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=0.23 s (789.6 files/s, 135795.9 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
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Python 133 4946 6265 14317
reStructuredText 24 1028 450 1833
TeX 2 67 0 789
Bourne Shell 7 82 69 402
SVG 1 0 0 396
YAML 11 45 75 374
make 2 29 6 151
CSS 1 50 10 130
Markdown 1 25 0 64
TOML 1 3 1 31
INI 1 0 0 5
-------------------------------------------------------------------------------
SUM: 184 6275 6876 18492
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 765
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1137/080716542 is OK
- 10.1137/1.9781611974997 is OK
- 10.1561/2200000016 is OK
- 10.1007/s10851-010-0251-1 is OK
- 10.1117/12.766355 is OK
- 10.1002/cpa.20042 is OK
- 10.1137/09076934x is OK
- 10.1016/0898-1221(76)90003-1 is OK
- 10.1109/TIP.2017.2713099 is OK
- 10.1109/LSP.2017.2763583 is OK
- 10.1109/MSP.2020.3016905 is OK
- 10.1007/978-0-387-40065-5 is OK
- 10.1561/2400000003 is OK
- 10.1561/2400000003 is OK
- 10.1109/iccv.2011.6126441 is OK
- 10.1109/TCI.2016.2599778 is OK
- 10.1109/GlobalSIP.2013.6737048 is OK
- 10.1090/s0025-5718-2012-02598-1 is OK
- 10.1109/TIP.2017.2662206 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:
@vitorsr, @DanNixon, and @lucaferranti - Thanks for agreeing to review this submission. This is the review thread for the paper. All of our communications will happen here from now on.
As you can see above, you each should use the command @editorialbot generate my checklist
to create your review checklist. @editorialbot commands need to be the first thing in a new comment.
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, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#4722
so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.
We aim for reviews to be completed within about 2-4 weeks. Please let me know if either of you require some more time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period of time.
Please feel free to ping me (@danielskatz) if you have any questions/concerns.
π @vitorsr, @DanNixon, and @lucaferranti - It's great to see you all have started your reviews. However, I don't see any open issues, so I wonder if you can let me know where you are, and anything that might be blocking you from making progress that either I or the authors can act on. Thanks!
Apologies for the delay. This whole week I have been travelling for work. I'll carry the review during the upcoming week
π @vitorsr, @DanNixon, and @lucaferranti - Can let me know where you are, and anything that might be blocking you from making progress that either I or the authors can act on? Thanks!
Sorry, have not had a chance to look at this over the past week, should be able to get the rest of my review done this week.
π @DanNixon - any update?
π @lucaferranti - any update?
π @vitorsr - how is your review going?
Apologies for the huge delay, pretty busy period. I have now allocated Saturday 8th morning (European time) to this.
Small side-comment: when I previously reviewed to JOSS, I was put as assignee on the review issue. This was very helpful, because I generally start and end my workday by checking what is assigned to me on github and so I did not forget about it (it also made finding the issue easier). Has something changed? Personally, I think it would help reviewers to have them as assignees in the issue.
Hi @danielskatz, this is a somewhat large project and I am carefully reviewing it piecewise as time allows. Please let me know if there is any urgency.
On Wed, Oct 5, 2022 at 4:53 AM Luca Ferranti @.***> wrote:
Apologies for the huge delay, pretty busy period. I have now allocated Saturday 8th morning (European time) to this.
Small side-comment: when I previously reviewed to JOSS, I was put as assignee on the review issue. This was very helpful, because I generally start and end my workday by checking what is assigned to me on github and so I did not forget about it (it also made finding the issue easier). Has something changed? Personally, I think it would be helpful
β Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4722#issuecomment-1268078802, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJW2VYPZ33QLTA5YIUZPKDLWBUXYTANCNFSM6AAAAAAQBW2OXM . You are receiving this because you were mentioned.Message ID: @.***>
Hi @danielskatz, this is a somewhat large project and I am carefully reviewing it piecewise as time allows. Please let me know if there is any urgency.
no, just checking to make sure progress is happening...
π @vitorsr - do you have any update on your status?
@DanNixon - do you have any update on your status?
π @lucaferranti - do you have any update on your status?
Hi @danielskatz, I will be concluding my review shortly. The project is spotless. Any and all comments that I would have are mainly curiosities with reference to the subject itself in my capacity as a signal processing researcher, not as a reviewer with reference to the project code submitted to JOSS.
On Thu, Oct 20, 2022 at 2:03 PM Daniel S. Katz @.***> wrote:
π @vitorsr https://github.com/vitorsr - do you have any update on your status?
β Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4722#issuecomment-1285879871, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJW2VYP6PJNKGXV4SGXFSHDWEF3MVANCNFSM6AAAAAAQBW2OXM . You are receiving this because you were mentioned.Message ID: @.***>
A small note on my review. I could not easily provision a GPU and I have had to do it on my personal computer, so my peruse has been bound to CPU-only testing (as the authors do in their CI).
On Thu, Oct 20, 2022 at 2:03 PM Daniel S. Katz @.***> wrote:
π @vitorsr https://github.com/vitorsr - do you have any update on your status?
β Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4722#issuecomment-1285879871, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJW2VYP6PJNKGXV4SGXFSHDWEF3MVANCNFSM6AAAAAAQBW2OXM . You are receiving this because you were mentioned.Message ID: @.***>
@editorialbot generate pfg
I'm sorry human, I don't understand that. You can see what commands I support by typing:
@editorialbot commands
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Dear @danielskatz and @bwohlberg π ,
First, I would like to start by sincerely apologizing for the huuuge delay in carrying my review. I have been a lot of deadlines and being the software pretty big it took a while to go through the code and examples. Again, I am very sorry for the delay, but finally I got there.
So, in general I would say the software and the paper have an exceptionally high quality and I definitely recommend for publication.
The software is very well documented and I particularly like how it supports both binder and colab to allow users to start playing with the examples. I have also run the examples locally and they seem to work appropriately.
The paper is in general well written. I only have one comment:
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1137/080716542 is OK
- 10.1137/1.9781611974997 is OK
- 10.1561/2200000016 is OK
- 10.1007/s10851-010-0251-1 is OK
- 10.1117/12.766355 is OK
- 10.1002/cpa.20042 is OK
- 10.1137/09076934x is OK
- 10.1016/0898-1221(76)90003-1 is OK
- 10.1109/TIP.2017.2713099 is OK
- 10.1109/LSP.2017.2763583 is OK
- 10.1109/MSP.2020.3016905 is OK
- 10.1007/978-0-387-40065-5 is OK
- 10.1561/2400000003 is OK
- 10.1561/2400000003 is OK
- 10.1109/iccv.2011.6126441 is OK
- 10.1109/TCI.2016.2599778 is OK
- 10.1109/GlobalSIP.2013.6737048 is OK
- 10.1090/s0025-5718-2012-02598-1 is OK
- 10.1109/TIP.2017.2662206 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Regarding the references, the list of DOIs above seems quite longer than the list of references in the paper, indeed the references.bib
seem to have several references which are not cited in the paper. Could you clarify on their role?
@danielskatz I presume the references file should only contain the references which are actually used in the paper? Can you comment from an editor perspective on this?
@lucaferranti - regarding the references, our reference checker checks everything in the bib file, so references that are not used in the paper don't need to be there, but as long as they aren't causing problems in the check, they won't cause any problems anywhere else either
Dear @danielskatz and @bwohlberg π ,
First, I would like to start by sincerely apologizing for the huuuge delay in carrying my review. I have been a lot of deadlines and being the software pretty big it took a while to go through the code and examples. Again, I am very sorry for the delay, but finally I got there.
So, in general I would say the software and the paper have an exceptionally high quality and I definitely recommend for publication.
The software is very well documented and I particularly like how it supports both binder and colab to allow users to start playing with the examples. I have also run the examples locally and they seem to work appropriately.
The paper is in general well written. I only have one comment:
- [ ] currently there is no comparison with other software in the fields. The authors mention in the statement of need that there are other packages overlapping with SCICO functionalities and a few also support execution on GPU, but they don't mention by name any other library. I would encourage the authors to expand and cite relevant software in the field; ideally also comparing SCICO to them in more details, e.g. in table form.
Thanks for these comments. @bwohlberg, it looks like there is just one thing here for you to respond to
Thank you @lucaferranti and @danielskatz. The requested comparison with other software can be found in section Related Packages on this docs page (I suspect that @lucaferranti did not notice it because it was added relatively recently). We have not intentionally included any references that are not cited at least once (some may only be cited in a single example script), but it is possible that such references have inadvertently been created during changes to the docs.
Hi all, apologies from me also that my review has taken longer than I said it would, a few things came up that meant I only had the odd bit of time in the evenings to look at the software itself.
Anyway, I am happy with what I have seen and don't have any significant comments beyond what has already been said. The project is very well put together with good documentation and extensive examples/use cases.
@DanNixon - you have an item in your checklist that is unchecked. Can you check it off, or let us know what you would need done in order to do so?
@vitorsr - you have a few items left in your checklist unchecked. Can you check them off, or let us know what you would need in order to do so (which could include more time on your part, or actions from the author)?
All done. My only concern is that the JAX dependency seems a bit fragile - is there any plan to "future-proof" this requirement?
All done. My only concern is that the JAX dependency seems a bit fragile - is there any plan to "future-proof" this requirement?
We have experienced some issues with changes in jaxlib
and jax
breaking parts of our code, but a recent re-write of the BlockArray
implementation has made that much less frequent. The project requirements.txt
file includes both minimum and maximum jaxlib
/ jax
version numbers to ensure that the user installs versions of these dependencies that are known to function correctly with scico
, and we've set up a weekly job in the project CI to check whether there are any compatibility issues with any new jaxlib
/ jax
releases. We're open to suggestions, though, if there's anything else that could be done that we've overlooked.
π @vitorsr, @DanNixon, @lucaferranti - you've all now checked off all your review items, which I presume means that you think this can be accepted. Please confirm this is the case.
Yes. The submission has no acceptance blockers and meets all acceptance criteria.
On Tue, Oct 25, 2022 at 10:35 AM Daniel S. Katz @.***> wrote:
π @vitorsr https://github.com/vitorsr, @DanNixon https://github.com/DanNixon, @lucaferranti https://github.com/lucaferranti - you've all now checked off all your review items, which I presume means that you think this can be accepted. Please confirm this is the case.
β Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4722#issuecomment-1290569779, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJW2VYIAS5VTCY5AXP5TYDDWE7O2TANCNFSM6AAAAAAQBW2OXM . You are receiving this because you were mentioned.Message ID: @.***>
Yes, also happy for the submission to be accepted.
confirm the submission is ready for publication
great, thanks all.
π @bwohlberg - at this point could you:
I can then move forward with the next steps, which will include me proofreading the paper, perhaps suggesting changes, then accepting and publishing the submission.
Thank you @vitorsr, @DanNixon, and @lucaferranti for your reviews.
@danielskatz: We released version 0.0.3 about a month ago (well after the review had started) and have only made minor changes since then. Would it be OK to use that tagged release for the process outlined above? Also, any objections to some minor changes (e.g. correcting a reference, updating a description of the repo) being made to the paper itself at this stage?
Both of those are fine.
The tag is v0.0.3 and the Zenodo doi is 10.5281/zenodo.7255839.
@editorialbot generate pdf
Submitting author: !--author-handle-->@bwohlberg<!--end-author-handle-- (Brendt Wohlberg) Repository: https://github.com/lanl/scico Branch with paper.md (empty if default branch): joss-paper Version: v0.0.3 Editor: !--editor-->@danielskatz<!--end-editor-- Reviewers: @vitorsr, @DanNixon, @lucaferranti Archive: 10.5281/zenodo.7255839
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
@vitorsr & @DanNixon & @lucaferranti, 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 @danielskatz 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
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π Checklist for @DanNixon
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