[REVIEW]: 'KinOpt: A Python package for chemical kinetics analysis and optimization'

[editorialbot]

Submitting author: @alan-tabore (Alan Taboré)
Repository: https://github.com/alan-tabore/KinOpt
Branch with paper.md (empty if default branch): joss_branch
Version: v1.0
Editor: @rkurchin
Reviewers: @mbkumar, @jranalli
Archive: Pending

Status

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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) 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

@mbkumar & @jranalli, 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 @rkurchin 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 @jranalli

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[editorialbot]

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

✅ OK DOIs

- 10.1007/s00289-022-04462-1 is OK
- 10.1002/macp.200700100 is OK
- 10.1002/(SICI)1096-987X(199702)18:3<393::AID-JCC9>3.0.CO;2-P is OK
- 10.1002/pen.20046 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/0040-6031(76)80056-1 is OK
- 10.1002/cjce.23060 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- 10.1016/j.polymer.2010.09.073 may be a valid DOI for title: Modeling diffusion-control in the cure kinetics of...

❌ INVALID DOIs

- 10.1002/1096-987X(20010130)22:2<178::AID-JCC5>3.0.CO;2- is INVALID

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.67 s (168.2 files/s, 206802.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          11           1154           1711          60541
Text                            10             45              0          40154
HTML                            38           7632            112          22095
CSS                             13            368             80           1723
Qt                               1              0              0           1273
JavaScript                      11            127            195            812
reStructuredText                18            122             95            194
TeX                              1             11              0            151
Markdown                         2             53              0            105
SVG                              3              0              0             85
YAML                             2              7              7             32
DOS Batch                        1              8              1             26
TOML                             1              1              0             21
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           113           9532           2208         127221
-------------------------------------------------------------------------------

Commit count by author:

    36	Alan Taboré

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 657

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

[editorialbot]

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

[jranalli]

Review checklist for @jranalli

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/alan-tabore/KinOpt?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@alan-tabore) 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?

[jranalli]

I ran into a few issues, so here's the concerns I have.

Must Fix - areas that failed to meet JOSS criteria:

• Some issues with installation instructions, detailed in Issue Link
• Community Guidelines: No community guidelines or contribution instructions. This doesn't need to be extensive, just seek examples from small projects Issue Link.
• Functionality/Automated Tests: three of the included tests failed detailed in Issue Link.
• Automated tests: the project doesn't use CI and lacks explicit instructions for running the tests. Issue Link.

My opinions that aren't necessary to fix to meet JOSS criteria but may be viewed as constructive suggestions

• Include some default options. Issue Link
• Paper: The paper is well written. I think there could be some improvement with respect to its accessibility for a "non-sepcialist audience."
• Example usage: the API docs based on the dosctrings are good, and the video tutorials for the GUI are good, but it would be nice to include an example of how to perform the analysis from code/script.
• Consider improving the code coverage to include some of the other modules.