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=0.45 s (917.5 files/s, 63155.3 lines/s)
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Language files blank comment code
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Python 392 3425 2767 19755
Markdown 3 185 0 1157
YAML 11 54 16 387
TeX 1 38 0 275
JSON 1 0 0 92
TOML 1 0 0 2
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SUM: 409 3702 2783 21668
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 1913
Failed to discover a Statement of need
section in paper
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1002/qj.441 is OK
- 10.1145/2833157.2833162 is OK
- 10.5194/npg-24-535-2017 is OK
- 10.5194/gmd-8-1677-2015 is OK
- 10.1175/1520-0469(1967)024<0688:CDGBC>2.0.CO;2 is OK
- 10.5194/acp-18-7313-2018 is OK
- 10.5194/gmd-10-1817-2017 is OK
- 10.21105/joss.00755 is OK
- 10.1029/2018MS001285 is OK
- 10.5194/gmd-13-5119-2020 is OK
- 10.5194/gmd-13-1335-2020 is OK
- 10.1002/2017MS000930 is OK
- 10.5194/gmd-11-3623-2018 is OK
- 10.1007/978-3-030-77964-1_2 is OK
- 10.1002/qj.1913 is OK
- 10.1029/2002JD002673 is OK
- 10.1007/s10546-020-00595-w is OK
- 10.1002/fld.1071 is OK
- 10.1029/2019MS001689 is OK
- 10.21105/joss.02807 is OK
- 10.1038/s41467-019-12982-0 is OK
- 10.1175/JAS3980 is OK
- 10.21105/joss.03219 is OK
- 10.1002/essoar.10510248.1 is OK
- 10.5194/acp-16-2083-2016 is OK
- 10.5194/gmd-13-4107-2020 is OK
- 10.1029/1999JD901161 is OK
- 10.1038/nature22806 is OK
- 10.1126/science.aad4889 is OK
- 10.5194/gmd-9-1455-2016 is OK
- 10.1175/1520-0450(1978)017<0320:ATDPIC>2.0.CO;2 is OK
- 10.1016/0307-904X(84)90088-X is OK
- 10.1017/CBO9781139165389 is OK
- 10.1039/c3fd00035d is OK
MISSING DOIs
- 10.21105/joss.03896 may be a valid DOI for title: PyMPDATA v1: Numba-accelerated implementation of MPDATA with examples in Python, Julia and Matlab
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@dhhagan Please remove me as a reviewer. I am an author on this paper.
@editorialbot remove @claresinger as reviewer
@claresinger removed from the reviewers list!
@editorialbot add @emmasimp as reviewer
@emmasimp added to the reviewers list!
@dhhagan can you check if the reviewers are now properly set? Let me know if you need any help
@emmasimp Can you generate your checklist by running "@editorialbot generate my checklist"? Thanks!
@dhhagan Please remove me as a reviewer. I am an author on this paper.
Sorry about that mistake!
Apologies for the length of time it has taken for this review.
After looking over the code and paper, I'm happy to report that it looks to be in great shape to me. The paper is well written and describes the new functionality well, the API documentation is easy to find and useful, and the test coverage of the code seems good.
The one thing I would note is that there is not any discussion of the 'state of the field' in this paper. The version 1 paper does list other implementations of these routines, which are also noted in the README document for the code repository. But it would be useful here to have a short note on what extra (if any) open source packages have been added since v1, and if any other software tools have overlapping functionality specifically with the new features described in this paper.
Sorry for the delay in getting this review done!
Overall I think the paper and code are very well written. I found the code and documentation easy to understand and get up and running with the model. I wish more software was documented in a way that allowed me to install and run the model within a matter of minutes!
I agree with Doug that the only thing missing is a bit more detail in the paper of how the new features of PySDM v2 fit in to the wider picture of similar models available (or whether or not any exist).
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Thanks for adding the state of the field section to the paper. It looks good to me now, I'm happy for the paper to be published.
I agree with Doug, happy for the paper to be published :)
Thank you!
One question for the editors we have is how to technically handle the fact that the project has recently moved from github.com/atmos-cloud-sim-uj
to github.com/open-atmos
. There is a redirect, so the previous link does work, but it would be great to promote the new location on the JOSS website next to the paper. @dhhagan @Kevin-Mattheus-Moerman is there a way to change such piece of metadata? Thanks
@editorialbot set github.com/open-atmos as repository
Done! repository is now github.com/open-atmos
@editorialbot generate pdf
:warning: An error happened when generating the pdf.
@slayoo like that ☝️. All should be good. Let us know if the branch should be changed.
@editorialbot set https://github.com/open-atmos as repository
Done! repository is now https://github.com/open-atmos
@editorialbot generate pdf
Looks like it couldn't find paper. Let @dhhagan know where it is found.
:warning: An error happened when generating the pdf.
@editorialbot set https://github.com/open-atmos/PySDM as repository
I'm sorry @slayoo, I'm afraid I can't do that. That's something only editors are allowed to do.
@Kevin-Mattheus-Moerman I think you maybe need to set https://github.com/open-atmos/PySDM as the repository (the whole path, not just the org)
@editorialbot set https://github.com/open-atmos/PySDM as repository
Done! repository is now https://github.com/open-atmos/PySDM
@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 generate pdf
(changed my affiliation order from "5,3" to "3,5" + added two commas in the text)
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@dhhagan @Kevin-Mattheus-Moerman Now that the two reviewers have expressed their approval, can we initiate the next steps in the publication?
@dhhagan @Kevin-Mattheus-Moerman can you please update us on the next steps needed for publication
@dhhagan @Kevin-Mattheus-Moerman please update us on the status of this review, thanks!
@slayoo apologies for the delay. It seems @dhhagan might be overlooking these notifications. I'll try to email him. I'll take over as editor if he doesn't respond.
Actually, I'll take it from here.
Thank you, @Kevin-Mattheus-Moerman
@editorialbot generate pdf
Submitting author: !--author-handle-->@edejong-caltech<!--end-author-handle-- (Emily de Jong) Repository: https://github.com/open-atmos/PySDM Branch with paper.md (empty if default branch): Version: v2.16 Editor: !--editor-->@dhhagan<!--end-editor-- Reviewers: @douglowe, @emmasimp Archive: 10.5281/zenodo.7640495
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.)
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@claresinger & @douglowe, 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:
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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 ✨
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