[REVIEW]: GiNaCDE: the high-performance F-expansion and First Integral Methods with C++ library for solving Nonlinear Differential Equations

[whedon]

Submitting author: @mithun218 (Mithun Bairagi)
Repository: https://github.com/mithun218/GiNaCDE
Branch with paper.md (empty if default branch):
Version: v1.5.0
Editor: @meg-simula
Reviewers: @peanutfun, @carstenbauer
Archive: 10.5281/zenodo.6366056

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Markdown: [![status](https://joss.theoj.org/papers/340d71bea413f1f5677108636bf38665/status.svg)](https://joss.theoj.org/papers/340d71bea413f1f5677108636bf38665)

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Review checklist for @peanutfun

✨ 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

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@mithun218) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• 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?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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 @carstenbauer

✨ 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

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@mithun218) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• 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?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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]

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

⚠️ JOSS reduced service mode ⚠️

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[whedon]

Wordcount for paper.md is 962

[whedon]

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

OK DOIs

- 10.1016/S0375-9601(02)01775-9 is OK
- 10.1155/2013/104894 is OK
- 10.1016/j.chaos.2005.10.007 is OK
- 10.1016/S0960-0779(03)00102-4 is OK
- 10.1016/S0375-9601(01)00825-8 is OK
- 10.15388/NA.17.4.14052 is OK
- 10.1016/j.amc.2010.04.026 is OK
- 10.1006/jsco.2001.0494 is OK
- 10.1016/j.jmaa.2010.08.050 is OK
- 10.1016/0010-4655(96)00104-X is OK
- 10.1016/S0010-4655(02)00559-3 is OK
- 10.1016/j.jsc.2003.09.004 is OK
- 10.1016/j.cpc.2004.08.007 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.19 s (227.5 files/s, 68429.5 lines/s)
-----------------------------------------------------------------------------------
Language                         files          blank        comment           code
-----------------------------------------------------------------------------------
C++                                 23           1943            679           7981
TeX                                  2            144             15            925
C/C++ Header                        11            221            106            643
CMake                                3             54             64            219
Markdown                             3             47              0            167
YAML                                 1              1              4             18
Windows Resource File                1              0              0              1
-----------------------------------------------------------------------------------
SUM:                                44           2410            868           9954
-----------------------------------------------------------------------------------


Statistical information for the repository '5677997e600bb1d677520f81' was
gathered on 2021/11/03.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
mithun218                        3         12874           1301          100.00

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
mithun218                 11573           89.9          0.0                6.81

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[meg-simula]

👋🏼 @mithun218 @peanutfun @carstenbauer 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#3885 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.

Please feel free to ping me (@meg-simula ) if you have any questions/concerns.

[peanutfun]

Hi @mithun218 👋 I'll review your software in the next couple of days, and open up issues in the repository as I go along. Some of them might only be suggestions and you won't have to resolve all of them to get your submission accepted (from my side). Once I'm finished, I'll hence report back here and summarize the issues with respect to the review criteria and the checklist above.

Happy coding!

[peanutfun]

@mithun218 Before I can summarize I need a bit of clarification on how to use and interpret the output of GiNaCDE. I very much like the extensive documentation you provide, with an in-depth look at the mathematical methods and clear instructions on how to use GiNaCDE. However, it does not explain how to use the resulting output (files). That's why I have some trouble verifying if the software computes the correct solutions.

Admittedly, I am not too familiar with the methods you use and the problems you try to solve, so I might have a wrong impression or perspective. Considering the example usage you propose in the README.md, how would a typical workflow look like after calculating a solution? In particular: What to do with the resulting output .txt file? Its contents do not seem self-explanatory to me.

GiNaCDE provides the option to output either in the Maple or the Mathematica format. However, the output files also contain plain text and cannot simply be "imported" into either of the programs (Please, correct me if I'm wrong!). How could I use the output of GiNaCDE in them? Would I need to copy-paste the expressions, leaving out the text? How do I get a "computational" representation of the results to continue on with?

I myself own neither of the programs. How can I make use of the results in my case?

[mithun218]

@peanutfun thanks so much for your review and comments.
I am happy to edit the paper to incorporate your comments.

The GiNaCDE software determines exact solutions with calculating steps, and the results are saved in an output .txt file in the Maple or the Mathematica format. In order to use the output exact solutions in Maple or Mathematica software, we have to copy the exact solutions with the conditions of solutions (which are also provided in the output .txt file) from the output .txt file. Then, we can verify the exact solutions using Maple or Mathematica software. To verify the exact solutions at first, we have to substitute the exact solutions with the corresponding conditions of the solutions into the input NLPDE and then simplify it. After simplification, if it is equal to zero, then the solution is correct. Otherwise, the solution is not valid.

Besides the output .txt file, the solutions of the NLPDE and the corresponding conditions are also collected by the variables solutionClt and constraints. We have explained about these variables in the section 11. INPUT AND OUTPUT OF LIBRARY of the documentation file. Using these variables, one can easily locate and copy the solutions with the conditions of the solutions in the Maple or the Mathematica software.

Unfortunately, currently, GiNaCDE is unable to verify the solutions without Maple or the Mathematica software. But this will be a very interesting feature of the GiNaCDE if the GiNaCDE itself is able to verify the solutions. Now I am planning that I shall add this feature in the next release of GiNaCDE but this will take some time.

I will try to resolve all the above issues (mentioned by you) in the next few days.

[peanutfun]

@mithun218 thank you for your quick reply. Indeed, I missed the part on solutionClt and constraints. Let me summarize my review and get back to my question:

You obviously put a lot of effort into implementing the F-expansion and first integral methods in an open-source framework. Your documentation focuses strongly on the intricate mathematics involved in these methods, and admittedly, they are a bit out of my reach (I'm a physicist 🙈 ). Your paper makes a good point why GiNaCDE is needed, especially in the open-source context. And I really like the GUI, it works intuitively and is a great option for users that are less familiar with the command line and C++ programming.

While GiNaCDE probably serves you well in your own workflow, the focus shifts from functionality to usability when it comes to a software publication. The goal is to address a wider audience for the software, and even people who are unfamiliar with the methods (like me) need to quickly understand how the software is installed, how they interact with it, how they use its results in their own workflow, and that everything works as intended. I find that GiNaCDE as a software package lacks this wider perspective to some degree.

Most importantly, it is very difficult for me (as somebody unfamiliar with the mathematics) to verify the results of GiNaCDE. This verification is best done automatically in tests, but as I pointed out in mithun218/GiNaCDE#3, the currently implemented tests do not verify the results. In your reply you point out that Maple or Mathematica are required for this. But you also state that

To verify the exact solutions at first, we have to substitute the exact solutions with the corresponding conditions of the solutions into the input NLPDE and then simplify it. After simplification, if it is equal to zero, then the solution is correct. Otherwise, the solution is not valid.

Isn't this procedure also possible within GiNaCDE? Could this be used to test your results in a general way? If not, you could have the tests compute solutions for relatively simple ODEs or PDEs, and then evaluate the resulting expressions for some known function values like roots, maxima, etc. I focus on this because (automated) tests for verifying the software are part of the JOSS review criteria, and I cannot check this off until there is at least a manual procedure documented on how to verify the results of the library.

Also with regard to usability, I think the installation instructions need to be improved to account for different operating systems, and the usage instructions should show how other CMake projects can incorporate GiNaCDE. This leads me to the following list of issues we need to resolve to match the JOSS review criteria from my perspective:

Issues for meeting review criteria

• Improve the automated tests to verify computation results (or add manual instructions on how to do so): Make tests actually check the computation results mithun218/GiNaCDE#3
• Simplify installation instructions for Linux, and possibly add instructions for macOS and Windows: Add OS-dependent installation instructions mithun218/GiNaCDE#5
• Add instructions on how to use GiNaCDE in downstream modules: Support and advertise usage in downstream build systems mithun218/GiNaCDE#8
• Incorporate or conclusively reject suggestions to the JOSS paper: Improve the JOSS paper mithun218/GiNaCDE#12

Personally, I consider all other issues I opened in the GiNaCDE repository non-crucial for accepting your submission.

[mithun218]

@meg-simula Please check the following information:

1. The version tag of the archived version is v1.5.0
2. The DOI of the Zenodo archived version is 10.5281/zenodo.6366056

Please let me know if I have missed something.

[mithun218]

@meg-simula I have addressed all the points you mentioned here. Please review and if I have missed anything please let me know.

[meg-simula]

@editorialbot set 10.5281/zenodo.6366056 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.6366056

[meg-simula]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1016/S0375-9601(02)01775-9 is OK
- 10.1155/2013/104894 is OK
- 10.1016/j.chaos.2005.10.007 is OK
- 10.1016/S0960-0779(03)00102-4 is OK
- 10.1016/S0375-9601(01)00825-8 is OK
- 10.15388/NA.17.4.14052 is OK
- 10.1016/j.amc.2010.04.026 is OK
- 10.1006/jsco.2001.0494 is OK
- 10.1016/j.jmaa.2010.08.050 is OK
- 10.1016/0010-4655(96)00104-X is OK
- 10.1016/S0010-4655(02)00559-3 is OK
- 10.1016/j.jsc.2003.09.004 is OK
- 10.1016/j.cpc.2004.08.007 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉 openjournals/joss-papers#3145

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3145, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@mithun218 – I've made some fixes to the citation formatting in the PR: mithun218/GiNaCDE#40

[mithun218]

@mithun218 – I've made some fixes to the citation formatting in the PR: mithun218/GiNaCDE#40

Thanks @arfon, the pull request has been merged.

[mithun218]

@arfon We have made a tagged release of the software, and the version tag of the archived version is v1.5.0. But I have seen a problem that here the version is still showing v1.0.0.

[arfon]

@editorialbot set v1.5.0 as version

[editorialbot]

Done! version is now v1.5.0

[arfon]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1016/S0375-9601(02)01775-9 is OK
- 10.1155/2013/104894 is OK
- 10.1016/j.chaos.2005.10.007 is OK
- 10.1016/S0960-0779(03)00102-4 is OK
- 10.1016/S0375-9601(01)00825-8 is OK
- 10.15388/NA.17.4.14052 is OK
- 10.1016/j.amc.2010.04.026 is OK
- 10.1006/jsco.2001.0494 is OK
- 10.1016/j.jmaa.2010.08.050 is OK
- 10.1016/0010-4655(96)00104-X is OK
- 10.1016/S0010-4655(02)00559-3 is OK
- 10.1016/j.jsc.2003.09.004 is OK
- 10.1016/j.cpc.2004.08.007 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉 openjournals/joss-papers#3159

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3159, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03885 joss-papers#3160
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03885
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@peanutfun, @carstenbauer – many thanks for your reviews here and to @meg-simula for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@mithun218 – your paper is now accepted and published in JOSS ⚡🚀💥

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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HTML:
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reStructuredText:
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[peanutfun]

@mithun218 congratulations! 🎉

[mithun218]

Huge thank you to @peanutfun and @carstenbauer  for your reviews, and @meg-simula  and @arfon for your editorial work. Much appreciated! 🎉