[REVIEW]: pymgpipe: microbiome metabolic modeling in Python

[editorialbot]

Submitting author: @ym2877 (Yoli Meydan)
Repository: https://github.com/korem-lab/pymgpipe
Branch with paper.md (empty if default branch): joss-paper
Version: v0.16.10
Editor: @fboehm
Reviewers: @cumbof, @ammaraziz
Archive: 10.5281/zenodo.8169484

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/3f284f37987438428fd09ad3d5bd4871/status.svg)](https://joss.theoj.org/papers/3f284f37987438428fd09ad3d5bd4871)

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) by leaving comments 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.)

Reviewer instructions & questions

@cumbof & @ammaraziz, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @fboehm know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @cumbof

📝 Checklist for @ammaraziz

[editorialbot]

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

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

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.15 s (235.1 files/s, 330326.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              1              0              0          22191
JSON                             1              0              0          19849
MUMPS                            1              0              0           4599
Python                          21            435            120           2264
TeX                              1             23              0            233
YAML                             4             10             10            146
Jupyter Notebook                 2              0            339            120
Markdown                         2             33              0            102
reStructuredText                 3             26             47             31
-------------------------------------------------------------------------------
SUM:                            36            527            516          49535
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 925

[editorialbot]

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

OK DOIs

- 10.1007/s13105-015-0390-3 is OK
- 10.1038/s41586-020-2896-2 is OK
- 10.1038/s41467-019-10927-1 is OK
- 10.1101/318485 is OK
- 10.1101/361907 is OK
- 10.1093/bioinformatics/btac003 is OK
- 10.1038/nbt.1614 is OK
- 10.1038/nprot.2009.203 is OK
- 10.1038/s41587-022-01628-0 is OK
- 10.1093/nar/gkz1054 is OK
- 10.1093/nar/gky537 is OK
- 10.1101/2021.06.14.448190 is OK
- 10.1186/s40168-019-0689-3 is OK
- 10.1080/19490976.2021.1915673 is OK
- 10.2139/ssrn.3305554 is OK
- 10.1186/s12915-020-00775-7 is OK
- 10.1186/1752-0509-7-74 is OK
- 10.21105/joss.00139 is OK
- 10.1186/s12859-020-03711-2 is OK
- 10.1016/j.ymben.2003.09.002 is OK
- 10.4161/gmic.22370 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[cumbof]

Review checklist for @cumbof

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 https://github.com/korem-lab/pymgpipe?
• 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 (@ym2877) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[fboehm]

@cumbof @ammaraziz - how are the reviews going? @ammaraziz - please feel free to create your checklist using the syntax specified above. Please let me know if you have any questions. Thanks!

[fboehm]

@cumbof & @ammaraziz - please create your checklists, if you haven't had a chance to do so yet. Please feel free to keep it up to date as you work through the review criteria. If you have any questions about the software or the review process, please feel free to discuss them here, in this thread.