Closed editorialbot closed 11 months ago
Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.
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Software report:
github.com/AlDanial/cloc v 1.88 T=0.04 s (1149.7 files/s, 133103.6 lines/s)
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Language files blank comment code
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Julia 26 476 94 2683
Markdown 10 333 0 972
TeX 1 33 0 336
YAML 4 3 4 124
TOML 3 3 0 33
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SUM: 44 848 98 4148
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 1216
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1088/0022-3719/17/33/005 is OK
- 10.1038/nphys2592 is OK
- 10.1103/physreve.63.011206 is OK
- 10.1063/1.58544 is OK
- 10.1103/revmodphys.76.785 is OK
- 10.1063/5.0155142 is OK
- 10.1039/c7sm00852j is OK
- 10.1023/A:1019991729106 is OK
- 10.1088/0953-8984/3/26/022 is OK
- 10.1093/acprof:oso/9780199235346.001.0001 is OK
- 10.1103/PhysRevE.67.021502 is OK
- 10.1103/PhysRevLett.104.255704 is OK
- 10.3389/fphy.2018.00097 is OK
- 10.1063/5.0149764 is OK
- 10.1103/PhysRevE.75.031503 is OK
- 10.1103/PhysRevLett.105.125701 is OK
- 10.1103/PhysRevE.106.064136 is OK
- 10.48550/arXiv.2306.03992 is OK
- 10.1145/355841.355847 is OK
- 10.1103/PhysRevA.29.2765 is OK
- 10.1103/PhysRevE.96.062608 is OK
- 10.1103/PhysRevLett.129.145501 is OK
- 10.48550/arXiv.2307.03443 is OK
- 10.1103/PhysRevE.104.044608 is OK
- 10.1088/1742-5468/2005/05/P05013 is OK
- 10.1103/PhysRevE.56.2932 is OK
- 10.1103/PhysRevE.81.041502 is OK
- 10.1103/PhysRevE.93.012603 is OK
- 10.1103/PhysRevE.62.1856 is OK
- 10.1103/PhysRevLett.10.321 is OK
- 10.1103/PhysRevE.82.011504 is OK
- 10.1103/PhysRevE.62.8004 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 @mstimberg - can you help me understand what's going on with this? I don't see any progress in the last month, and I only see 1 assigned reviewer, so I'm a little confused
HI @mstimberg - can you help me understand what's going on with this? I don't see any progress in the last month, and I only see 1 assigned reviewer, so I'm a little confused
Hi @danielskatz. I was away for all of August (see https://github.com/openjournals/joss-reviews/issues/5718#issuecomment-1664423068) and will carry things forward from next week on. I opened the review issue for the single reviewer that agreed so far so that they could already start, since they said that they'd have time late August/early September (https://github.com/openjournals/joss-reviews/issues/5718#issuecomment-1664842419) but might not be available later. As soon as I find someone, I'll add the second reviewer here.
Great, thanks!
@IlianPihlajamaa apologies for the slow progress, I am back from vacation and will carry things forward. I have contacted additional potential reviewers, hopefully at least one of them will accept.
@epspebble how are looking things from your side, did you find time to look at the software/paper yet? Please be reminded that JOSS reviews can be iterative, i.e. feel free to open issues or comment here as soon as you come across concerns β there is no need to gather everything into a single review text as commonly done for traditional journals. In the same vein, please generate your checklist and feel free to tick boxes in your checklist whenever you are sure about them (the two in the beginning β conflict of interest and code of conduct β would be good first candidates π ). Thank you for your time π !
@editorialbot add @dawbarton as reviewer
Thanks again @dawborton for having agreed to review (and no worries about not having time in the next 2β3 weeks).
@dawbarton added to the reviewers list!
:wave: @epspebble, @dawbarton how are things going with the reviews? Please let me know if there is anything I can do from my side to help advance things :pray:
Hi Marcel,
September has been very busy as I mentioned to you earlier. Thereβll be a big push coming as Canadian thanksgiving is around the corner!
Simon
On Mon, Oct 2, 2023 at 1:01 AM Marcel Stimberg @.***> wrote:
π @epspebble https://github.com/epspebble, @dawbarton https://github.com/dawbarton how are things going with the reviews? Please let me know if there is anything I can do from my side to help advance things π
β Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5737#issuecomment-1742565006, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA7VGRZTE3UJ5WUQ3PTQ3QLX5JYG3ANCNFSM6AAAAAA3EL25NY . You are receiving this because you were mentioned.Message ID: @.***>
Hi Marcel,
Just double checking with you here concerning the bullet points under "Software paper".
IMO, the author has made some effort towards helping a "diverse, non-specialist" audience to understand how to use the software, but I think the software is made to solve a specialist class of problem, namely Mode Coupling Theory. Does the nature of this software allows us to forgive the lack of diversity? I do not see examples of integro-differential equations in the software paper that do not arise from Mode Coupling Theory (MCT). In fact, that's only one example, but that seem sophisticated enough for people working in MCT.
The next question is just a quick confirmation. I simply checked "State of the Field" because I am persuaded by the author that indeed there are no comparable software that is convenient to do this (except "in-house integrators"). The similar enough situation is discussed here: https://discourse.julialang.org/t/integro-differential-equation-and-2nd-order-differential-equation/78799/9 (which requires some extra setup)
So, can we just check this item whenever indeed there are no replacements? Do we need to do a more extensive search?
Simon
Hi @epspebble, thanks for your questions. Here's my take:
IMO, the author has made some effort towards helping a "diverse, non-specialist" audience to understand how to use the software, but I think the software is made to solve a specialist class of problem, namely Mode Coupling Theory. Does the nature of this software allows us to forgive the lack of diversity? I do not see examples of integro-differential equations in the software paper that do not arise from Mode Coupling Theory (MCT). In fact, that's only one example, but that seem sophisticated enough for people working in MCT.
In my opinion, it is not necessary that a "diverse, non-specialist" audience is able to use the software β as you say, this software is very specialized and someone not interested in Mode Coupling Theory will have no use for it. What is important is that someone from outside this specialization is able to figure out the "high-level functionality and purpose of the software", i.e. what the software is about. I think the authors successfully do this in their Summary section, by explaining what MCT is and why it needs special algorithms β but of course this is up to you to judge as a reviewer.
So, can we just check this item whenever indeed there are no replacements? Do we need to do a more extensive search?
If you are convinced by the authors' review of the state of the field and don't see any major omission, you can check this item. If you are not very familiar with software in this sub-field, I'd indeed recommend doing a search. But of course the "state of the field" isn't required to be exhaustive, it is important to compare to other "commonly used" software β or state that there isn't any.
Hope that helps! Don't hesitate to contact me for further questions if necessary.
Overall, this is a good submission and I'd be keen for this to be published in JOSS. I don't have a background in MCT and don't know the literature in this area, but the general approach/methods are well within my area of expertise. All the examples provided work in the latest version of the software and all tests pass. The documentation and paper are generally very well written.
My comments are all really minor. The only thing that is missing are the community guidelines - at least, I didn't spot any.
ExponentiallyDecayingKernel
"We would like to thank @dawbarton for going through the paper and the software documentation. Below we address their comments and suggestions.
Through our response and changes, we hope to have adequately addressed the comments.
@mstimberg What should I do to update the submitted manuscript, other than editing the paper.md file in our github repository?
What should I do to update the submitted manuscript, other than editing the paper.md file in our github repository?
You can make a comment asking @editorialbot generate pdf
, and it will generate the new manuscript for you. Otherwise let me know and I can trigger it for you.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Great; all looks good from my perspective.
:wave: @epspebble how is the review coming along from your side?
Nothing happened so far. But I plan to take a look at my notes this weekend. It's been a very busy time for me!
Not having a background in MCT, I am pleasantly impressed by the level of detail the authors put in the documentation to explain how to use the software - they are both succinct and precise. With their help, I have successfully walked through the examples, modifying them and re-run with slightly different sets of parameters with success. I also commend the abundance of references put at appropriate places, including function docstrings. I am happy to recommend acceptance of this work to JOSS.
I have not found any major errors other than typos (e.g. "succesful" should be "successful" in the paper, "assumtions" should be "assumptions" in MCT.md)
Thanks a lot, @epspebble, for taking the time to go through the examples in the documentation. We are delighted by the kind words and positive recommendation! We have fixed the typos as pointed out.
@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 so much @dawbarton and @epspebble for your reviews. Since both reviewers accepted the manuscript/software in its current state, I will now proceed with the final steps before publication.
@IlianPihlajamaa please have a look at the checklist below, and take care of the tasks listed for authors (if necessary). Note that for technical reasons, you cannot tick off things in the checklist, so please don't worry about it.
@editorialbot set <DOI here> as archive
@editorialbot set <version here> as version
@editorialbot generate pdf
@editorialbot check references
and ask author(s) to update as needed@editorialbot recommend-accept
@mstimberg I accidentally checked one of your tasks and now I cannot undo that.
@mstimberg I accidentally checked one of your tasks and now I cannot undo that.
@IlianPihlajamaa I don't see anything checked, so seems to be ok?
The software version is: 0.8.1. The Zenodo doi is: 10.5281/zenodo.10036791.
Hi @IlianPihlajamaa thanks for checking off the items in the list, and apologies for taking so long to do the final review. I've opened a PR that fixes a few minor things (mostly capitalization in the bibliography) in IlianPihlajamaa/ModeCouplingTheory.jl#42. Apart from that, all is good from my side. Note that you do not have to release a new version and create a new archive, given that the changes only apply to the paper. As soon as this is done, I'll recommend the acceptance and trigger the final approval by the editor-in-chief.
Great, thanks! I just merged it.
@editorialbot set 10.5281/zenodo.10036791 as archive
Done! archive is now 10.5281/zenodo.10036791
@editorialbot set 0.8.1 as version
Done! version is now 0.8.1
@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 recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1088/0022-3719/17/33/005 is OK
- 10.1103/PhysRevA.34.5059 is OK
- 10.1038/nphys2592 is OK
- 10.1103/physreve.63.011206 is OK
- 10.1063/1.58544 is OK
- 10.1103/revmodphys.76.785 is OK
- 10.1063/5.0155142 is OK
- 10.1039/c7sm00852j is OK
- 10.1023/A:1019991729106 is OK
- 10.1088/0953-8984/3/26/022 is OK
- 10.1093/acprof:oso/9780199235346.001.0001 is OK
- 10.1103/PhysRevE.67.021502 is OK
- 10.1103/PhysRevLett.104.255704 is OK
- 10.3389/fphy.2018.00097 is OK
- 10.1063/5.0149764 is OK
- 10.1103/PhysRevE.75.031503 is OK
- 10.1103/PhysRevLett.105.125701 is OK
- 10.1103/PhysRevE.106.064136 is OK
- 10.48550/arXiv.2306.03992 is OK
- 10.1145/355841.355847 is OK
- 10.1103/PhysRevA.29.2765 is OK
- 10.1103/PhysRevE.96.062608 is OK
- 10.1103/PhysRevLett.129.145501 is OK
- 10.48550/arXiv.2307.03443 is OK
- 10.1103/PhysRevE.104.044608 is OK
- 10.1088/1742-5468/2005/05/P05013 is OK
- 10.1103/PhysRevE.56.2932 is OK
- 10.1103/PhysRevE.81.041502 is OK
- 10.1103/PhysRevE.93.012603 is OK
- 10.1103/PhysRevE.62.1856 is OK
- 10.1103/PhysRevLett.10.321 is OK
- 10.1103/PhysRevE.82.011504 is OK
- 10.1103/PhysRevE.62.8004 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:wave: @openjournals/csism-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/4746, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
π @IlianPihlajamaa - I'm the track editor who will finish the processing of this submission. I've proofread the paper, and have a couple of small changes to request: https://github.com/IlianPihlajamaa/ModeCouplingTheory.jl/pull/43 Please merge this, or let me know what you disagree with, then we can continue the acceptance and publication process.
I've approved the changes and merged them. Thanks for proofreading!
@editorialbot recommend-accept
Submitting author: !--author-handle-->@IlianPihlajamaa<!--end-author-handle-- (Ilian Pihlajamaa) Repository: https://github.com/IlianPihlajamaa/ModeCouplingTheory.jl Branch with paper.md (empty if default branch): Version: 0.8.1 Editor: !--editor-->@mstimberg<!--end-editor-- Reviewers: @epspebble, @dawbarton Archive: 10.5281/zenodo.10036791
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
@epspebble, 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 @mstimberg 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 @dawbarton
π Checklist for @epspebble