Closed whedon closed 3 years ago
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @vigji it looks like you're currently assigned to review this paper :tada:.
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To fix this do the following two things:
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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@whedon generate pdf
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.3389/fninf.2011.00034 is OK
- 10.3233/APC190017 is OK
- 10.1103/physrevx.10.021002 is OK
- 10.17815/jlsrf-2-121 is OK
- 10.3389/fnana.2018.00075 is OK
- 10.1016/j.neuroimage.2015.02.020 is OK
- 10.1098/rsif.2015.0734 is OK
- 10.1145/2833157.2833162 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Software report (experimental):
github.com/AlDanial/cloc v 1.88 T=0.34 s (347.2 files/s, 110372.8 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
SVG 4 2 2 21804
Python 49 1601 1480 4518
C++ 15 692 202 2978
C/C++ Header 19 304 69 1451
Markdown 4 115 0 275
CMake 5 39 36 201
YAML 3 16 21 180
Jupyter Notebook 2 0 418 176
Bourne Shell 10 30 14 165
make 2 34 10 145
TeX 1 8 0 100
reStructuredText 3 17 80 9
-------------------------------------------------------------------------------
SUM: 117 2858 2332 32002
-------------------------------------------------------------------------------
Statistical information for the repository '845d1dee56dd4b12c318a43e' was
gathered on 2021/02/15.
The following historical commit information, by author, was found:
Author Commits Insertions Deletions % of changes
fmatuschke 658 30396 17112 100.00
Below are the number of rows from each author that have survived and are still
intact in the current revision:
Author Rows Stability Age % in comments
fmatuschke 13295 43.7 11.1 6.30
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Thank you so much, @vigji for accepting to review this. I want to find at least one more reviewer, but since you started reviewing already, please feel free to indeed get started.
Please read the instructions above. If you have trouble ticking things off in the list above, remember you need to click to "accept" here: https://github.com/openjournals/joss-reviews/invitations! Any questions, feedback on the paper, etc., please post here. Any very code-specific questions, suggestions, etc., please use the issues in the code repo and link to them from this thread, so we can all keep track of them. 🌸
For examples of how this process plays out feel free to skim previous reviews, such as: #2285 and #2348. ☺️
@whedon add @glyg as reviewer
OK, @glyg is now a reviewer
👋 @glyg welcome! Make sure to read the instructions above, accept the invitation, etc.
I'll link here below all issues related to this review:
https://github.com/3d-pli/fastpli/issues/1
https://github.com/3d-pli/fastpli/issues/2
https://github.com/3d-pli/fastpli/issues/3
https://github.com/3d-pli/fastpli/issues/4
@whedon add @RealPolitiX as reviewer
OK, @RealPolitiX is now a reviewer
Oooh, and also: 👋 @RealPolitiX welcome! Make sure to read the instructions above, accept the invitation, etc.
Thank you all again!
Hey @vigji, @glyg, @RealPolitiX, when you all get a chance can you post your ETAs for your reviews — thanks! 🌸
Hi @oliviaguest I plan to make some progress on that at the end of the week, not sure how far I'll be able to get, but I'll update on Friday with an ETA
Hey @oliviaguest ! I did most of my comments on the package via issues in the repo, will write a complete report once they will all be addressed - If I got the procedure right!
Hi all
First, congrats @fmatuschke on the software, it is a really nice piece of work. I opened several issues on fastPLI repo for technical concerns.
Here are aspects more related to the paper itself:
Here I failed to see a review of other similar software or efforts. The cited literature focuses on the authors' team. Although I understand the imaging modality is specific, is it not used in other settings? Simulation of IRM data is alluded to, maybe this adjacent field has more references? As is it is hard to situate this work in the general field of brain/neuron imagery. A more scholarly (minor) question: I know 2 photons / second harmonics generation methods are also used to image bi-refringent tissues. Could fastPLI be adapted to modeling this modality? Are there comparable modeling efforts for these techniques?
Some revision of the writing should be made. @oliviaguest should I provide a detailed list of typos and such?
As stated in the first section, a review of the field or references to contributions from outside the authors' team (unless I missed something) would be welcome.
I opened 4 issues
The first 2 require minor efforts #7, #8 and are cosmetic.
The next 2 (#9, #10 ) would improve the software distribution and visualization, but I don't consider they need to be solved prior to publication.
In summary, I think this paper should be published pending the minor revisions in paper.md outlined above.
:wave: @vigji, please update us on how your review is going (this is an automated reminder).
@vigji I'd prefer if you post them all here now so I (and others) can see and comment too, if need be. Thanks!
@glyg thanks for the compliment. Since this is my first official attempt at releasing software, it means a lot. All the issues you opened in the software repository were commented by me. They are nice suggestions for improvements. As for the missing discussion of other software, I definitely failed to address that. I will add this as soon as possible and let you all know.
@whedon re-invite @RealPolitiX as reviewer
OK, the reviewer has been re-invited.
@realpolitix please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations
The paper from @fmatuschke is well-written apart from a few minor grammar errors in the first paragraph. The references are thorough. I think due to the novelty of the measurement technique used for reconstruction of neuronal fibers, it's not used elsewhere in general. You can probably cite some of the references from OpenPolScope, since it's related, and discuss your unique context.
As for the software, I opened issue #11. The wiki looks nicely written.
I added the missing section about the software compares mentioned by @glyg. Additionally I fixed some typos I found.
Thank you @RealPolitiX for opening https://github.com/3d-pli/fastpli/issues/11. I fixed it.
Just a small summary for @all. I have addressed all the issues so far. The main changes since the opening of the review are a complete rework of my Wiki and API documentation.
@fmatuschke thanks for the update. Can you please all — @vigji, @glyg, @RealPolitiX — make sure everything that has not yet been ticked off is and/or discuss any (new) changes you might be looking for? Ta! ☺️
Looks good to me now :smile:
I assume the other two reviewers are not checking their notifications, so I will email them now.
I am very sorry, yes, I was missing the notifications!
I went again through the repository. For the review, I opened 6 issues (https://github.com/3d-pli/fastpli/issues/1, https://github.com/3d-pli/fastpli/issues/2, https://github.com/3d-pli/fastpli/issues/3, https://github.com/3d-pli/fastpli/issues/4, https://github.com/3d-pli/fastpli/issues/5, https://github.com/3d-pli/fastpli/issues/6) concerning installation, automatic testing, clarity of the documentation, and internal organisation and naming consistency in the package. All of them have been thoroughly addressed by the author. Kudos to the new wiki, it is extensive and very readable now! I could successfully install the package and ran the tests.
I checked the last version of the manuscript and it looks good to me. I don't have the expertise in the subject of interest to suggest other related packages and publications that should be discussed in the paper, but the literature now discussed in the context of fibres models seems good to me!
All my issues have been addressed and I have no further requirements for the paper to be published. Nice job @fmatuschke !
@fmatuschke when you feel everything has been decided to be "ready", let me know (get whedon to compile the most recent PDF, etc.)... and I'll pop back in here and move this along. ☺️
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@fmatuschke is it looking good? ☺️ If so, can you deposit the code in zenodo or similar and post the DOI back here?
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@all I fixed hopefully the last typo and one reference in the paper. @oliviaguest I published the software in zenodo with the DOI: 10.5281/zenodo.4720075
@whedon set 10.5281/zenodo.4720075 as archive
OK. 10.5281/zenodo.4720075 is the archive.
@whedon check references
@whedon check repository
Software report (experimental):
github.com/AlDanial/cloc v 1.88 T=0.50 s (227.7 files/s, 75484.8 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
SVG 4 2 2 21804
Python 46 1506 1724 4006
C++ 15 692 199 2978
C/C++ Header 19 304 69 1451
Jupyter Notebook 4 0 794 369
Markdown 4 129 0 312
CMake 5 42 38 208
TeX 1 15 0 180
make 2 34 10 159
YAML 3 10 19 147
Bourne Shell 7 25 10 116
reStructuredText 3 18 85 11
-------------------------------------------------------------------------------
SUM: 113 2777 2950 31741
-------------------------------------------------------------------------------
Statistical information for the repository 'ad085f14f1572dcad7d76238' was
gathered on 2021/04/26.
The following historical commit information, by author, was found:
Author Commits Insertions Deletions % of changes
fmatuschke 680 31099 18181 100.00
Below are the number of rows from each author that have survived and are still
intact in the current revision:
Author Rows Stability Age % in comments
fmatuschke 12929 41.6 13.1 6.19
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.3389/fninf.2011.00034 is OK
- 10.3233/APC190017 is OK
- 10.1103/physrevx.10.021002 is OK
- 10.17815/jlsrf-4-121-1 is OK
- 10.3389/fnana.2018.00075 is OK
- 10.1016/j.neuroimage.2015.02.020 is OK
- 10.1098/rsif.2015.0734 is OK
- 10.1145/2833157.2833162 is OK
- 10.1103/physreve.83.041804 is OK
- 10.3389/fninf.2017.00005 is OK
- 10.1016/j.neuroimage.2019.02.055 is OK
- 10.1364/opex.13.004420 is OK
- 10.1117/1.3241986 is OK
- 10.1016/j.optcom.2020.126113 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@whedon generate pdf
@whedon accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.3389/fninf.2011.00034 is OK
- 10.3233/APC190017 is OK
- 10.1103/physrevx.10.021002 is OK
- 10.17815/jlsrf-4-121-1 is OK
- 10.3389/fnana.2018.00075 is OK
- 10.1016/j.neuroimage.2015.02.020 is OK
- 10.1098/rsif.2015.0734 is OK
- 10.1145/2833157.2833162 is OK
- 10.1103/physreve.83.041804 is OK
- 10.3389/fninf.2017.00005 is OK
- 10.1016/j.neuroimage.2019.02.055 is OK
- 10.1364/opex.13.004420 is OK
- 10.1117/1.3241986 is OK
- 10.1016/j.optcom.2020.126113 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:
: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/2262
If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2262, then you can now move forward with accepting the submission by compiling again with the flag deposit=true
e.g.
@whedon accept deposit=true
@fmatuschke I have proofread your paper and have some very minor comments which I hope you can address:
It allows contrasting fibers and fiber tracts and ultimately reconstructing 3D nerve fiber orientations
, some words seem missing. Should this be something like It provides image contrast for fibers and fiber tracts, and ultimately enables reconstruction of 3D nerve fiber orientations
?Different types of simulation...
to Different types of simulations...
Once you have considered the above please call @whedon generate pdf
to update the paper. I will then review the changes and process acceptance when ready.
One more important note relates to the Zenodo archive
Fiber Architecture Simulation Toolbox for 3D-PLI
but this should match the paper and be changed to fastPLI: A Fiber Architecture Simulation Toolbox for3D-PLI
. You can manually change this on Zenodo. The version tag for the Zenodo archive is 1.1.0
. I will therefore assume we should update the version tag here also. I will do this shortly below :point_down:.
Thanks.
@whedon set 1.1.0 as version
OK. 1.1.0 is the version.
Dear @Kevin-Mattheus-Moerman, I change all three of your comments. Thanks for your help. Regarding the version number. Yes, it is now officially 1.1. Thanks to the reviewers I changed quite a bit, so I had to increase the minor version. I have also corrected the title in the Zenodo archive.
Submitting author: @fmatuschke (Felix Matuschke) Repository: https://github.com/3d-pli/fastpli Version: 1.1.0 Editor: @oliviaguest Reviewers: @vigji, @glyg, @RealPolitiX Archive: 10.5281/zenodo.4720075
: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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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.)
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@vigji, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
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✨ 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 ✨
Review checklist for @glyg
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
Review checklist for @vigji
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
Review checklist for @RealPolitiX
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper