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=0.14 s (403.1 files/s, 269127.8 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
C/C++ Header 4 5306 7381 21414
Python 11 221 43 793
YAML 17 47 7 645
Markdown 7 252 0 494
R 4 46 99 182
C++ 3 44 19 132
TeX 1 9 0 99
Bourne Shell 4 21 21 58
Dockerfile 4 14 0 27
CMake 1 5 0 8
-------------------------------------------------------------------------------
SUM: 56 5965 7570 23852
-------------------------------------------------------------------------------
gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 674
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.21105/joss.03076 is OK
- 10.1146/annurev.fluid.010908.165248 is OK
- 10.1063/1.1699114 is OK
- 10.1145/3458817.3476150 is OK
- 10.1007/978-3-319-11259-6_23-1 is OK
- 10.4208/cicp.2009.v6.p826 is OK
- 10.7287/PEERJ.PREPRINTS.1686V1 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 @georgiastuart , @Himscipy ,
During the review, feel free to ask questions here to the authors directly if you need clarifications, or to me regarding the editorial part. If you open issues on the code's repository, please report them and/or their resolution here as well so that I can follow that part as well.
Thanks for reviewing for JOSS!
Hi @georgiastuart thanks for starting the review.
@Himscipy do you have any question regarding the editorial process?
-> @georgiastuart @Himscipy gentle reminder of the review in progress.
👋 Hi all - as the track editor here, I just wanted to check in on on the progress of this review after a couple of weeks with no changes
Thanks for the nudge @danielskatz , I'll get back to this ASAP.
@linusseelinger can you explain the contributions of Matthew Parno? He's listed as an author but not listed in the contributors list on GitHub.
@linusseelinger, you can disregard the above, I found Matt's contributions in the benchmarks repo.
A few questions / comments...
parameters
and config
function arguments and the return values for each method in the server? Apologies if I missed this in the docs somewhere.I intend to look at this again and try to set up an example with my own python-based model, but the above are my first impressions. Very cool work!
Also, please add community guidelines in a CONTRIBUTION.md
file or similar to the repository.
Another question, is UM-Bridge capable of using mpi-parallelized models?
@georgiastuart Thanks a lot for your comments!
Hi @georgiastuart, I accidentally edited your review checklist, my apologies for that. However, I have brought it back to the state where it was, but I would like you to cross-check it again. Thank you.
Hi @linusseelinger
Here few comments related to the software paper and repository;
Could you mention how the UM-Bridge compares with the existing state of the field tools for UQ in the paper? This will be useful in addressing one of the requirements (State of the field: Do the authors describe..) in the paper.
The repository needs unit tests /automated tests for code checking. I would recommend adding a unit test and also the code coverage as a software testing metric associated with the software repo. This will be useful for debugging and future development of the software.
@georgiastuart Examples now link to the respective source code (turns out pulling source files directly from the repo is not trivial in our docs system, so we'll go with plan B for now). Types are now better documented, in particular for Python client and server where it's not obvious to see what is expected. The Python code also enforces types by explicitly checking, so I hope that's sufficient to guide new users. I hope that covers your comments about docs / types?
@Himscipy Thank you for your feedback! I have added some tests to fully cover the C++ and Python clients beyond the examples we had. The server side should be fairly well-tested already (see protocol_conformity_1.0, which is run on every model). I'm hesitant about code coverage checks, since UM-Bridge includes a couple of different languages, and more are to come. Also, since the libraries are mostly protocol wrappers, full coverage is fairly easy to achieve. Will soon adapt the paper as requested!
Hi @linusseelinger thank you for addressing the comments from both reviewers so far.
@georgiastuart @Himscipy can you assess the update?
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@Himscipy Btw, last update of paper includes the improvements you requested.
@georgiastuart @Himscipy can you have a look at @linusseelinger 's update ?
@georgiastuart @Himscipy it is over a month since the update by the authors, may I ask you to proceed with the review?
Hi @pdebuyl Thank you for the reminder. I will finalize the review by COB today.
Hi @pdebuyl , I have looked at the latest changes and gone through the reviewers checklist for the paper. Thank you for providing the opportunity for reviewing the submission.
@linusseelinger the updated submission looks good, good luck!
Hi @Himscipy thanks a lot for completing the review! I had seen your first message but not the second, sorry about this.
@georgiastuart can you assess the changes since your review?
Apologies, I went on maternity leave before finishing this.
I am satisfied by the response from the authors!
Hi @georgiastuart thank you for completing the review!
@linusseelinger I'll proceed (not before 10 days, sorry) to the subsequent editorial steps.
@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
- 10.21105/joss.03076 is OK
- 10.1146/annurev.fluid.010908.165248 is OK
- 10.1063/1.1699114 is OK
- 10.1145/3458817.3476150 is OK
- 10.1007/978-3-319-11259-6_23-1 is OK
- 10.4208/cicp.2009.v6.p826 is OK
- 10.7287/PEERJ.PREPRINTS.1686V1 is OK
- 10.12688/openreseurope.14445.2 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Hi @linusseelinger I read the paper and tested a few of the examples. Everything ran flawlessly and I have no further comments or recommendations.
Can you
@pdebuyl Thanks a lot! Here's the DOI: 10.5281/zenodo.7743819
@editorialbot set 10.5281/zenodo.7743819 as archive
Done! Archive is now 10.5281/zenodo.7743819
@editorialbot set 1.2.2 as version
Done! version is now 1.2.2
@editorialbot set v1.2.2 as version
Done! version is now v1.2.2
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.21105/joss.03076 is OK
- 10.1146/annurev.fluid.010908.165248 is OK
- 10.1063/1.1699114 is OK
- 10.1145/3458817.3476150 is OK
- 10.1007/978-3-319-11259-6_23-1 is OK
- 10.4208/cicp.2009.v6.p826 is OK
- 10.7287/PEERJ.PREPRINTS.1686V1 is OK
- 10.12688/openreseurope.14445.2 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/4061, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
👋 @linusseelinger - I'm the track editor who will take over at this point. While proofreading the paper, I found some small changes that I think are needed: please merge https://github.com/UM-Bridge/umbridge/pull/12 or let me know what you disagree with, then we can proceed to acceptance and publication
Submitting author: !--author-handle-->@linusseelinger<!--end-author-handle-- (Linus Seelinger) Repository: https://github.com/UM-Bridge/umbridge Branch with paper.md (empty if default branch): Version: v1.2.2 Editor: !--editor-->@pdebuyl<!--end-editor-- Reviewers: @georgiastuart, @Himscipy Archive: 10.5281/zenodo.7743819
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
@georgiastuart & @Himscipy, 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 @pdebuyl know.
✨ 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 ✨
Checklists
📝 Checklist for @georgiastuart
📝 Checklist for @Himscipy