Closed editorialbot closed 7 months ago
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Software report:
github.com/AlDanial/cloc v 1.88 T=0.14 s (551.3 files/s, 161325.7 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
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Python 43 1906 3802 5504
Jupyter Notebook 18 0 7722 1653
TeX 1 27 0 563
XML 1 0 19 448
YAML 6 18 19 141
reStructuredText 2 92 74 126
Ruby 1 28 12 106
Markdown 1 39 0 96
JSON 1 0 0 51
TOML 1 3 0 30
DOS Batch 1 8 1 26
make 1 4 7 9
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SUM: 77 2125 11656 8753
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gitinspector failed to run statistical information for the repository
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1017/S0022112010001217 is OK
- 10.1137/1.9781611974508 is OK
- 10.1146/annurev-fluid-030121-015835 is OK
- 10.1016/j.arcontrol.2009.12.001 is OK
- 10.1007/978-0-387-40065-5 is OK
- 10.1017/9781108380690 is OK
- 10.1137/21M1401243 is OK
- 10.1063/1.4772195 is OK
- 10.1007/s00332-017-9437-7 is OK
- 10.1146/annurev-fluid-011212-140652 is OK
- 10.1063/1.4993854 is OK
- 10.1007/BF02532251 is OK
- 10.1038/s41467-017-00030-8 is OK
- 10.1007/978-3-662-04323-3_15 is OK
- 10.1017/S0022112009992059 is OK
- 10.1002/9781118535561 is OK
- 10.48550/arXiv.1710.09668 is OK
- 10.1137/18M1225409 is OK
- 10.1063/1.5011399 is OK
- 10.1038/s41467-017-02388-1 is OK
- 10.1098/rspa.2017.0844 is OK
- 10.1103/PhysRevLett.120.024102 is OK
- 10.1137/19M1274067 is OK
- 10.1016/j.jcp.2018.10.045 is OK
- 10.1073/pnas.1906995116 is OK
- 10.1126/science.aaw4741 is OK
- 10.1007/s00466-019-01711-5 is OK
- 10.1137/130932715 is OK
- 10.1016/j.cma.2016.03.025 is OK
- 10.1016/j.physd.2020.132401 is OK
- 10.1073/pnas.1118984109 is OK
- 10.1073/pnas.1620045114 is OK
- 10.1073/pnas.0609476104 is OK
- 10.1126/science.1165893 is OK
- 10.1038/ncomms9133 is OK
- 10.1073/pnas.1517384113 is OK
- 10.1007/s00332-015-9258-5 is OK
- 10.1126/sciadv.1602614 is OK
- 10.3934/jcd.2015005 is OK
- 10.1038/s41467-018-07210-0 is OK
- 10.1137/18M1177846 is OK
- 10.48550/arXiv.1710.04340 is OK
- 10.1017/jfm.2021.271 is OK
- 10.1016/j.ifacol.2016.10.250 is OK
- 10.1109/TAC.2020.2978039 is OK
- 10.1007/978-3-030-35713-9 is OK
- 10.1088/2632-2153/abf0f5 is OK
- 10.1016/j.automatica.2019.05.016 is OK
- 10.1137/20M1325678 is OK
- 10.21105/joss.02104 is OK
- 10.1137/17M115414X is OK
- 10.1016/j.physd.2004.06.015 is OK
- 10.1137/19M1267246 is OK
- 10.1137/15M1013857 is OK
- 10.1088/2632-2153/ac3de0 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Wordcount for paper.md
is 1267
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Hi @pswpswpsw, a few comments about the paper:
Figure 3
should be shrinked and it would be preferrable to move it closer to where it is referenced, I've found it unpleasant to move up and down to understand what you were talking about.Figure 1
is quite detached from the context of the paper. It seems to me that it's neither referenced nor explained in the body, and it is too dense of information.Figure 2
as for Figure 3
, I would shrink it and make it better integrated with the body.@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Hi @fandreuz, thank you for your time reviewing! I just finished the revised paper. Please take a look.
Hi @pswpswpsw, thanks for updating the paper:
There's a typo/rendering problem at L93. I propose to remove "the" before "PyKoopman" in L51.
About Statement of need: please try to condense it. I propose to have a detailed explanation of all features supported in PyKoopman only in one place, namely the Features section. In Statement of need I'd like to see only 1/2 sentences about high-level features of your package, 1/2 sentences for comparison with state of the art (e.g. other open source packages like PyDMD) and much less citations. I would say there's not much need for many citations in Statement of need as anyway you will go into details in Features, so I propose to keep only the critical ones.
Hi @fandreuz, Thanks for the second round review.
pykoopman
. Now I have added them to the revised version. Please take a look. I just corrected the typo/rendering issues and also removed the "the" before Pykoopman.
For statement of need, the revised version now only has one sentence about comparison to pydmd
:
Compared to implementation of DMD (e.g.,
PyDMD
[@demo2018pydmd]) which can be viewed as a linear projection of Koopman operator,PyKoopman
offers a comprehensive set of nonlinear projection methods.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@pswpswpsw has the package PyKoopman
been used in academic papers?
@ulf1 Hi Ulf, first I want to thank you for pointing out the issues. I learned a lot.
To answer your question, not yet (because we just officially released the paper) but soon I will have a few papers that uses this pykoopman. I believe the community will also start to use our package for benchmark.
@editorialbot generate pdf
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:
@olexandr-konovalov dear editor, looks like the review has been completed? Shall we move forward?
@fandreuz and @ulf1, could you please confirm if the review is completed? I don't see that all checkboxes have been checked, so it's not yet finished from my perspective. Could you please revisit your checklists and update their state? Thanks!
Hi @pswpswpsw, as I said in my last comment I still feel the full detailed summary for each dependency is not needed and it should be cut. Not sure what's the opinion of @ulf1 here.
I also feel 11 pages is quite a lot for JOSS, in general I would:
I've checked all the other points.
@olexandr-konovalov @pswpswpsw @fandreuz Hello, I finished my review. I like the jupyter demo notebooks to explain how to call the package's classes, and the unit tests. The dependencies, including version ranges, have been fixed. I agree with @fandreuz that the PDF is very lengthy. I recommend this submission for publication.
@editorialbot generate pdf
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Hi @fandreuz , thanks for the reply. I have
Hope this would work. Thanks.
Looks good for me @olexandr-konovalov, thanks @pswpswpsw.
@olexandr-konovalov dear editor, can we move forward with the current status?
@fandreuz @ulf1 thank you for the reviews. So, can you please explicitly confirm your recommendation to accept the submission of the latest version?
Hi @olexandr-konovalov, sure. I recommend the paper for submission
I recommend the latest submission for publication
@olexandr-konovalov looks like both reviewers have agreed. Shall we move forward?
Thanks @fandreuz and @ulf1 - yes, @pswpswpsw, I have now to follow this process, let me try to find some time next week...
@olexandr-konovalov Hi Editor, I have done my part issuing a tag v1.0.9 and uploaded it on https://zenodo.org/records/10633346
@editorialbot create post-review checklist
I'm sorry @pswpswpsw, I'm afraid I can't do that. That's something only editors are allowed to do.
@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
@editorialbot generate pdf
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1017/S0022112010001217 is OK
- 10.1137/1.9781611974508 is OK
- 10.1146/annurev-fluid-030121-015835 is OK
- 10.1016/j.arcontrol.2009.12.001 is OK
- 10.1007/978-0-387-40065-5 is OK
- 10.21105/joss.03994 is OK
- 10.1017/9781108380690 is OK
- 10.1137/21M1401243 is OK
- 10.1063/1.4772195 is OK
- 10.1007/s00332-017-9437-7 is OK
- 10.1146/annurev-fluid-011212-140652 is OK
- 10.1063/1.4993854 is OK
- 10.1007/BF02532251 is OK
- 10.1038/s41467-017-00030-8 is OK
- 10.1007/978-3-662-04323-3_15 is OK
- 10.1017/S0022112009992059 is OK
- 10.1002/9781118535561 is OK
- 10.48550/arXiv.1710.09668 is OK
- 10.1137/18M1225409 is OK
- 10.1063/1.5011399 is OK
- 10.1038/s41467-017-02388-1 is OK
- 10.1098/rspa.2017.0844 is OK
- 10.1103/PhysRevLett.120.024102 is OK
- 10.1137/19M1274067 is OK
- 10.1016/j.jcp.2018.10.045 is OK
- 10.1073/pnas.1906995116 is OK
- 10.1126/science.aaw4741 is OK
- 10.1007/s00466-019-01711-5 is OK
- 10.1137/130932715 is OK
- 10.1016/j.cma.2016.03.025 is OK
- 10.1016/j.physd.2020.132401 is OK
- 10.1073/pnas.1118984109 is OK
- 10.1073/pnas.1620045114 is OK
- 10.1073/pnas.0609476104 is OK
- 10.1126/science.1165893 is OK
- 10.1038/ncomms9133 is OK
- 10.1073/pnas.1517384113 is OK
- 10.1007/s00332-015-9258-5 is OK
- 10.1126/sciadv.1602614 is OK
- 10.3934/jcd.2015005 is OK
- 10.1038/s41467-018-07210-0 is OK
- 10.1137/18M1177846 is OK
- 10.48550/arXiv.1710.04340 is OK
- 10.1017/jfm.2021.271 is OK
- 10.1016/j.ifacol.2016.10.250 is OK
- 10.1109/TAC.2020.2978039 is OK
- 10.1007/978-3-030-35713-9 is OK
- 10.1088/2632-2153/abf0f5 is OK
- 10.1016/j.automatica.2019.05.016 is OK
- 10.1137/20M1325678 is OK
- 10.21105/joss.02104 is OK
- 10.1137/17M115414X is OK
- 10.1016/j.physd.2004.06.015 is OK
- 10.1137/19M1267246 is OK
- 10.1137/15M1013857 is OK
- 10.1088/2632-2153/ac3de0 is OK
MISSING DOIs
- 10.21105/joss.00530 may be a valid DOI for title: PyDMD: Python dynamic mode decomposition
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot generate pdf
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1017/S0022112010001217 is OK
- 10.1137/1.9781611974508 is OK
- 10.1146/annurev-fluid-030121-015835 is OK
- 10.1016/j.arcontrol.2009.12.001 is OK
- 10.1007/978-0-387-40065-5 is OK
- 10.21105/joss.00530 is OK
- 10.21105/joss.03994 is OK
- 10.1017/9781108380690 is OK
- 10.1137/21M1401243 is OK
- 10.1063/1.4772195 is OK
- 10.1007/s00332-017-9437-7 is OK
- 10.1146/annurev-fluid-011212-140652 is OK
- 10.1063/1.4993854 is OK
- 10.1007/BF02532251 is OK
- 10.1038/s41467-017-00030-8 is OK
- 10.1007/978-3-662-04323-3_15 is OK
- 10.1017/S0022112009992059 is OK
- 10.1002/9781118535561 is OK
- 10.48550/arXiv.1710.09668 is OK
- 10.1137/18M1225409 is OK
- 10.1063/1.5011399 is OK
- 10.1038/s41467-017-02388-1 is OK
- 10.1098/rspa.2017.0844 is OK
- 10.1103/PhysRevLett.120.024102 is OK
- 10.1137/19M1274067 is OK
- 10.1016/j.jcp.2018.10.045 is OK
- 10.1073/pnas.1906995116 is OK
- 10.1126/science.aaw4741 is OK
- 10.1007/s00466-019-01711-5 is OK
- 10.1137/130932715 is OK
- 10.1016/j.cma.2016.03.025 is OK
- 10.1016/j.physd.2020.132401 is OK
- 10.1073/pnas.1118984109 is OK
- 10.1073/pnas.1620045114 is OK
- 10.1073/pnas.0609476104 is OK
- 10.1126/science.1165893 is OK
- 10.1038/ncomms9133 is OK
- 10.1073/pnas.1517384113 is OK
- 10.1007/s00332-015-9258-5 is OK
- 10.1126/sciadv.1602614 is OK
- 10.3934/jcd.2015005 is OK
- 10.1038/s41467-018-07210-0 is OK
- 10.1137/18M1177846 is OK
- 10.48550/arXiv.1710.04340 is OK
- 10.1017/jfm.2021.271 is OK
- 10.1016/j.ifacol.2016.10.250 is OK
- 10.1109/TAC.2020.2978039 is OK
- 10.1007/978-3-030-35713-9 is OK
- 10.1088/2632-2153/abf0f5 is OK
- 10.1016/j.automatica.2019.05.016 is OK
- 10.1137/20M1325678 is OK
- 10.21105/joss.02104 is OK
- 10.1137/17M115414X is OK
- 10.1016/j.physd.2004.06.015 is OK
- 10.1137/19M1267246 is OK
- 10.1137/15M1013857 is OK
- 10.1088/2632-2153/ac3de0 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@olexandr-konovalov Hi Editor, I just fixed the missing DOI issue.
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@olexandr-konovalov Hi Editor, I have ensured our page on zenodo (https://zenodo.org/records/10633346) has the correct author list and ORCID. I have completed the following.
@pswpswpsw wonderful, thanks - helps me a lot!
Submitting author: !--author-handle-->@pswpswpsw<!--end-author-handle-- (Shaowu Pan) Repository: https://github.com/dynamicslab/pykoopman Branch with paper.md (empty if default branch): Version: v1.1.0 Editor: !--editor-->@olexandr-konovalov<!--end-editor-- Reviewers: @ulf1, @fandreuz Archive: 10.5281/zenodo.10685233
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
@ulf1 & @fandreuz, 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 @olexandr-konovalov 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 @fandreuz
📝 Checklist for @ulf1