for instructions on how to generate your own review checklist. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.
The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues directly in the software repository. If you do so, please mention this thread so that a link is created (and I can keep an eye on what is happening). Please also feel free to comment and ask questions in this thread. It is often easier to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.
Please feel free to ping me (@csoneson) if you have any questions or concerns. Thanks!
Hello @csoneson @adamltyson @Yannan-Chen
Thanks for organizing the review process and agreeing to review our submission!
A quick update: thanks to @adamltyson's issue, we have now migrated PyView to Python 3.10 and made a new release. We request you to use this release when reviewing.
We are looking forward to your issues, comments, questions and reviews!
Thanks!
Hey @ajkswamy, as I play with the software, I'm going to raise issues on anything that I come across. Just letting you know that some of these will likely be personal preference, or may not affect the software from a user's point of view (e.g. https://github.com/galizia-lab/pyview/issues/23). Don't feel like all of these must be addressed for the JOSS submission, so feel free to close/ignore these.
The paper itself looks good. It may be nice to cite the suite2p pre-print for consistency (e.g. the CaImAn paper is cited).
Hey @ajkswamy, I saw that you added a tutorial PDF. The software is much, much easier to understand now. Considering how much work has gone into this software, and it's broad functionality, it would be a shame if it's not used by more people. I would recommend documenting everything as comprehensively as the tutorial, and make it as easy to find for new users as possible.
However, there are very few tools that couldn't do with a bit more documentation (including all of mine!), so considering the installation procedure is also much improved, I'm now happy to recommend acceptance! :tada: cc @csoneson.
Thank you @adamltyson!
Hi @csoneson , In this submission, the authors provide a software offering a wide range of features for working with calcium imaging data interactively. The tool is user-friendly and easy to install, with clear and straightforward documentation. Overall, Iām happy to recommend this tool to be accepted by JOSS!
Thank you @Yannan-Chen!
@ajkswamy - as both reviewers have given their ok, I'll take a quick look through the submission as well, and get back to you with the next steps.
@editorialbot generate pdf
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.7554/elife.61834 is OK
- 10.3389/fninf.2016.00006 is OK
- 10.1016/j.jneumeth.2009.06.031 is OK
- 10.1111/ejn.12558 is OK
- 10.1038/8144 is OK
- 10.1201/9781420039429.ch13 is OK
- 10.7554/elife.38173 is OK
- 10.1152/physiol.00032.2007 is OK
- 10.3389/fncel.2018.00128 is OK
- 10.1109/cvprw.2016.78 is OK
- 10.1038/srep21841 is OK
- 10.1007/s00359-017-1209-1 is OK
- 10.1007/s00441-020-03385-5 is OK
- 10.1016/j.conb.2018.11.004 is OK
- 10.1016/j.cmpb.2019.104991 is OK
- 10.1371/journal.pcbi.1005526 is OK
- 10.1046/j.1460-9568.1999.00826.x is OK
- 10.1038/nmeth.2019 is OK
- 10.1016/j.bpj.2017.09.040 is OK
- 10.1016/j.neuroimage.2014.04.041 is OK
- 10.1186/1471-2105-14-s18-s4 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:
Hi @ajkswamy - sorry for the delay. I had a quick look through the paper, and at the moment it is a bit too long for JOSS standards. In particular, see here:
The paper should be between 250-1000 words. Authors submitting papers significantly longer than 1000 words may be asked to reduce the length of their paper.
Your paper currently:
Wordcount for paper.md is 2603
Can you see if you can bring the paper a bit closer to the suggested length? In particular some of the technical content could perhaps be moved to the documentation, and I think some of the non-technical sections can be made more concise without losing too much information. Thanks!
@csoneson Thanks for the message. We are looking into it and it might take a week or two. I will update you here once we are done revising the manuscript.
@csoneson Thanks again for your suggestions. We have accordingly revised the manuscript to bring down the word count to ~1600 words. Here is summary of changes:
Please have a look and let me know if any further changes are needed to the manuscript, the code repo or its wiki. Thanks!
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Thanks @ajkswamy - this looks good! I made a PR with some small modifications, please check and merge if you agree.
The next steps then are:
I can then move forward with accepting the submission.
Hi @csoneson. Thanks for your PR with improvements to the manuscript. We have accepted the PR and made a new release: v1.3.
The same version of the code has been archived with G-Node Infrastructure services (GIN): https://doi.org/10.12751/g-node.ezh5w2
@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 references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.7554/elife.61834 is OK
- 10.3389/fninf.2016.00006 is OK
- 10.1016/j.jneumeth.2009.06.031 is OK
- 10.1111/ejn.12558 is OK
- 10.1038/8144 is OK
- 10.1201/9781420039429 is OK
- 10.7554/elife.38173 is OK
- 10.1152/physiol.00032.2007 is OK
- 10.3389/fncel.2018.00128 is OK
- 10.1109/cvprw.2016.78 is OK
- 10.1038/srep21841 is OK
- 10.1007/s00359-017-1209-1 is OK
- 10.1007/s00441-020-03385-5 is OK
- 10.1016/j.conb.2018.11.004 is OK
- 10.1016/j.cmpb.2019.104991 is OK
- 10.1371/journal.pcbi.1005526 is OK
- 10.1046/j.1460-9568.1999.00826.x is OK
- 10.1038/nmeth.2019 is OK
- 10.1016/j.bpj.2017.09.040 is OK
- 10.1016/j.neuroimage.2014.04.041 is OK
- 10.1186/1471-2105-14-s18-s4 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@editorialbot set 1.3 as version
Done! version is now 1.3
@editorialbot set 10.12751/g-node.ezh5w2 as archive
Done! Archive is now 10.12751/g-node.ezh5w2
Thanks @ajkswamy - this looks good to me. I'm going to hand over to the track EiC for the final steps. Thanks for submitting to JOSS!
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.7554/elife.61834 is OK
- 10.3389/fninf.2016.00006 is OK
- 10.1016/j.jneumeth.2009.06.031 is OK
- 10.1111/ejn.12558 is OK
- 10.1038/8144 is OK
- 10.1201/9781420039429 is OK
- 10.7554/elife.38173 is OK
- 10.1152/physiol.00032.2007 is OK
- 10.3389/fncel.2018.00128 is OK
- 10.1109/cvprw.2016.78 is OK
- 10.1038/srep21841 is OK
- 10.1007/s00359-017-1209-1 is OK
- 10.1007/s00441-020-03385-5 is OK
- 10.1016/j.conb.2018.11.004 is OK
- 10.1016/j.cmpb.2019.104991 is OK
- 10.1371/journal.pcbi.1005526 is OK
- 10.1046/j.1460-9568.1999.00826.x is OK
- 10.1038/nmeth.2019 is OK
- 10.1016/j.bpj.2017.09.040 is OK
- 10.1016/j.neuroimage.2014.04.041 is OK
- 10.1186/1471-2105-14-s18-s4 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:wave: @openjournals/bcm-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/3952, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
@editorialbot accept
Doing it live! Attempting automated processing of paper acceptance...
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ššš š Toot for this paper š ššš
šØšØšØ THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! šØšØšØ
Here's what you must now do:
Any issues? Notify your editorial technical team...
@adamltyson, @Yannan-Chen ā many thanks for your reviews here and to @csoneson for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you āØ
@ajkswamy ā your paper is now accepted and published in JOSS :zap::rocket::boom:
: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:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.04936/status.svg)](https://doi.org/10.21105/joss.04936)
HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04936">
<img src="https://joss.theoj.org/papers/10.21105/joss.04936/status.svg" alt="DOI badge" >
</a>
reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04936/status.svg
:target: https://doi.org/10.21105/joss.04936
This is how it will look in your documentation:
We need your help!
The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:
@adamltyson @Yannan-Chen Thanks for taking the time to review our software and manuscript. Your input has helped improve them a lot!
@csoneson @arfon Thanks for a great editorial process and the opportunity to publish in JOSS. It was the most transparent and the best structured review process I have experienced!
Submitting author: !--author-handle-->@ajkswamy<!--end-author-handle-- (Ajayrama Kumaraswamy) Repository: https://github.com/galizia-lab/pyview Branch with paper.md (empty if default branch): joss Version: 1.3 Editor: !--editor-->@csoneson<!--end-editor-- Reviewers: @adamltyson, @Yannan-Chen Archive: 10.12751/g-node.ezh5w2
Status
Status badge code:
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
@adamltyson & @Yannan-Chen, 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 @csoneson know.
āØ 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 āØ
Checklists
š Checklist for @adamltyson
š Checklist for @Yannan-Chen