[REVIEW]: Segmenteverygrain: A Python module for segmentation of grains in a variety of image types

[editorialbot]

Submitting author: @zsylvester (Zoltan Sylvester)
Repository: https://github.com/zsylvester/segmenteverygrain
Branch with paper.md (empty if default branch):
Version: v0.2.2
Editor: @anastassiavybornova
Reviewers: @pr4deepr, @elliesch, @jessepisel
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/3adb1bac50434eb701915a59d65eba40/status.svg)](https://joss.theoj.org/papers/3adb1bac50434eb701915a59d65eba40)

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

@pr4deepr & @elliesch, 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 @anastassiavybornova 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 @elliesch

[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:

@editorialbot commands

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 1.98  T=0.04 s (521.7 files/s, 193162.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           5            281            785           1377
TeX                              1             32              0            478
Jupyter Notebook                 3              0           3793            259
Text                             3             32              0            206
Markdown                         2             57              0            144
YAML                             4             10             10            106
reStructuredText                 3             60             92             53
-------------------------------------------------------------------------------
SUM:                            21            472           4680           2623
-------------------------------------------------------------------------------

Commit count by author:

   210	Zoltan Sylvester

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 955

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

[editorialbot]

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

✅ OK DOIs

- 10.1046/j.1365-2117.1996.00253.x is OK
- 10.1111/sed.12049 is OK
- 10.1002/esp.4760 is OK
- 10.1002/esp.5545 is OK
- 10.1029/2006JF000549 is OK
- 10.48550/arXiv.2304.02643 is OK
- 10.5194/esurf-10-953-2022 is OK
- 10.1371/journal.pone.0229839 is OK
- 10.1029/2021JF006260 is OK
- 10.1016/j.earscirev.2024.104699 is OK
- 10.1111/j.1365-3091.2008.00977.x is OK
- 10.1016/j.marpetgeo.2020.104518 is OK
- 10.1002/esp.1877 is OK
- 10.1002/esp.5755 is OK
- 10.5194/esurf-6-583-2018 is OK
- 10.1002/esp.4787 is OK
- 10.57035/journals/sdk.2024.e22.1594 is OK
- 10.1038/s41467-024-50147-w is OK
- 10.1029/2023JE008013 is OK
- 10.48550/arXiv.1505.04597 is OK
- 10.48550/arXiv.2408.00714 is OK
- 10.1038/s41592-020-01018-x is OK
- 10.7717/peerj.453 is OK
- 10.25080/TCWV9851 is OK
- 10.2110/sepmcsp.13.06 is OK
- 10.17612/rn6g-fq64 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Evaluation of 3d beach profiles: A new method for ...
- No DOI given, and none found for title: Pillow (PIL Fork) Documentation
- No DOI given, and none found for title: Rasterio: geospatial raster I/O for Python program...
- No DOI given, and none found for title: Shapely: manipulation and analysis of geometric ob...
- No DOI given, and none found for title:  TensorFlow: Large-Scale Machine Learning on Heter...
- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python

❌ MISSING DOIs

- 10.1163/1574-9347_dnp_e612900 may be a valid DOI for title: Keras

❌ INVALID DOIs

- None

[editorialbot]

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

[anastassiavybornova]

@elliesch @pr4deepr hi again & thanks again for accepting to review this paper!

instructions on next steps for you as reviewers (starting by generating the checklist) are already posted by the editorialbot in the comments above. ping me if you need help or clarifications.

you can ping the submitting author @zsylvester if you have questions / comments along the way.

and lastly @zsylvester if applicable and relevant - you're welcome to tag your coauthors here.

i'll be checking in on your review conversation from time to time.

talk soon everyone!

[elliesch]

Review checklist for @elliesch

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/zsylvester/segmenteverygrain?
• 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 (@zsylvester) 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?

[anastassiavybornova]

@editorialbot add @jessepisel as reviewer

[editorialbot]

@jessepisel added to the reviewers list!

[anastassiavybornova]

@jessepisel huge thanks for agreeing to review this one! for getting started, see the comments above - and ping me if anything is unclear