Closed editorialbot closed 4 months ago
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Software report:
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Wordcount for paper.md
is 1514
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1137/141000671 is OK
- 10.21105/joss.04869 is OK
- 10.1029/2022MS002994 is OK
- 10.1109/TPAMI.2021.3097011 is OK
- 10.1214/13-STS421 is OK
- 10.21105/joss.04561 is OK
- 10.1137/19M1304891 is OK
- 10.1093/bioinformatics/btaa078 is OK
- 10.1088/1361-6420/ac99fa is OK
- 10.1029/2022MS003245 is OK
- 10.22541/essoar.170365299.96491153/v1 is OK
MISSING DOIs
- 10.1088/0266-5611/29/4/045001 may be a valid DOI for title: Ensemble Kalman methods for inverse problems
- 10.1109/allerton.2008.4797607 may be a valid DOI for title: Uniform approximation of functions with random bases
- 10.1214/10-sts327 may be a valid DOI for title: The Random Walk Metropolis: Linking Theory and Practice Through a Case Study
INVALID DOIs
- https://doi.org/10.1016/j.jcp.2020.109716 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1029/2020MS002454 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1029/2021MS002735 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1029/2022MS002997 is INVALID because of 'https://doi.org/' prefix
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Hello again! πβ¨
@matt-graham, @Vaibhavdixit02, @nluetts
FYI @odunbar
This is the review thread for the paper. All of our higher-level communications will happen here from now on, review comments and discussion can happen in the repository of the project (details below).
π Please read the "Reviewer instructions & questions" in the comment from our editorialbot (above).
β All reviewers get their own checklist with the JOSS requirements - you generate them as per the details in the editorialbot comment. As you go over the submission, please check any items that you feel have been satisfied.
π» The JOSS review is different from most other journals: The reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention the link to https://github.com/openjournals/joss-reviews/issues/6372 so that a link is created to this thread. That will also help me to keep track!
β Please also feel free to comment and ask questions on this thread if you are unsure about something!
π― We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule. NOTE: I am aware that some of you asked for some additional time due to having other obligations for now. That's no problem, please just communicate with me if your schedule for this review changes.
@Vaibhavdixit02 if you are done with your review (seems like it from your checkmarks), I'd appreciate if you could write a short summary whether you recommend this paper for acceptance or/and if some points still need to be addressed.
Same for @matt-graham once you are finished, please π
@nluetts I know that you will only be able to really get started on this in early March, please keep me updated should anything change with that.
@sappelhoff the package is quite well-developed and has comprehensive documentation and usage tutorials. It is a novel implementation as well so from my end it is a clear accept. The points raised by Matt are reasonable and I am following those issues barring which I don't have any other comments here.
@nluetts I know that you will only be able to really get started on this in early March, please keep me updated should anything change with that.
All fine, @sappelhoff , I just started with the review.
@matt-graham may I ask you for an update on your ongoing review, please? What are the outstanding points, and the approximate timeline for them?
@sappelhoff - I've currently got no spare capacity due to other commitments so will not be able to look at this again till next week. I saw that the authors responded to the issues I previously raised but haven't had a chance to look through their responses to two of the issues yet. I also have some minor feedback on the paper which I haven't yet had a chance to transcribe in to an issue.
@matt-graham @nluetts just to check in with you: Are there any blockers that are holding you back from completing your reviews? Are you able to share an approximate date with us of when you might finish the last steps? Thanks!
@sappelhoff The cold season has taken its toll on me a little, but I resumed the review now and have some time during this week, so I try to provide all my feedback by Friday. Apropos feedback, when I have questions and feedback to the JOSS paper draft itself, am I supposed to open an issue over at https://github.com/CliMA/CalibrateEmulateSample.jl or comment in this issue?
Sorry to hear that, get well soon @nluetts! Thanks for your updated schedule as well. Please open issues at https://github.com/CliMA/CalibrateEmulateSample.jl also when it's about the JOSS paper draft π
Apologies for the delay in finishing off my review. I have opened an issue with some minor suggestions for changes to text to paper (and have therefore left a couple of items on reviewer checklist unticked but just to be clear I don't have any concerns about overall quality of writing). @odunbar has addressed everything in the other issues I raised so from my perspective it is only the minor changes to the paper that are outstanding.
Hi everyone! Thanks for all the comments on the documentation, examples and manuscript. I believe as of now we have addressed all points raised, with PRs documenting all changes that link to the issues above. Let me know if any item was missed.
I'd like to make one additional change related to adding one further author to the paper. @nefrathenrici . Though they have not made visible direct contributions to the exact CES repository so far, Nat has been involved in a lot of recent decisionmaking, and added other auxilliary code such as pipelines to enable automated workflows for CalibrateEmulateSample needs for HPC applications, with various PRs to our sister repositories. I think as Nat is also primed to play more of a role moving forwards with CalibrateEmulateSample.jl they will prove a responsible and reliable steward for this codebase in future.
I will link an issue/PR adding Nat to the code here once this is done.
I think our docs and examples have definitely benefited from your reviews, and should hopefully help future users!
Cheers, Ollie
@sappelhoff : @odunbar addressed all points I raised with regard to the paper and the documentation of the package, so I ticked off the remaining items on my checklist. I agree with @Vaibhavdixit02 conclusions and recommend this paper for acceptance.
Thanks a lot @nluetts for your final verdict.
And thanks @odunbar for the update.
Once @matt-graham has finished the last steps, we can move on to a final evaluation by me and the next steps.
Once @matt-graham has finished the last steps, we can move on to a final evaluation by me and the next steps.
@sappelhoff - I've now completed my reviewer checklist and the authors have addressed all the points I raised, so I think everything now ready for your final evaluation.
Thanks a lot @matt-graham, and also @nluetts and @Vaibhavdixit02 again for completing your reviews! π
@nluetts I could not find you in our reviewer database. If you enjoyed the process of reviewing for JOSS, we'd be very grateful if you considered signing up for potential future services as a reviewerπ ... You can do that here: https://reviewers.joss.theoj.org/join
@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
@odunbar please let me know once you finished your items from the list above: https://github.com/openjournals/joss-reviews/issues/6372#issuecomment-2043015005
I will then work on my final items, and then it's (hopefully) finally time to ship it!
Hi @sappelhoff
v0.5.1
has been tagged and released Let me know if there are any issues
@sappelhoff (just in case this didn't ping you)
Hi @odunbar thanks for the ping -- I have it on my list and will get to it in time -- latest next Monday β but perhaps earlier if I can squeeze it in.
@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
- 10.1137/141000671 is OK
- 10.21105/joss.04869 is OK
- 10.1029/2022MS002994 is OK
- 10.1109/TPAMI.2021.3097011 is OK
- 10.1214/13-STS421 is OK
- 10.21105/joss.04561 is OK
- 10.1137/19M1304891 is OK
- 10.1093/bioinformatics/btaa078 is OK
- 10.1088/1361-6420/ac99fa is OK
- 10.1029/2022MS003245 is OK
- 10.22541/essoar.170365299.96491153/v1 is OK
- 10.21105/joss.05428 is OK
MISSING DOIs
- No DOI given, and none found for title: Handbook of Approximate Bayesian Computation
- 10.1201/9781315117195-8 may be a valid DOI for title: High-Dimensional ABC
- No DOI given, and none found for title: Supervised Calibration and Uncertainty Quantificat...
- No DOI given, and none found for title: Gaussian processes for machine learning
- 10.1088/0266-5611/29/4/045001 may be a valid DOI for title: Ensemble Kalman methods for inverse problems
- No DOI given, and none found for title: Random Features for Large-Scale Kernel Machines.
- 10.1109/allerton.2008.4797607 may be a valid DOI for title: Uniform approximation of functions with random bas...
- 10.1214/10-sts327 may be a valid DOI for title: The Random Walk Metropolis: Linking Theory and Pra...
- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
- No DOI given, and none found for title: GaussianProcesses. jl: A Nonparametric Bayes Packa...
- No DOI given, and none found for title: Equation of state calculations by fast computing m...
- 10.1088/1475-7516/2023/10/021 may be a valid DOI for title: Fast and robust Bayesian Inference using Gaussian ...
- 10.1111/rssb.12482 may be a valid DOI for title: The Barker proposal: combining robustness and effi...
- No DOI given, and none found for title: The No-U-Turn sampler: adaptively setting path len...
INVALID DOIs
- https://doi.org/10.1016/j.jcp.2020.109716 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1029/2020MS002454 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1029/2021MS002735 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1029/2022MS002997 is INVALID because of 'https://doi.org/' prefix
@odunbar sorry for the delay. Here is a list of comments from my side. I would appreciate a response to all of them (preferably with links to the commits in which you addressed them), and if you don't want to follow my suggestions on a particular point, I'd appreciate a reason for why not.
N. Efrat-Henrici
is the only co-author with an abbreviated first namee.g.
with or without comma after. Currently, you sometimes use e.g.,
and sometimes just e.g.
. I would recommend to follow the APA guidelines on this, which say to use latin abbreviations (also i.e.
) only in parentheses (e.g., here) and with commas, and not in flowing text like, for example, here. See: https://apastyle.apa.org/style-grammar-guidelines/abbreviations/latin ... ultimately this is up to you, but please be consistent(e.g., the Ensemble Kalman65 Sampler (Dunbar, Lopez-Gomez, et al., 2022; Garbuno-Inigo et al., 2020))
please reformat them to not use nested parentheses --> (e.g., the Ensemble Kalman65 Sampler; Dunbar, Lopez-Gomez, et al., 2022; Garbuno-Inigo et al., 2020)
Research projects using the package
section into a bullet list for improved readability and to avoid the awkward parentheses.the pipeline has three stages, most easily explained in reverse ........
Thanks!
@editorialbot set 10.5281/zenodo.10946875 as archive
Done! archive is now 10.5281/zenodo.10946875
@editorialbot set v0.5.1 as version
Done! version is now v0.5.1
Thank you for the comments, I'll get to it.
Regarding the author name, I asked them to provide a name that they wished to be stated on the manuscript and this is what they provided, which I respected. I'm happy to ask them again (but I am only really comfortable changing it if they are however).
@sappelhoff I've addressed your comments.
Please see https://github.com/CliMA/CalibrateEmulateSample.jl/pull/305 for the details of line-by-line changes etc.
The points I was unable to (fully) address
N. Efrat-Henrici
PS Do I need to release a new version and get a new Zenodo link now or is this OK?
Thanks a lot @odunbar, I'll have a look later today.
PS Do I need to release a new version and get a new Zenodo link now or is this OK?
nope, this is fine as is, because the changes were all more in terms of the paper.
@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
- 10.1137/141000671 is OK
- 10.1201/9781315117195 is OK
- 10.1201/9781315117195-8 is OK
- 10.1016/j.jcp.2020.109716 is OK
- 10.21105/joss.04869 is OK
- 10.1029/2022MS002994 is OK
- 1721.1/145140 is OK
- 10.1142/S0129065704001899 is OK
- 10.1088/0266-5611/29/4/045001 is OK
- 10.1109/allerton.2008.4797607 is OK
- 10.1109/TPAMI.2021.3097011 is OK
- 10.1214/13-STS421 is OK
- 10.1214/10-sts327 is OK
- 10.1029/2020MS002454 is OK
- 10.1029/2021MS002735 is OK
- 10.1029/2022MS002997 is OK
- 10.18637/jss.v102.i01 is OK
- 10.21105/joss.04561 is OK
- 10.1137/19M1304891 is OK
- 10.1093/bioinformatics/btaa078 is OK
- 10.1088/1361-6420/ac99fa is OK
- 10.1029/2022MS003245 is OK
- 10.22541/essoar.170365299.96491153/v1 is OK
- 10.1063/1.1699114 is OK
- 10.21105/joss.05428 is OK
- 10.1088/1475-7516/2023/10/021 is OK
- 10.1111/rssb.12482 is OK
MISSING DOIs
- No DOI given, and none found for title: Random Features for Large-Scale Kernel Machines.
- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
- No DOI given, and none found for title: The No-U-Turn sampler: adaptively setting path len...
INVALID DOIs
- None
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1137/141000671 is OK
- 10.1201/9781315117195 is OK
- 10.1201/9781315117195-8 is OK
- 10.1016/j.jcp.2020.109716 is OK
- 10.21105/joss.04869 is OK
- 10.1029/2022MS002994 is OK
- 1721.1/145140 is OK
- 10.1142/S0129065704001899 is OK
- 10.1088/0266-5611/29/4/045001 is OK
- 10.1109/allerton.2008.4797607 is OK
- 10.1109/TPAMI.2021.3097011 is OK
- 10.1214/13-STS421 is OK
- 10.1214/10-sts327 is OK
- 10.1029/2020MS002454 is OK
- 10.1029/2021MS002735 is OK
- 10.1029/2022MS002997 is OK
- 10.18637/jss.v102.i01 is OK
- 10.21105/joss.04561 is OK
- 10.1137/19M1304891 is OK
- 10.1093/bioinformatics/btaa078 is OK
- 10.1088/1361-6420/ac99fa is OK
- 10.1029/2022MS003245 is OK
- 10.22541/essoar.170365299.96491153/v1 is OK
- 10.1063/1.1699114 is OK
- 10.21105/joss.05428 is OK
- 10.1088/1475-7516/2023/10/021 is OK
- 10.1111/rssb.12482 is OK
MISSING DOIs
- No DOI given, and none found for title: Random Features for Large-Scale Kernel Machines.
- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
- No DOI given, and none found for title: The No-U-Turn sampler: adaptively setting path len...
INVALID DOIs
- None
:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.
Element doi: [facet 'pattern'] The value '1721.1/145140' is not accepted by the pattern '10\.[0-9]{4,9}/.{1,200}'.
@openjournals/dsais-eics I wanted to recommend this paper for acceptance, but I get the above error for a DOI: 1721.1/145140
... However, this DOI does seem to resolve correctly: https://doi.org/1721.1/145140
How shall we proceed?
Submitting author: !--author-handle-->@odunbar<!--end-author-handle-- (Oliver Dunbar) Repository: https://github.com/CliMA/CalibrateEmulateSample.jl Branch with paper.md (empty if default branch): Version: v0.5.1 Editor: !--editor-->@sappelhoff<!--end-editor-- Reviewers: @matt-graham, @Vaibhavdixit02, @nluetts Archive: 10.5281/zenodo.10946875
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
@matt-graham & @Vaibhavdixit02 & @nluetts, 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 @sappelhoff 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 @matt-graham
π Checklist for @nluetts
π Checklist for @Vaibhavdixit02