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=0.10 s (331.1 files/s, 111252.9 lines/s)
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Language files blank comment code
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Jupyter Notebook 2 0 2763 2512
Python 13 778 1355 2330
TeX 1 25 0 315
DOS Batch 1 36 2 243
make 2 32 6 199
Markdown 3 52 0 167
YAML 5 9 20 113
reStructuredText 5 32 52 43
Bourne Again Shell 1 1 0 2
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SUM: 33 965 4198 5924
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 684
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1016/j.jneumeth.2014.11.012 is OK
- 10.1109/ICDSP.2007.4288544 is OK
- 10.1007/PL00007990 is OK
- 10.1007/s005290050005 is OK
- 10.1073/pnas.1017041108 is OK
- 10.48550/arXiv.2201.11941 is OK
- 10.1101/2021.02.03.429582 is OK
- 10.1016/j.neuroimage.2008.02.020 is OK
- 10.2307/2287238 is OK
- 10.1016/0013-4694(83)90235-3 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1007/BF00198091 is OK
- 10.1016/S0165-0270(03)00052-9 is OK
- 10.1007/978-3-662-58485-9_11 is OK
- 10.1002/(sici)1097-0193(1999)8:4<194::aid-hbm4>3.0.co;2-c is OK
- 10.1523/JNEUROSCI.0854-21.2021 is OK
- 10.1016/j.clinph.2004.04.029 is OK
- 10.1103/PhysRevLett.100.234101 is OK
- 10.1002/hbm.20346 is OK
- 10.3389/fnsys.2021.645709 is OK
- 10.1016/j.neuroimage.2011.01.055 is OK
- 10.1016/j.neuroimage.2010.01.073 is OK
- 10.3389/fnins.2013.00267 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 @AJQuinn, @sappelhoff, and @EtienneCmb π Thanks again for agreeing to review this submission ! The review will take place in this issue, and you can generate your individual reviewer checklists by asking editorialbot directly with @\editorialbot generate my checklist
.
In working through the checklist, you're likely to have specific feedback on Spectral Connectivity. Whenever possible, please open relevant issues on the linked software repository (and cross-link them with this issue) rather than discussing them here. This helps to make sure that feedback is translated into actionable items to improve the software !
If you aren't sure how to get started, please see the Reviewing for JOSS guide -- and, of course, feel free to ping me with any questions !
@editorialbot generate my checklist
Hm, you might need to just create a new comment @AJQuinn -- I'm not sure that it will respond to edited comments ! Sorry for the confusion.
@emdupre I have completed my review. All issues that I raised have been addressed to my full satisfaction. I believe that spectral_connectivity
is a valuable package that will serve the community well, as already evidenced in several publications. I recommend this paper for publication in JOSS.
For details, please see my checklist and all my linked issues and PRs in this review thread.
π Hi @AJQuinn, I wanted to make sure you weren't facing issues in getting started on your review ? Please let me know if there's anything I can do to help, and thank you again for agreeing to review Spectral Connectivity !
π Hi @EtienneCmb, I just wanted to check in and see how this review is going for you. Please let me know if I can answer any questions that might help in finalizing your review ! And thanks again for agreeing to review Spectral connectivity for JOSS.
Hi @emdupre @edeno - Apologies for the long delay, my review is in progress and should be completed tomorrow. I'm impressed overall. This is a useful package though I think the documentation needs a bit of work.
I've added some issues on the docs and will complete some comments on the code and paper tomorrow.
Thank you, @AJQuinn ! Please let me know when you have completed your review, or if you consider your first pass complete and you are waiting on author revisions.
I'm also just noting that I have been corresponding with @EtienneCmb via email, and he confirmed that he should have his finalized review within the next week at the latest.
Hi @emdupre my review is finished. I'm impressed with the package. It works well and the code is high quality. There are some similar packages with overlapping functionality but I think spectral_connectivity
is a strong addition to the field with several unique features. I felt parts of the documentation were lacking a bit and have outlined some suggestions for this in the linked comments. Happy to proceed once these are actioned.
Hi @emdupre, I completed my review. This package has several originalities justifying its existence and its importance, especially for the neurophysiological community. Among those originalities, the possibility to choose collapsing axes is an important feature for performing, for example, single-trial and dynamic estimations of the connectivity. As raised by @AJQuinn, the documentation can be improved. I still have two issues opened on GPU computations and comparison with other software.
Dear @emdupre, the last issue regarding performance claims has been addressed. From my side, this package checks all the boxes. I recommend this manuscript for publication in JOSS.
Hi @AJQuinn, I believe I have addressed your issues with the documentation. Please see the updated documentation.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Thank you @edeno for actioning these reviewer comments, and @EtienneCmb and @sappelhoff (who I see I have not yet thanked !! π ) for confirming your completed reviews !
While we wait for additional comments from @AJQuinn , I'll perform a few editorial checks.
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1016/j.jneumeth.2014.11.012 is OK
- 10.1109/ICDSP.2007.4288544 is OK
- 10.1007/PL00007990 is OK
- 10.1007/s005290050005 is OK
- 10.1073/pnas.1017041108 is OK
- 10.48550/arXiv.2201.11941 is OK
- 10.1101/2021.02.03.429582 is OK
- 10.1016/j.neuroimage.2008.02.020 is OK
- 10.2307/2287238 is OK
- 10.1016/0013-4694(83)90235-3 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1007/BF00198091 is OK
- 10.1016/S0165-0270(03)00052-9 is OK
- 10.1007/978-3-662-58485-9_11 is OK
- 10.1002/(sici)1097-0193(1999)8:4<194::aid-hbm4>3.0.co;2-c is OK
- 10.1523/JNEUROSCI.0854-21.2021 is OK
- 10.1016/j.clinph.2004.04.029 is OK
- 10.1103/PhysRevLett.100.234101 is OK
- 10.1002/hbm.20346 is OK
- 10.3389/fnsys.2021.645709 is OK
- 10.1016/j.neuroimage.2011.01.055 is OK
- 10.1016/j.neuroimage.2010.01.073 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.3389/978-2-88919-608-1 is OK
- 10.22541/au.159363438.81020330 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Hi all - @edeno et al have gone above and beyond in addressing my comments and I'm very happy to recommend spectral_connectivity for publication.
The documentation changes are excellent - I think this will be a massive benefit for future users. Thank you for your efforts.
Thank you for confirming, @AJQuinn !
@edeno , I've finished reviewing the software and paper, and I'm also very happy with the submission. I do have a few editorial requests on the paper itself :
CliffUnifyingPairwiseInteractions2022
reference, could you please update the bib entry as:
@article{CliffUnifyingPairwiseInteractions2022,
doi = {10.48550/ARXIV.2201.11941},
url = {https://arxiv.org/abs/2201.11941},
author = {Cliff, Oliver M. and Lizier, Joseph T. and Tsuchiya, Naotsugu and Fulcher, Ben D.},
title = {Unifying Pairwise Interactions in Complex Dynamics},
year = {2022},
eprint={2007.01941},
archivePrefix={arXiv},
primaryClass={cs.LG}
}
Rokem2020
reference, could you please update the bib entry as:
@software{Rokem2020,
author = {Rokem, Ariel and Ivanov, Paul and Perez, Fernando and Trumpis, Mike and Gramfort, Alex },
title = {Nitime: timeseries analysis for neuroscience data},
url = {https://github.com/nipy/nitime},
version = {0.9},
date = {2020-12-19},
}
assuming you did intend to cite the 0.9 release, otherwise please amend as appropriate !
SchlaflyPythonpracticingneuroscientist2020
reference, could you please update the entry as:
@article{SchlaflyPythonpracticingneuroscientist2020,
doi = {10.22541/au.159363438.81020330},
url = {https://doi.org/10.22541%2Fau.159363438.81020330},
year = {2020},
month = {jul},
publisher = {Authorea, Inc.},
author = {Emily Schlafly and Anthea Cheung and Samantha W Michalka and Paul A Lipton and Caroline Moore Kochlacs and Jason Bohland and Uri T Eden and Mark Kramer},
title = {Python for the practicing neuroscientist: an online educational resource}
}
Following their "Cite as" recommendation ?
file
fields from the paper.bib fileAfter making these edits, could you then please :
I can then move forward with processing the submission π
Hi @emdupre:
Thank you so much for your work and to all the reviewers. The process has been very educational.
I have:
@editorialbot generate pdf
@editorialbot set v1.1.0 as version
Done! version is now v1.1.0
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot set 10.5281/zenodo.7416614 as archive
Done! Archive is now 10.5281/zenodo.7416614
Thank you, @edeno !
I noticed that the metadata on the archive has several small discrepancies from the paper metadata. In particular, could you please update the title to :
Spectral Connectivity: a python package for computing multitaper spectral estimates and frequency-domain brain connectivity measures on the CPU and GPU
and double-check that the author information lists names and surnames correctly ? From my rendering, these appear inverted in the final citation (i.e., excerpting from the bib file):
author = {Eric, Denovellis and
Maxym, Myroshnychenko and
Mehrad, Sarmashghi and
Emily, Stephen},
You can update these without creating a new archive by editing the existing archive's metadata as described here.
Ah yes. Silly mistake by me. Should be fixed now.
Thank you ! I see that the author name changes have updated but not the title of the archive. Could you please confirm that ?
Sorry, I misunderstood what the title referred to. It should be fixed now?
Thank you ; this now looks right on my end !
I'm now happy to recommend Spectral Connectivity to the EIC team for publication, and I just want to add my congratulations to you on such an impressive effort ! π
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1016/j.jneumeth.2014.11.012 is OK
- 10.1109/ICDSP.2007.4288544 is OK
- 10.1007/PL00007990 is OK
- 10.1007/s005290050005 is OK
- 10.1073/pnas.1017041108 is OK
- 10.48550/ARXIV.2201.11941 is OK
- 10.1101/2021.02.03.429582 is OK
- 10.1016/j.neuroimage.2008.02.020 is OK
- 10.2307/2287238 is OK
- 10.1016/0013-4694(83)90235-3 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1007/BF00198091 is OK
- 10.1016/S0165-0270(03)00052-9 is OK
- 10.1007/978-3-662-58485-9_11 is OK
- 10.1002/(sici)1097-0193(1999)8:4<194::aid-hbm4>3.0.co;2-c is OK
- 10.1523/JNEUROSCI.0854-21.2021 is OK
- 10.1016/j.clinph.2004.04.029 is OK
- 10.1103/PhysRevLett.100.234101 is OK
- 10.1002/hbm.20346 is OK
- 10.3389/fnsys.2021.645709 is OK
- 10.1016/j.neuroimage.2011.01.055 is OK
- 10.1016/j.neuroimage.2010.01.073 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.3389/978-2-88919-608-1 is OK
- 10.22541/au.159363438.81020330 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/3787, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
I found a couple of small typos that I fixed. We are happy how it looks otherwise.
@edeno I am the AEiC for this track and here to help process this work for acceptance in JOSS. I have reviewed the archive and the paper and all seems in order. I only have one minor editorial point:
United States of America
instead of USA
. Please let me know when you've worked on the above. Thanks.
Hi @Kevin-Mattheus-Moerman,
I added the affiliation country to the archive and the paper.md. Please let me know if there's another place it should be added.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@edeno all looks good now so we'll proceed with acceptance. Thanks
Submitting author: !--author-handle-->@edeno<!--end-author-handle-- () Repository: https://github.com/Eden-Kramer-Lab/spectral_connectivity Branch with paper.md (empty if default branch): Version: v1.1.0 Editor: !--editor-->@emdupre<!--end-editor-- Reviewers: @AJQuinn, @sappelhoff, @EtienneCmb Archive: 10.5281/zenodo.7416614
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
@AJQuinn & @sappelhoff & @EtienneCmb, 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 @emdupre know.
β¨ 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 β¨
Checklists
π Checklist for @AJQuinn
π Checklist for @sappelhoff
π Checklist for @EtienneCmb