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[REVIEW]: SMBLtoODEpy: A software program for converting SBML models into ODE models in Python #1643
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Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @SirSharpest, @marouenbg it looks like you're currently assigned to review this paper 🎉. ⭐ Important ⭐ If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿 To fix this do the following two things:
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@ashleefv I have made my comments as a new issue on the relevant github page: AnabelSMRuggiero/sbmltoodepy#1 Most are minor, and possibly non-issues. Though, I feel that the clarifications I mentioned for the manuscript would be important to readers. As would being explicit in which python versions are supported. Finally, I feel strongly about unit-testing being done to software engineering standards, but I understand that this has at least been addressed using their own method. @mgymrek if there is anything else, prior to author response, please let me know and I'll promptly proceed with. |
Thanks @SirSharpest and @marouenbg. These comments look reasonable. |
Responses to Reviewer 1's comments (Issue 1):General CommentsWe now specify that the supported versions of python are 3.5, 3.6, and 3.7. Added comment to README.md about installing from source. TestingPyTest could be a good fit for our project, but we expect to include if we have a major update in the future. Software checked on:We now specify that the supported versions of python are 3.5, 3.6, and 3.7. Software styleRemoved all of the "import *" statements. While the updated code on this github repo has been updated, we plan on updating the package on PyPI once all reviewer comments have been addressed. Running the provided Tutorial.mdWe addressed the comments by
Community guidelinesWe do not see the scope of the project for others' to make pull requests or suggest features. Paper ClarificationsIn our paper, we compare our work to two other pieces of software. COPASI- The comparison was intended simply to validate the results of the models generated by SBMLtoODEpy. COPASI uses ODEPACK for its Time Course calculations, which is the same library that scipy's odeint function uses. If the calculations agree, then that suggests SBMLtoODEpy has generated the correct equations. Furthermore, the targeted niche for SBMLtoODEpy is not the same as COPASI. Systems Biology Format Converter (SBFC)- SBFC is a better software to compare SBMLtoODEpy to. SBFC converts SBML models into various programming and modeling languages, but notably excludes Python. This gap SBFC's functionality is specifically the target niche of SBMLtoODEpy. Additionally, SBMLtoODEpy is designed to generate code that can be incorporated into other python projects. The Octave/MATLAB scripts generated by SBFC implement the model that neither accept arguments nor return any values. SBMLtoODEpy generates code that implements the model as a class with most methods and members intended to be accessible to other code. The paper has been updated to better convey the scope and intent of the comparisons. |
Responses to Reviewer 2's commentsComment 1 (Issue 2)Since we expect users to take and modify or use the code generated by SBMLtoODEpy in ways we can't predict, the burden of applying SED-ML or KiSAO will have to be on the user. Additionally most SBML components are stored as entries in dictionaries that are members of the class implementing the model. Currently rules and initial assignments are not implemented this way and annotations stored in the SBML model are not retained. We plan to address these in a future update. We updated the paper to expand on the comparison to COPASI. My comment to reviewer #1 addresses the comparison to COPASI and Systems Biology Format Converter in more depth. Comment 2 (Issue 3)We looked into the suggestion and are currently not interested in using Travis-CI. Travis-CI does not play well with PyPI accounts with non-alphanumeric characters in its password. Additionally, any updates to SBMLtoODEpy will change the code generated by it and may require different interfacing with user code. Because of this, we want only want a new version of our code pushed when we are absolutely certain its ready for public use. Building and pushing a new version of our code to PyPI is already a simple process with setuptools and twine. We did set up a code ocean capsule and tested our code on Ubuntu 16.04 and 18.04. We're not planning on publishing the capsule as we do not believe it to be a good fit to publish this project on code ocean. However, we are glad the reviewer provided this suggestion because it may be a good fit for some of our other projects that involve simulation experiments. Comment 3 (Issue 4)We have added in both the readme and tutorial to our documentation page. While we see the value in a troubleshooting section of the documentation, we think we need user feedback before creating it. We plan on adding a changelog section to the documentation as part of finishing addressing reviewer feedback, if future edits are made. |
@whedon generate pdf |
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@whedon generate pdf |
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Approved the new article proof. We have concluded our responses to the reviewers' comments. |
Thanks @ashleefv for addressing these comments. Also, I noticed you mentioned you mentioned for community guidelines that you do not envision contributions from others to the project. However this is an important aspect of open source projects. Even if you do not envision new features, it's possible a user could find a bug and want to contribute a fix for example. To address this point you could simply add a blurb to the readme suggesting users to contact you or submit a pull request if they would like to contribute a change. |
I just checked all the boxes on my side. The authors did address the comments either through new commits and/or provided reasonable explanations for sticking to their initial choices. Great job! |
Perfect, thanks @marouenbg and @SirSharpest for the reviews! |
@whedon generate pdf |
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@whedon check references |
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@mgymrek We have updated the Hindmarsh url, fixed the noted typo, finalized the revised pypi release, and created a new zenodo doi for this updated release: https://zenodo.org/record/3441677#.XYLMoyhKjZs |
@whedon set v1.0.3 as version |
OK. v1.0.3 is the version. |
@whedon set 10.5281/zenodo.3441677 as archive |
OK. 10.5281/zenodo.3441677 is the archive. |
@openjournals/joss-eics We are ready to accept this submission! |
@whedon accept |
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Check final proof 👉 openjournals/joss-papers#974 If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#974, then you can now move forward with accepting the submission by compiling again with the flag
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@whedon accept deposit=true |
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🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦 |
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Woohoo!! Congrats @ashleefv on your publication and thank you to reviewers @SirSharpest and @marouenbg!! |
🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉 If you would like to include a link to your paper from your README use the following code snippets:
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I recently got the feedback that our acronym in the first word of the title reversed the B & M. It should be SBMLtoODEpy. Additionally this accidental reversal of the letters appeared one other time int he document. Can this be corrected? |
@mgymrek We aren't sure if our title issue and internal typo can be updated. We accidentally switched the letters B&M in the title of our paper and in one other place (I'm fine if that internal typo is not corrected, but the title would be best to fix.). I never caught the error because it blended together for me visually. Someone just commented on our github repository pointing out the issue. |
@ashleefv - please make the necessary changes to your |
@arfon I have updated paper.md in the repository: https://github.com/SMRuggiero/sbmltoodepy |
@ashleefv - this was fixed in openjournals/joss-papers@5f08ae3 although the paper might take a few hours to show as updated on the JOSS website as there's caching in place. |
Submitting author: @ashleefv (Ashlee N. Ford Versypt)
Repository: https://github.com/SMRuggiero/sbmltoodepy
Version: v1.0.3
Editor: @mgymrek
Reviewer: @SirSharpest, @marouenbg
Archive: 10.5281/zenodo.3441677
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Review checklist for @SirSharpest
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paper.md
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Conflict of interest
Code of Conduct
General checks
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Documentation
Software paper
paper.md
file include a list of authors with their affiliations?The text was updated successfully, but these errors were encountered: