Joss-reviews: [REVIEW]: MicroBenthos: a modeling framework for microbial benthic ecology

[whedon]

Submitting author: @achennu (Arjun Chennu)
Repository: https://github.com/achennu/microbenthos
Version: v0.9
Editor: @lheagy
Reviewer: @leouieda
Archive: 10.5281/zenodo.1240940

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

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@leouieda, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @lheagy know.

Review checklist for @leouieda

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 (v0.8.2)?
• [x] Authorship: Has the submitting author (@achennu) 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?
• [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 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]

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

:star: Important :star:

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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For a list of things I can do to help you, just type:

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[lheagy]

👋 Hi @leouieda, here is the review issue. I will jump in on this one and add comments as well, but I will leave the check-list up to you. Please let me know if you have any questions!

[leouieda]

@lheagy OK, will do :+1:

[achennu]

Thanks @leouieda

I have been rerunning the software on some previous model definition files. Found some bugs in the user's CLI interface due to a refactor. I've starting adding commits to the develop branch with these minor fixes.

@lheagy Can you clarify about this checkbox?
Version: Does the release version given match the GitHub release (v0.8.2)?

That version is no longer actual (0.9). I intend that the final version after the review should somehow be referenced?

[achennu]

Just realized the version number may be a non-issue, since a designated version needs to be put on an archival site after review.

[lheagy]

@achennu, I can update the version referenced in the github issue. And correct, it will also be included on the archival site

[achennu]

@lheagy @leouieda
Thanks for your inputs on the repo. I've made the changes you've indicated thus far. Travis builds are passing. Once you indicate that the JOSS review is through, I'll bump version, release and create an archive on zenodo.

[lheagy]

Thanks @achennu! @leouieda: just checking in, when do you think you will have time to take a look at this review?

[leouieda]

@achennu @lheagy I'll get to this week. Sorry for the delay @achennu.

[achennu]

@leouieda Thanks for the update. Do let me know if you need any info.

[leouieda]

@achennu @lheagy I just went through the tutorials and documentation and everything works great. Really nice work @achennu! I particularly liked the microbial groups tutorial. I checked all of the boxes above and added a couple of issues to the repository with minor comments.

A question that I have is regarding the simulation output in the HDF5 file. Is the file format a standard in your field or this a custom microbenthos format? I'm wondering if people who don't program in Python would be able to analyze the data somewhere else (R, Matlab, etc). I see that there is a export model command but there isn't much information in the docs about that. I don't know if this is a desirable feature or most users will just be happy with the output video and plots (these are great, by the way).

[lheagy]

Thanks @leouieda! In your opinion, should these issues be addressed before the paper is published?

[leouieda]

@lheagy maybe just achennu/microbenthos#6 but that's just a single word

[achennu]

Thanks @leouieda ! I'm glad you enjoyed it.

The export model command is used to validate an input file by the user. That command writes out the validated YAML string to stdout, which can of course be piped to a file for further use.

HDF5 is a widely used standard format for storing scientific data. It contains many useful features: it is self-documenting, supports structured metadata, can be resized, etc. The specifications for it are codified by the HDF group. I use the vanilla h5py library to read and write to this format, but there are other libraries that build on it like pytables. There are of course readers in matlab, R, C++, etc. In fact, there is the java based GUI called hdfview to inspect it, though I'm partial to vitables written in python. With these, one can double click the file, inspects the hierarchy, the nodes, the metadata attached, etc. For microbenthos, the HDF5 format serves as a good archival output target. It is not tied down to the microbenthos software, or even python for that matter. The produced data can be consumed in whatever way serves the user's needs best: export to video, export to frames, open as interactive visualization, or read and analyze in their tool of choice.

I hope this satisfies all your concerns. Thanks for taking the time and giving useful feedback.

[leouieda]

@achennu OK, thanks for the clarification!

@lheagy I don't have any more comments. I think this is good to go :rocket:

[lheagy]

Thanks @leouieda for your review!

@achennu, could you please archive your software (eg. on zenodo or similar) and post the doi here?

[achennu]

Thank you @leouieda !

@lheagy I have created an archive on zenodo: http://doi.org/10.5281/zenodo.1240940

[arfon]

@whedon set 10.5281/zenodo.1240940 as archive

[whedon]

OK. 10.5281/zenodo.1240940 is the archive.

[arfon]

@leouieda - many thanks for your review here and to @lheagy for editing this submission ✨

@achennu - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00674 :zap: :rocket: :boom:

[whedon]

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

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