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[PRE REVIEW]: GD-VAEs Package: Geometric Dynamic Variational Autoencoders #5630

Closed editorialbot closed 1 year ago

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@atzberg<!--end-author-handle-- (Paul J. Atzberger) Repository: https://github.com/gd-vae/gd-vae Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@matthewfeickert<!--end-editor-- Reviewers: Pending Managing EiC: George K. Thiruvathukal

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Markdown: [![status](https://joss.theoj.org/papers/4394956a220aa26c956c043ee587d251/status.svg)](https://joss.theoj.org/papers/4394956a220aa26c956c043ee587d251)

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editorialbot commented 1 year ago

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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editorialbot commented 1 year ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (637.6 files/s, 158225.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          22            925            832           2555
TeX                              1            129              0           2269
Markdown                         7            117              0            681
Jupyter Notebook                 3              0            696            460
Bourne Shell                     2              6              7              8
-------------------------------------------------------------------------------
SUM:                            35           1177           1535           5973
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 1 year ago

Wordcount for paper.md is 4749

gkthiruvathukal commented 1 year ago

@editorialbot invite @matthewfeickert as editor

editorialbot commented 1 year ago

Invitation to edit this submission sent!

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1126/science.1127647 is OK
- 10.1016/j.physd.2013.09.002 is OK
- 10.1002/jcc.540040211 is OK
- 10.2172/10176421 is OK
- 10.1038/nature14956 is OK
- 10.1557/mrs.2011.30 is OK
- 10.1016/j.jsb.2006.10.023 is OK
- 10.1098/rsta.2008.0219 is OK
- 10.1038/s43588-021-00034-x is OK
- 10.1007/978-3-319-01905-5_60-2 is OK
- 10.1088/1361-651x/ab7150 is OK
- 10.1007/978-3-540-28650-9_4 is OK
- 10.1016/0079-6816(93)90013-l is OK
- 10.1021/acsomega.8b01393 is OK
- 10.5281/zenodo.7945271 is OK
- 10.1007/978-3-662-04323-3 is OK
- 10.1016/0005-1098(95)00120-8 is OK
- 10.1146/annurev-control-053018-023744 is OK
- 10.1080/00207720802083018 is OK
- 10.1017/9781108380690.012 is OK
- 10.1109/TSP.2015.2432731 is OK
- 10.1146/annurev-fluid-011212-140652 is OK
- 10.1007/978-3-319-22470-1_3 is OK
- 10.1137/1.9781611974829.ch3 is OK
- 10.1017/S0022112010001217 is OK
- 10.1115/1.3662552 is OK
- 10.1109/ICASSP.2019.8683411 is OK
- 10.1109/ASSPCC.2000.882463 is OK
- 10.1063/1.5043720 is OK
- 10.1137/1.9781611974508 is OK
- 10.3934/jcd.2014.1.391 is OK
- 10.1007/s10955-019-02272-w is OK
- 10.1016/j.acha.2018.08.002 is OK
- 10.1109/MCS.2019.2938121 is OK
- 10.1063/5.0002051 is OK
- 10.1073/pnas.1916012117 is OK
- 10.1214/aoms/1177699147 is OK
- 10.1214/aoms/1177729694 is OK
- 10.1002/047174882X is OK
- 10.1016/j.jcp.2020.109340 is OK
- 10.1162/neco.1997.9.8.1735 is OK
- 10.3115/v1/D14-1179 is OK
- 10.1073/pnas.1906995116 is OK
- 10.48550/ARXIV.2107.14362 is OK
- 10.1103/physreve.97.062412 is OK
- 10.24963/ijcai.2020/375 is OK
- 10.1175/1520-0493(1915)43<163:SRROTM>2.0.CO;2 is OK
- 10.1063/1.1841255 is OK
- 10.1063/1.1668896 is OK
- 10.1201/9780429492563 is OK
- 10.1016/C2009-0-61160-0 is OK
- 10.21105/joss.02158 is OK
- 10.1103/PhysRevX.10.031056 is OK
- 10.1073/pnas.1517384113 is OK
- 10.1126/science.1165893 is OK
- 10.48550/ARXIV.2012.03448 is OK
- 10.1080/01621459.2017.1285773 is OK

MISSING DOIs

- 10.2139/ssrn.4455789 may be a valid DOI for title: SDYN-GANs: Adversarial Learning Methods for Multistep Generative Models for General Order Stochastic Dynamics
- 10.1038/s41467-018-07210-0 may be a valid DOI for title: Deep learning for universal linear embeddings of nonlinear dynamics
- 10.1016/j.jcp.2019.06.056 may be a valid DOI for title: Deep learning of dynamics and signal-noise decomposition with time-stepping constraints
- 10.1609/aaai.v31i1.10779 may be a valid DOI for title: Structured Inference Networks for Nonlinear State Space Models
- 10.1007/s11263-007-0056-x may be a valid DOI for title: On the Local Behavior of Spaces of Natural Images
- 10.1007/978-1-4612-2974-2_5 may be a valid DOI for title: The Self-Intersections of a Smooth n-Manifold in 2n-Space
- 10.1561/9781680839135 may be a valid DOI for title: Dynamical Variational Autoencoders: A Comprehensive Review
- 10.1109/humanoids.2016.7803340 may be a valid DOI for title: Dynamic movement primitives in latent space of time-dependent variational autoencoders
- 10.1007/bf00337288 may be a valid DOI for title: Self-organized formation of topologically correct feature maps
- 10.1007/3-540-61510-5_31 may be a valid DOI for title: GTM: A Principled Alternative to the Self-Organizing Map
- 10.1007/s11263-013-0676-2 may be a valid DOI for title: A Klein-Bottle-Based Dictionary for Texture Representation
- 10.1109/ijcnn52387.2021.9533735 may be a valid DOI for title: RL-GEP: symbolic regression via gene expression programming and reinforcement learning

INVALID DOIs

- https://doi.org/10.1016/j.jcp.2019.108973 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/S0764-4442(97)84778-7 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.automatica.2010.10.013 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cma.2020.112990 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cviu.2016.09.002 is INVALID because of 'https://doi.org/' prefix
editorialbot commented 1 year ago

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

gkthiruvathukal commented 1 year ago

@atzberg Please correct the above issues in your paper at the earliest opportunity. I have invited an editor for this submission.

atzberg commented 1 year ago

Thanks, I'll fix this DOI item today.

On Fri, Jul 7, 2023 at 7:43 PM George K. Thiruvathukal < @.***> wrote:

@atzberg https://github.com/atzberg Please correct the above issues in your paper at the earliest opportunity. I have invited an editor for this submission.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5630#issuecomment-1626541350, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACBHSZWCZNCWGJRRNDMB7BDXPDCLRANCNFSM6AAAAAA2CRYH7A . You are receiving this because you were mentioned.Message ID: @.***>

atzberg commented 1 year ago

@editorialbot check references

atzberg commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1126/science.1127647 is OK
- 10.1016/j.physd.2013.09.002 is OK
- 10.1002/jcc.540040211 is OK
- 10.2172/10176421 is OK
- 10.1038/nature14956 is OK
- 10.1557/mrs.2011.30 is OK
- 10.1016/j.jsb.2006.10.023 is OK
- 10.1098/rsta.2008.0219 is OK
- 10.1038/s43588-021-00034-x is OK
- 10.1007/978-3-319-01905-5_60-2 is OK
- 10.1088/1361-651x/ab7150 is OK
- 10.1007/978-3-540-28650-9_4 is OK
- 10.1016/0079-6816(93)90013-l is OK
- 10.1021/acsomega.8b01393 is OK
- 10.5281/zenodo.7945271 is OK
- 10.48550/arXiv.2302.03663 is OK
- 10.1007/978-3-662-04323-3 is OK
- 10.1016/0005-1098(95)00120-8 is OK
- 10.1146/annurev-control-053018-023744 is OK
- 10.1080/00207720802083018 is OK
- 10.1017/9781108380690.012 is OK
- 10.1109/TSP.2015.2432731 is OK
- 10.1038/s41467-018-07210-0 is OK
- 10.1146/annurev-fluid-011212-140652 is OK
- 10.1007/978-3-319-22470-1_3 is OK
- 10.1137/1.9781611974829.ch3 is OK
- 10.1016/j.jcp.2019.06.056 is OK
- 10.1017/S0022112010001217 is OK
- 10.48550/arXiv.1511.07367 is OK
- 10.1016/j.jcp.2019.108973 is OK
- 10.1115/1.3662552 is OK
- 10.1016/S0764-4442(97)84778-7 is OK
- 10.1109/ICASSP.2019.8683411 is OK
- 10.1109/ASSPCC.2000.882463 is OK
- 10.1063/1.5043720 is OK
- 10.1137/1.9781611974508 is OK
- 10.3934/jcd.2014.1.391 is OK
- 10.1007/s10955-019-02272-w is OK
- 10.1016/j.acha.2018.08.002 is OK
- 10.1109/MCS.2019.2938121 is OK
- 10.1016/j.automatica.2010.10.013 is OK
- 10.1063/5.0002051 is OK
- 10.1073/pnas.1916012117 is OK
- 10.1214/aoms/1177699147 is OK
- 10.1609/aaai.v31i1.10779 is OK
- 10.1214/aoms/1177729694 is OK
- 10.1002/047174882X is OK
- 10.1007/s11263-007-0056-x is OK
- 10.2307/1969265 is OK
- 10.1016/j.jcp.2020.109340 is OK
- 10.1162/neco.1997.9.8.1735 is OK
- 10.3115/v1/D14-1179 is OK
- 10.1073/pnas.1906995116 is OK
- 10.1016/j.cma.2020.112990 is OK
- 10.48550/ARXIV.2107.14362 is OK
- 10.1103/physreve.97.062412 is OK
- 10.1561/9781680839135 is OK
- 10.1109/humanoids.2016.7803340 is OK
- 10.1007/bf00337288 is OK
- 10.1007/3-540-61510-5_31 is OK
- 10.24963/ijcai.2020/375 is OK
- 10.1175/1520-0493(1915)43<163:SRROTM>2.0.CO;2 is OK
- 10.1007/s11263-013-0676-2 is OK
- 10.1016/j.cviu.2016.09.002 is OK
- 10.1063/1.1841255 is OK
- 10.1063/1.1668896 is OK
- 10.1201/9780429492563 is OK
- 10.1016/C2009-0-61160-0 is OK
- 10.21105/joss.02158 is OK
- 10.1103/PhysRevX.10.031056 is OK
- 10.1073/pnas.1517384113 is OK
- 10.1126/science.1165893 is OK
- 10.48550/ARXIV.2012.03448 is OK
- 10.1080/01621459.2017.1285773 is OK
- 10.1109/ijcnn52387.2021.9533735 is OK

MISSING DOIs

- 10.1109/ijcnn52387.2021.9533735 may be a valid DOI for title: RL-GEP: symbolic regression via gene expression programming and reinforcement learning

INVALID DOIs

- None
editorialbot commented 1 year ago

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

atzberg commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1126/science.1127647 is OK
- 10.1016/j.physd.2013.09.002 is OK
- 10.1002/jcc.540040211 is OK
- 10.2172/10176421 is OK
- 10.1038/nature14956 is OK
- 10.1557/mrs.2011.30 is OK
- 10.1016/j.jsb.2006.10.023 is OK
- 10.1098/rsta.2008.0219 is OK
- 10.1038/s43588-021-00034-x is OK
- 10.1007/978-3-319-01905-5_60-2 is OK
- 10.1088/1361-651x/ab7150 is OK
- 10.1007/978-3-540-28650-9_4 is OK
- 10.1016/0079-6816(93)90013-l is OK
- 10.1021/acsomega.8b01393 is OK
- 10.5281/zenodo.7945271 is OK
- 10.48550/arXiv.2302.03663 is OK
- 10.1007/978-3-662-04323-3 is OK
- 10.1016/0005-1098(95)00120-8 is OK
- 10.1146/annurev-control-053018-023744 is OK
- 10.1080/00207720802083018 is OK
- 10.1017/9781108380690.012 is OK
- 10.1109/TSP.2015.2432731 is OK
- 10.1038/s41467-018-07210-0 is OK
- 10.1146/annurev-fluid-011212-140652 is OK
- 10.1007/978-3-319-22470-1_3 is OK
- 10.1137/1.9781611974829.ch3 is OK
- 10.1016/j.jcp.2019.06.056 is OK
- 10.1017/S0022112010001217 is OK
- 10.48550/arXiv.1511.07367 is OK
- 10.1016/j.jcp.2019.108973 is OK
- 10.1115/1.3662552 is OK
- 10.1016/S0764-4442(97)84778-7 is OK
- 10.1109/ICASSP.2019.8683411 is OK
- 10.1109/ASSPCC.2000.882463 is OK
- 10.1063/1.5043720 is OK
- 10.1137/1.9781611974508 is OK
- 10.3934/jcd.2014.1.391 is OK
- 10.1007/s10955-019-02272-w is OK
- 10.1016/j.acha.2018.08.002 is OK
- 10.1109/MCS.2019.2938121 is OK
- 10.1016/j.automatica.2010.10.013 is OK
- 10.1063/5.0002051 is OK
- 10.1073/pnas.1916012117 is OK
- 10.1214/aoms/1177699147 is OK
- 10.1609/aaai.v31i1.10779 is OK
- 10.1214/aoms/1177729694 is OK
- 10.1002/047174882X is OK
- 10.1007/s11263-007-0056-x is OK
- 10.2307/1969265 is OK
- 10.1016/j.jcp.2020.109340 is OK
- 10.1162/neco.1997.9.8.1735 is OK
- 10.3115/v1/D14-1179 is OK
- 10.1073/pnas.1906995116 is OK
- 10.1016/j.cma.2020.112990 is OK
- 10.48550/ARXIV.2107.14362 is OK
- 10.1103/physreve.97.062412 is OK
- 10.1561/9781680839135 is OK
- 10.1109/humanoids.2016.7803340 is OK
- 10.1007/bf00337288 is OK
- 10.1007/3-540-61510-5_31 is OK
- 10.24963/ijcai.2020/375 is OK
- 10.1175/1520-0493(1915)43<163:SRROTM>2.0.CO;2 is OK
- 10.1007/s11263-013-0676-2 is OK
- 10.1016/j.cviu.2016.09.002 is OK
- 10.1063/1.1841255 is OK
- 10.1063/1.1668896 is OK
- 10.1201/9780429492563 is OK
- 10.1016/C2009-0-61160-0 is OK
- 10.21105/joss.02158 is OK
- 10.1103/PhysRevX.10.031056 is OK
- 10.1073/pnas.1517384113 is OK
- 10.1126/science.1165893 is OK
- 10.48550/ARXIV.2012.03448 is OK
- 10.1080/01621459.2017.1285773 is OK
- 10.1109/ijcnn52387.2021.9533735 is OK
- 10.1109/ijcnn52387.2021.9533735 is OK

MISSING DOIs

- None

INVALID DOIs

- None
atzberg commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

atzberg commented 1 year ago

Thanks for your help with this manuscript. The doi issue should now be resolved. The paper should be ready for review.

gkthiruvathukal commented 1 year ago

@atzberg Thank you for attending to these issues. I'm still waiting for @matthewfeickert to respond to my invitation. Please stay tuned.

matthewfeickert commented 1 year ago

@gkthiruvathukal I have been on holiday and am currently traveling for work. I can accpet this review, but I will not have time to allocate to finding reviewers for this review until next week at the earliest.

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot assign @matthewfeickert as editor

editorialbot commented 1 year ago

Assigned! @matthewfeickert is now the editor

Kevin-Mattheus-Moerman commented 1 year ago

@matthewfeickert thanks, starting to pick this up next week or when you are back is fine. Thanks!

matthewfeickert commented 1 year ago

Apologies for the delay. I have returned from work travel and can start finding reviewers for the submission this week.

matthewfeickert commented 1 year ago

@gkthiruvathukal @Kevin-Mattheus-Moerman @atzberg I'm going to suggest that this submission be withdrawn and resubmitted when it is ready for review. At the moment it fails multiple checks on the reviewer checklist that would keep it from being accepted, so I don't want to spend reviewer time giving the same critiques that I will give now.

Here are two examples of problems (I stopped doing a spot check after noticing them) as of https://github.com/gd-vae/gd-vae/tree/6fe11fef6d31f15282270c954b42d4a6c6f87073:

@atzberg my recommendation is to reread the Submitting a paper to JOSS docs and to read over the JOSS Review criteria to make sure that you have addresses everything a reviewer will check for before resubmitting. To be very clear, we heartily welcome your resubmission and I think that this could be a great JOSS publication!

atzberg commented 1 year ago

@matthewfeickert https://github.com/matthewfeickert Thanks for these comments and feedback. For ease of use, I had set it up with a wheel (.whl) (for PyPI) for installation with pip, but I can also add a ./src local installation process, which sounds like a good idea. Thanks for the reference to PEP 518. I can do this very soon, if we could keep this same submission going. I can update the git repo accordingly. Also, feel free to email me if any other items come to mind or suggestions for getting the package ready. Thanks!

On Fri, Aug 4, 2023 at 11:29 AM Matthew Feickert @.***> wrote:

@gkthiruvathukal https://github.com/gkthiruvathukal @Kevin-Mattheus-Moerman https://github.com/Kevin-Mattheus-Moerman @atzberg https://github.com/atzberg I'm going to suggest that this submission be withdrawn and resubmitted when it is ready for review. At the moment it fails multiple checks on the reviewer checklist that would keep it from being accepted, so I don't want to spend reviewer time giving the same critiques that I will give now.

Here are two examples of problems (I stopped doing a spot check after noticing them) as of https://github.com/gd-vae/gd-vae/tree/6fe11fef6d31f15282270c954b42d4a6c6f87073 :

  • There are no tests at all. (Examples are no tests.)
  • The source code is not installable locally as there is no PEP 518 https://peps.python.org/pep-0518/ compliant build backend specification file (i.e., setup.py, pyproject.toml).

@atzberg https://github.com/atzberg my recommendation is to reread the Submitting a paper to JOSS docs https://joss.readthedocs.io/en/latest/submitting.html and to read over the JOSS Review criteria https://joss.readthedocs.io/en/latest/review_criteria.html#review-criteria to make sure that you have addresses everything a reviewer will check for before resubmitting. To be very clear, we heartily welcome your resubmission and I think that this could be a great JOSS publication!

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5630#issuecomment-1666021315, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACBHSZQEB3C7ETHNCWTUA6TXTU5QXANCNFSM6AAAAAA2CRYH7A . You are receiving this because you were mentioned.Message ID: @.***>

matthewfeickert commented 1 year ago

For ease of use, I had set it up with a wheel (.whl) (for PyPI) for installation with pip, but I can also add a ./src local installation process, which sounds like a good idea.

@atzberg I'm not really sure what you mean by this. Your project on PyPI has a wheel and a sdist (https://pypi.org/project/gd-vae-pytorch/1.0.4/#files) but rather importantly there is no way to verify, or even indicate, where this v1.0.4 distribution was built from given that your repository has no tags in it at all: https://github.com/gd-vae/gd-vae/tags

The important thing is that there is the ability to actually build the project, which is not there. How did you create the sdist and wheel in the first place?

I can do this very soon, if we could keep this same submission going

No. You are missing a full test suite. This is not a trivial thing to do. You should resubmit when you're ready and take the time to read the review guidelines I shared and make sure that the work you're submitting is in a state that the reviewers can easily approve it.

Kevin-Mattheus-Moerman commented 1 year ago

@atzberg given the above we will now proceed to reject this submission. Note however that @matthewfeickert has given clear guidelines in terms of preparing this work for a re-submission if that is of interest. If so, we would welcome it.

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot reject

editorialbot commented 1 year ago

Paper rejected.