[REVIEW]: OPEM (Open Source PEM Fuel Cell Simulation Tool)

whedon commented 6 years ago

Submitting author: @sepandhaghighi (Sepand Haghighi) Repository: https://github.com/ECSIM/opem Version: v0.8 Editor: @katyhuff Reviewer: @nnadeau Archive: 10.5281/zenodo.1311905

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Review checklist for @nnadeau

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: Does the release version given match the GitHub release (v0.8)?
[x] Authorship: Has the submitting author (@sepandhaghighi) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] 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

[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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
[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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

whedon commented 6 years ago

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @nnadeau it looks like you're currently assigned as the reviewer for this paper :tada:.

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whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

--> Check article proof :page_facing_up: <--

engnadeau commented 6 years ago

Hi @sepandhaghighi and @katyhuff,

After performing an initial review, I have submitted the following issues:

Plagiarism

Unfortunately, https://github.com/ECSIM/opem/issues/47 appears to be a case of plagiarism in the documentation. Considering that the entirety of PEM.md is copied, permission should be granted from the original author. Otherwise the reader should be referred directly to the original source.

Paper

https://github.com/ECSIM/opem/issues/46

General syntax/grammer

The following issues reduce the readability of the documentation, examples, and paper:

Code Quality

The following issues describe desired improvements to the codebase:

sepandhaghighi commented 6 years ago

Hi @nnadeau Thank you for your time The issues have been fixed. ;-)

katyhuff commented 6 years ago

Thank you for this detailed review @nnadeau .

@sepandhaghighi : all of the issues remain open. Please bring them to closure through conversation with @nnadeau and I. I have left comments on most regarding whether I believe the issues have been sufficiently handled or whether I think the issue looks like it has truly been fixed.

Thanks for working quickly on these issues @sepandhaghighi . I am particularly concerned about the one regarding pem.md. The initial response by your team doesn't seem to recognize the gravity of plaigarism. I hope it will be handled well and swiftly.

engnadeau commented 6 years ago

@katyhuff @sepandhaghighi I'm still in the process of reviewing the actual codebase.

See https://github.com/ECSIM/opem/issues/50 for my initial observations regarding testing.

sepandhaghighi commented 6 years ago

@nnadeau @katyhuff

I merged develop and master branches and issues with fixed label closed automatically.

Thanks

engnadeau commented 6 years ago

@katyhuff @sepandhaghighi

My final review and opinion:

While the package has an obvious research application, it does not provide a significant contribution to the available open source software that either enables some new research challenges to be addressed or makes addressing research challenges significantly better (e.g., faster, easier, simpler). (https://joss.theoj.org/about#author_guidelines)

As the majority of function are simple one-liner multiplications, from my perspective, this is more of a minor, 'utility' package that would most likely be re-coded by most researchers using NumPy and SciPy. The most "novel" components are the pretty-print style outputs.

Moreover, the lack of good coding and Python practice makes this difficult for the open-source and research communities to extend and build upon this work. In its current form, this package is best suited for use in a single lab and research group.

@sepandhaghighi, while my overall review may be disappointing, I am very impressed by your team's effort and amazing documentation/README/website. I am also very pleased to see scientific contributions to the Python community. However, from a journal perspective, I cannot give my stamp of approval.

Best of luck with your future research!

sepandhaghighi commented 6 years ago

@katyhuff @nnadeau

Thanks for your time and deep review Your points about code style were very good and detailed and we will solve all of them. But about usage of this package really is not like this, we decided to create this package from some real problems in PEM research and focus on models to collect them in one package. OPEM designed for PEM researchers without programming knowledge, it is simple because we collected and solved equations outside of code. We spent about 10 months to collect and validate these models, now is really easy to re-code but this procedure is not. There is no package like OPEM that support all of these models in this style and I think we provide easier and simpler way in PEM analysis and we are in JOSS scope.

Best Regards Sepand Haghighi

kasraaskari commented 6 years ago

@nnadeau @katyhuff As @sepandhaghighi mentioned, in this project we worked on different models to develop a practical tool for evaluating the performance of PEMFC for PEM researchers without any programming knowledge. Usually, experimentalists in the lab do not have enough time (and money) to test different PEMFC with different conditions. For this, OPEM may be a useful tool for researchers to predict the performance of PEMFC without using so many complex equations. Also, there are many electrochemists and PEMFC researchers who know how to develop a simulator for predicting the performance of a PEMFC. So they can add the equations of their new model to OPEM and enhance the ability of our open source software.

Thanks for your kind consideration Kasra Askari

sepandhaghighi commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

--> Check article proof :page_facing_up: <--

arfon commented 6 years ago

@katyhuff - I think this review is waiting on your input.

katyhuff commented 6 years ago

Hi Folks, I'm sorry for the delay here. It took some time and exploration to determine whether there is really a fit concern for JOSS. @nnadeau , I thank you for your detailed and careful review. I understand your concern about this potentially being a minor utility rather than a tool enabling new research. However, after investigating a bit, I personally evaluate the work more generously. While it may only enable new research in this small subdomain, and perhaps only in this research group, I am convinced that it is more than a minor utility and will indeed, enable new research. I would like to approve this paper.

@sepandhaghighi @kasraaskari At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

sepandhaghighi commented 6 years ago

@katyhuff Thanks for your time.

Reviewed software DOI : 10.5281/zenodo.1311905

katyhuff commented 6 years ago

@whedon set 10.5281/zenodo.1311905 as archive

whedon commented 6 years ago

OK. 10.5281/zenodo.1311905 is the archive.

katyhuff commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

--> Check article proof :page_facing_up: <--

katyhuff commented 6 years ago

Thank you @nnadeau for reviewing this. Thank you @sepandhaghighi and @kasraaskari for the submission!

@arfon we're ready to accept this!

arfon commented 6 years ago

@nnadeau - many thanks for your review here and to @katyhuff for editing this submission ✨

@sepandhaghighi - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00676 :zap: :rocket: :boom:

whedon commented 6 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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sepandhaghighi commented 6 years ago

Thanks @arfon @katyhuff @nnadeau @whedon !

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