[REVIEW]: PySINDy: A comprehensive Python package for robust sparse system identification

whedon commented 2 years ago

Submitting author: @akaptano (Alan Kaptanoglu) Repository: https://github.com/dynamicslab/pysindy Version: v1.6.2 Editor: @sbenthall Reviewer: @henrykironde, @tuelwer Archive: 10.5281/zenodo.5842612

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Status

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Review checklist for @henrykironde

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@akaptano) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @tuelwer

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@akaptano) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

whedon commented 2 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @henrykironde, @tuelwer it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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whedon commented 2 years ago

Wordcount for paper.md is 1637

whedon commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1073/pnas.1517384113 is OK
- 10.1109/access.2018.2886528 is OK
- 10.1109/access.2020.3023625 is OK
- 10.21105/joss.02104 is OK
- 10.1126/science.1165893 is OK
- 10.5281/zenodo.1173754 is OK
- 10.1364/oe.24.030433 is OK
- 10.1063/1.5066099 is OK
- 10.1063/1.4977057 is OK
- 10.1016/j.ymssp.2018.08.033 is OK
- 10.1126/sciadv.1602614 is OK
- 10.1098/rspa.2016.0446 is OK
- 10.1137/16m1086637 is OK
- 10.1137/18m116798x is OK
- 10.1017/jfm.2017.823 is OK
- 10.1063/1.5018409 is OK
- 10.1016/j.ifacol.2016.10.249 is OK
- 10.1103/physreve.96.023302 is OK
- 10.1016/j.jcp.2018.10.045 is OK
- 10.1098/rspa.2018.0335 is OK
- 10.1016/j.jcp.2019.07.049 is OK
- 10.1007/s00162-020-00536-w is OK
- 10.1103/physreve.101.010203 is OK
- 10.1115/1.4043148 is OK
- 10.1137/130932715 is OK
- 10.1073/pnas.0609476104 is OK
- 10.1098/rspa.2020.0279 is OK
- 10.1103/PhysRevFluids.6.094401 is OK
- 10.1103/physreve.104.015206 is OK
- 10.1109/tmbmc.2016.2633265 is OK
- 10.1016/j.jcp.2021.110525 is OK
- 10.1103/physrevlett.120.024102 is OK
- 10.1016/j.cma.2016.03.025 is OK
- 10.1016/j.physd.2020.132401 is OK
- 10.1038/s41467-021-23479-0 is OK
- 10.1017/s0022112010001217 is OK
- 10.1098/rspa.2017.0844 is OK
- 10.1016/j.jcp.2017.07.050 is OK
- 10.1126/science.1165893 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 2 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.40 s (207.8 files/s, 93399.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          45           1969           2793           9567
Jupyter Notebook                16              0          13707           6692
TeX                              2             70              0            721
reStructuredText                 4            166            101            231
make                             1             33             13            223
Markdown                         4             42              0            206
Fortran 77                       1             38             44            132
YAML                             5              9              4            121
GLSL                             1             23             15            116
JSON                             2              0              0            108
Ruby                             1             28             12            106
TOML                             1              3              0             21
-------------------------------------------------------------------------------
SUM:                            83           2381          16689          18244
-------------------------------------------------------------------------------

Statistical information for the repository '64f2b7bdab3510f8fc665047' was
gathered on 2021/12/14.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Alan Kaptanoglu                 20          2308           1353            6.53
Brian                           12            25             27            0.09
Brian de Silva                   2            77             12            0.16
Jared Callaham                   7            70             37            0.19
Markus Quade                    75          2336            939            5.84
Taren Gorman                     1            15              0            0.03
TarenGorman                      3            49              6            0.10
Thomas Isele                     1            30              2            0.06
Thomasillo                       1           100              2            0.18
akaptano                       111         13161           4913           32.22
billtubbs                        2            18             17            0.06
briandesilva                   238          9679          11295           37.39
kopytjuk                         6           275            140            0.74
kpchamp                         81          2285            682            5.29
mq                              97          5050           1187           11.12

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Alan Kaptanoglu            1162           50.3          0.9                5.34
Jared Callaham               35           50.0          2.1               20.00
Markus Quade                409           17.5         23.1                6.36
TarenGorman                   2            4.1         47.7                0.00
akaptano                   6444           49.0          3.8                4.83
billtubbs                     6           33.3         19.3               16.67
briandesilva               5279           54.5         16.1                4.49
kopytjuk                    113           41.1         19.2                8.85
kpchamp                    1133           49.6         22.9                5.47
mq                           38            0.8         52.7                0.00

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

sbenthall commented 2 years ago

👋🏼 @akaptano @henrykironde @tuelwer this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements. 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, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#3994 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 any of you require some more time. We can also use Whedon (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 (@sbenthall ) if you have any questions/concerns.

akaptano commented 2 years ago

Hi @henrykironde and @tuelwer, thanks again for being willing to review this work! Just letting you know we are working on a the pde_optimization branch (now open as a pull request on the repo) that speeds up the PDE and weak form PDE functionality in the code by a factor of 10 or more by replacing for loops with a lot of numpy vectorization tricks. Feel free to check that out if you're interested or annoyed how slow the PDE-related code is on the main branch. This speedup should facilitate some really advanced SINDy for PDEs in the future.

Happy holidays! Alan

whedon commented 2 years ago

:wave: @tuelwer, please update us on how your review is going (this is an automated reminder).

whedon commented 2 years ago

:wave: @henrykironde, please update us on how your review is going (this is an automated reminder).

akaptano commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

akaptano commented 2 years ago

We have merged the PDE improvements into the main branch as v1.6. I have updated the paper to include Zach N. as an author (who did most of the PDE improvement work). Thanks!

tuelwer commented 2 years ago

@sbenthall @akaptano This is my review:

This submission deals with a major update to the PySINDy package, which has been previously published in JOSS [1]. PySINDy provides several implementations for the sparse identification of nonlinear dynamical systems, i.e., PySINDy performs sparse linear regression to estimate the function f describing the dynamical system from a dataset. To do so additional features are defined (by applying a library of basis functions to the data) to further improve the fit.

The authors are very clear about the contributions of their new version 1.6:

The new version of PySINDY is now able to handle systems of partial differential equations: PySINDy can now estimate systems that involve derivatives in up to three spatial dimensions in addition to the time derivative.
Version 1.6 also implements trapping SINDy algorithm for modeling fluid and plasma flows.
PySINDy now includes step-wise sparse regression (SSR) and forward regression orthogonal least squares (FROLS)

Remarks:

In my opinion these new features justify a new submission, however, an editor should check this, as I am not sure whether JOSS has any policies regarding submission for updated versions of previously published packages.
I had no problems installing the package on MacOS Monterey Version 12.0.1 and on Debian 4.19.208-1, but I got the following warning during installation of the dependencies: scikit-learn 1.0.2 does not provide the extra 'alldeps'
As far as I can see, there are tests covering the new features (e.g., the new PDE module is tested in conftest.py, FROLS and SSR are tested in test_optimizers.py). I was able to run the tests on MacOS, but I was required to re-install scikit-learn. (This might be related to the above mentioned problem.) One test failed (see issue https://github.com/dynamicslab/pysindy/issues/149).
The toolbox is very nicely documented and there are many JuPyter notebooks containing extensive examples. The results were reproducible. However, there are some missing dependencies (e.g., matplotlib in notebook '10_PDEFIND_examples') when running the notebooks on binder.
In some cases the computation of the solution can take some time. It would be good if the users could track the progress of the computation, but I am aware of the fact that this is probably not as easy to implement because PySINDy relies on other optimization toolboxes.
I liked the new tutorial videos on YouTube that very clearly explain the functionality of PySINDy.
The repository is quite large (697.3 MB according to MacOS). I would suggest that the authors spend some time looking into this. (Since rewriting the git history can cause more issues, I do not consider the large repository size a deal-breaker.)
The paper itself is very well-written and gives a nice introduction to the topic. It is quite long: 1637 words (JOSS guidelines suggest a paper length of 250-1000 words.), but given the complex nature of the discussed problem, I feel that the length is appropriate. The authors also did a good job at giving an overview over existing packages for SINDy.

Minor remarks:

Missing figure in Section "Documentation"
Documentation could be improved by typesetting the math in math mode, e.g., in : https://pysindy.readthedocs.io/en/latest/api/pysindy.optimizers.html#module-pysindy.optimizers.trapping_sr3
JuPyter notebooks in examples could be renamed such that they are sorted correctly (very minor remark)

Summary of my review: Overall, the submission is of high quality and I see a lot of value in this new version of PySINDy. That's why I would recommend to accept this submission into JOSS.

References: [1] de Silva et al., (2020). PySINDy: A Python package for the sparse identification of nonlinear dynamical systems from data. Journal of Open Source Software, 5(49), 2104, https://doi.org/10.21105/joss.02104

akaptano commented 2 years ago

Thanks for your review! I just pushed changes + a new release that updates according to your comments. It:

Fixes the complexity error you were seeing
Allows for a verbose=True/False option in all the optimizers, including the CVXPY ones, so folks can track the optimization progress (this was a very good idea!). I have added a couple unit tests for this, and updated the example 1 notebook with a simple example of its usage.
Added Matplotlib to requirements.txt in the main folder. This tells what binder which dependencies it needs. There are still some more advanced packages used in the later notebooks (notebooks 7, 8, etc.) that are not usable on binder but this is by design... we do not want the requirements.txt file to contain too many dependencies, and if users are using the advanced notebooks there are a number of other ways that users can access them, beyond online binder notebooks.
You are correct that the figure in the "Documentation" section does not render properly and we are frankly not sure how. This is because it is in a format to render correctly on the main GitHub repo page, but this then renders it incorrectly on the documentation page. For now, I have simply added a link to the file that users can follow.
Fixed the math formatting that you mentioned.

Let me know if you are satisfied with these changes. Thanks again!

akaptano commented 2 years ago

Added Andy Goldschmidt as an author for his work on the derivative package and added couple sentences about the new differentiation methods.

@whedon generate pdf

akaptano commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

tuelwer commented 2 years ago

@akaptano thank you for addressing my remarks!

@sbenthall I see no further issues with this submission!

akaptano commented 2 years ago

Thanks @tuelwer. A (hopefully last) update, made some minor changes to the paper file:

Added a link to the YouTube tutorials
Updated Figs 1 and 3 to differentiate between PDELibrary and the new WeakPDELibrary, and show the new GeneralizedLibrary class.
Added a reference to Urban Fasel's ensemble-SINDy paper.

akaptano commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

sbenthall commented 2 years ago

Great. Looks like the reviewers both recommend acceptance. We can move on to the next stage of the process, which is finalizing the submission.

sbenthall commented 2 years ago

@whedon check references

whedon commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1073/pnas.1517384113 is OK
- 10.1109/access.2018.2886528 is OK
- 10.1109/access.2020.3023625 is OK
- 10.21105/joss.02104 is OK
- 10.1126/science.1165893 is OK
- 10.5281/zenodo.1173754 is OK
- 10.1364/oe.24.030433 is OK
- 10.1063/1.5066099 is OK
- 10.1063/1.4977057 is OK
- 10.1016/j.ymssp.2018.08.033 is OK
- 10.1126/sciadv.1602614 is OK
- 10.1098/rspa.2016.0446 is OK
- 10.1137/16m1086637 is OK
- 10.1137/18m116798x is OK
- 10.1017/jfm.2017.823 is OK
- 10.1063/1.5018409 is OK
- 10.1016/j.ifacol.2016.10.249 is OK
- 10.1103/physreve.96.023302 is OK
- 10.1016/j.jcp.2018.10.045 is OK
- 10.1098/rspa.2018.0335 is OK
- 10.1016/j.jcp.2019.07.049 is OK
- 10.1007/s00162-020-00536-w is OK
- 10.1103/physreve.101.010203 is OK
- 10.1115/1.4043148 is OK
- 10.1137/130932715 is OK
- 10.1073/pnas.0609476104 is OK
- 10.1098/rspa.2020.0279 is OK
- 10.1103/PhysRevFluids.6.094401 is OK
- 10.1103/physreve.104.015206 is OK
- 10.1109/tmbmc.2016.2633265 is OK
- 10.1016/j.jcp.2021.110525 is OK
- 10.1103/physrevlett.120.024102 is OK
- 10.1016/j.cma.2016.03.025 is OK
- 10.1016/j.physd.2020.132401 is OK
- 10.1038/s41467-021-23479-0 is OK
- 10.1017/s0022112010001217 is OK
- 10.1098/rspa.2017.0844 is OK
- 10.1016/j.jcp.2017.07.050 is OK
- 10.1126/science.1165893 is OK

MISSING DOIs

- 10.1016/j.cpc.2007.03.009 may be a valid DOI for title: Numerical differentiation of experimental data: local versus global methods
- 10.1214/11-aos878 may be a valid DOI for title: The solution path of the generalized lasso

INVALID DOIs

- None

sbenthall commented 2 years ago

@akaptano Can you look at the reference summary above and confirm and add any missing DOI's please?

akaptano commented 2 years ago

@whedon generate pdf

akaptano commented 2 years ago

@whedon check references

whedon commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.cpc.2007.03.009 is OK
- 10.5402/2011/164564 is OK
- 10.1214/11-aos878 is OK
- 10.1073/pnas.1517384113 is OK
- 10.1109/access.2018.2886528 is OK
- 10.1109/access.2020.3023625 is OK
- 10.21105/joss.02104 is OK
- 10.1126/science.1165893 is OK
- 10.5281/zenodo.1173754 is OK
- 10.1364/oe.24.030433 is OK
- 10.1063/1.5066099 is OK
- 10.1063/1.4977057 is OK
- 10.1016/j.ymssp.2018.08.033 is OK
- 10.1126/sciadv.1602614 is OK
- 10.1098/rspa.2016.0446 is OK
- 10.1137/16m1086637 is OK
- 10.1137/18m116798x is OK
- 10.1017/jfm.2017.823 is OK
- 10.1063/1.5018409 is OK
- 10.1016/j.ifacol.2016.10.249 is OK
- 10.1103/physreve.96.023302 is OK
- 10.1016/j.jcp.2018.10.045 is OK
- 10.1098/rspa.2018.0335 is OK
- 10.1016/j.jcp.2019.07.049 is OK
- 10.1007/s00162-020-00536-w is OK
- 10.1103/physreve.101.010203 is OK
- 10.1115/1.4043148 is OK
- 10.1137/130932715 is OK
- 10.1073/pnas.0609476104 is OK
- 10.1098/rspa.2020.0279 is OK
- 10.1103/PhysRevFluids.6.094401 is OK
- 10.1103/physreve.104.015206 is OK
- 10.1109/tmbmc.2016.2633265 is OK
- 10.1016/j.jcp.2021.110525 is OK
- 10.1103/physrevlett.120.024102 is OK
- 10.1016/j.cma.2016.03.025 is OK
- 10.1016/j.physd.2020.132401 is OK
- 10.1038/s41467-021-23479-0 is OK
- 10.1017/s0022112010001217 is OK
- 10.1098/rspa.2017.0844 is OK
- 10.1016/j.jcp.2017.07.050 is OK
- 10.1126/science.1165893 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.cpc.2007.03.009 is OK
- 10.5402/2011/164564 is OK
- 10.1214/11-aos878 is OK
- 10.1073/pnas.1517384113 is OK
- 10.1109/access.2018.2886528 is OK
- 10.1109/access.2020.3023625 is OK
- 10.21105/joss.02104 is OK
- 10.1126/science.1165893 is OK
- 10.5281/zenodo.1173754 is OK
- 10.1364/oe.24.030433 is OK
- 10.1063/1.5066099 is OK
- 10.1063/1.4977057 is OK
- 10.1016/j.ymssp.2018.08.033 is OK
- 10.1126/sciadv.1602614 is OK
- 10.1098/rspa.2016.0446 is OK
- 10.1137/16m1086637 is OK
- 10.1137/18m116798x is OK
- 10.1017/jfm.2017.823 is OK
- 10.1063/1.5018409 is OK
- 10.1016/j.ifacol.2016.10.249 is OK
- 10.1103/physreve.96.023302 is OK
- 10.1016/j.jcp.2018.10.045 is OK
- 10.1098/rspa.2018.0335 is OK
- 10.1016/j.jcp.2019.07.049 is OK
- 10.1007/s00162-020-00536-w is OK
- 10.1103/physreve.101.010203 is OK
- 10.1115/1.4043148 is OK
- 10.1137/130932715 is OK
- 10.1073/pnas.0609476104 is OK
- 10.1098/rspa.2020.0279 is OK
- 10.1103/PhysRevFluids.6.094401 is OK
- 10.1103/physreve.104.015206 is OK
- 10.1109/tmbmc.2016.2633265 is OK
- 10.1016/j.jcp.2021.110525 is OK
- 10.1103/physrevlett.120.024102 is OK
- 10.1016/j.cma.2016.03.025 is OK
- 10.1016/j.physd.2020.132401 is OK
- 10.1038/s41467-021-23479-0 is OK
- 10.1017/s0022112010001217 is OK
- 10.1098/rspa.2017.0844 is OK
- 10.1016/j.jcp.2017.07.050 is OK
- 10.1126/science.1165893 is OK

MISSING DOIs

- None

INVALID DOIs

- None

akaptano commented 2 years ago

@sbenthall Okay looks like I fixed it!

henrykironde commented 2 years ago

@sbenthall I recommend that the submission gets accepted. The software is well packaged to the standard and satisfies substantial scholarly effort. However, we should confirm the submission as @tuelwer mentioned

an editor should check this, as I am not sure whether JOSS has any policies regarding submission for updated versions of previously published packages.

@akaptano thank you for submitting this package. The YouTube videos on PySINDy, made everything move smoothly, and I am sure the users find it easy to use the tool.

akaptano commented 2 years ago

Hopefully last thing... added funding acknowledgment for Zach

akaptano commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

akaptano commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

akaptano commented 2 years ago

Fixed two typos, sorry about that.

akaptano commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

sbenthall commented 2 years ago

Ok. I've checked in with the editors-in-chief, and resubmission is allowed if there's substantial scholarly effort and a genuinely new major release, which this is.

@akaptano, can you please:

make a tagged release
make an archive with a DOI on Zenodo or the like
report the version number and DOI here

akaptano commented 2 years ago

@sbenthall The new release is v1.6.2 and the DOI Zenodo archive is

DOI: 10.5281/zenodo.5842612

sbenthall commented 2 years ago

@whedon set 10.5281/zenodo.5842612 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5842612 is the archive.

sbenthall commented 2 years ago

@whedon set v1.6.2 as version

whedon commented 2 years ago

OK. v1.6.2 is the version.

sbenthall commented 2 years ago

Thank you @akaptano for the submission and @tuelwer and @henrykironde for the reviews.

I recommend this article for acceptance.

sbenthall commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago

Attempting dry run of processing paper acceptance...

whedon commented 2 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2910

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2910, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

whedon commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.cpc.2007.03.009 is OK
- 10.5402/2011/164564 is OK
- 10.1214/11-aos878 is OK
- 10.1073/pnas.1517384113 is OK
- 10.1109/access.2018.2886528 is OK
- 10.1109/access.2020.3023625 is OK
- 10.21105/joss.02104 is OK
- 10.1126/science.1165893 is OK
- 10.5281/zenodo.1173754 is OK
- 10.1364/oe.24.030433 is OK
- 10.1063/1.5066099 is OK
- 10.1063/1.4977057 is OK
- 10.1016/j.ymssp.2018.08.033 is OK
- 10.1126/sciadv.1602614 is OK
- 10.1098/rspa.2016.0446 is OK
- 10.1137/16m1086637 is OK
- 10.1137/18m116798x is OK
- 10.1017/jfm.2017.823 is OK
- 10.1063/1.5018409 is OK
- 10.1016/j.ifacol.2016.10.249 is OK
- 10.1103/physreve.96.023302 is OK
- 10.1016/j.jcp.2018.10.045 is OK
- 10.1098/rspa.2018.0335 is OK
- 10.1016/j.jcp.2019.07.049 is OK
- 10.1007/s00162-020-00536-w is OK
- 10.1103/physreve.101.010203 is OK
- 10.1115/1.4043148 is OK
- 10.1137/130932715 is OK
- 10.1073/pnas.0609476104 is OK
- 10.1098/rspa.2020.0279 is OK
- 10.1103/PhysRevFluids.6.094401 is OK
- 10.1103/physreve.104.015206 is OK
- 10.1109/tmbmc.2016.2633265 is OK
- 10.1016/j.jcp.2021.110525 is OK
- 10.1103/physrevlett.120.024102 is OK
- 10.1016/j.cma.2016.03.025 is OK
- 10.1016/j.physd.2020.132401 is OK
- 10.1038/s41467-021-23479-0 is OK
- 10.1017/s0022112010001217 is OK
- 10.1098/rspa.2017.0844 is OK
- 10.1016/j.jcp.2017.07.050 is OK
- 10.1126/science.1165893 is OK

MISSING DOIs

- None

INVALID DOIs

- None

openjournals / joss-reviews