[REVIEW]: PyForestScan: A Python Library for Calculating Forest Structural Metrics from LiDAR Point Cloud Data

editorialbot commented 2 weeks ago

Submitting author: !--author-handle-->@iosefa@mengqi-z<!--end-editor-- Reviewers: @npucino, @giswqs Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/61114708d8831867a7c7d7e1ef25947d"><img src="https://joss.theoj.org/papers/61114708d8831867a7c7d7e1ef25947d/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/61114708d8831867a7c7d7e1ef25947d/status.svg)](https://joss.theoj.org/papers/61114708d8831867a7c7d7e1ef25947d)

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

@npucino & @giswqs, 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 @mengqi-z 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 @giswqs

📝 Checklist for @npucino

editorialbot commented 2 weeks ago

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 commented 2 weeks ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1150.0 files/s, 112061.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          11            406            507           1246
TeX                              1             21              0            234
Markdown                         4             85              0            170
reStructuredText                 6            113             91            108
YAML                             4             18              0             92
XML                              6              0              0             55
DOS Batch                        1              8              1             26
Jupyter Notebook                 1              0            276             25
make                             1              4              7              9
INI                              1              0              0              6
-------------------------------------------------------------------------------
SUM:                            36            655            882           1971
-------------------------------------------------------------------------------

Commit count by author:

    34  iosefa
    22  Iosefa Percival
     4  benleamon

editorialbot commented 2 weeks ago

Paper file info:

📄 Wordcount for paper.md is 899

✅ The paper includes a Statement of need section

editorialbot commented 2 weeks ago

License info:

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

editorialbot commented 2 weeks ago

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

✅ OK DOIs

- 10.1016/j.foreco.2018.11.017 is OK
- 10.1016/j.foreco.2005.08.034 is OK
- 10.1016/S0034-4257(01)00281-4 is OK
- 10.1016/j.rse.2020.112061 is OK
- 10.2307/1934145 is OK
- 10.3390/rs12030413 is OK
- 10.1080/22797254.2024.2315413 is OK
- 10.1016/j.jenvman.2023.118709 is OK
- 10.1016/j.foreco.2021.119343 is OK
- 10.5281/ZENODO.13151991 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Airborne LiDAR Data Manipulation and Visualization...
- No DOI given, and none found for title: Efficient LiDAR processing software
- No DOI given, and none found for title: Global Mapper: GIS and Mapping Software
- No DOI given, and none found for title: FUSION/LDV: LiDAR Processing and Visualization Sof...

❌ MISSING DOIs

- 10.32614/cran.package.leafr may be a valid DOI for title: leafR: Calculates the Leaf Area Index (LAD) and Ot...

❌ INVALID DOIs

- None

editorialbot commented 2 weeks ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mengqi-z commented 2 weeks ago

👋 @iosefa, @npucino, and @giswqs, Welcome to the review thread for the paper. All communication regarding this submission will take place here.

Please start by reading the "Reviewer instructions & questions" in the first comment above.

Reviewers, please create your checklists outlining JOSS requirements. As you assess the submission, mark any items you believe have been satisfied. Additionally, refer to the JOSS reviewer guidelines linked at the top of this thread.

Our aim is to collaborate with authors to help them meet our criteria. Reviewers are encouraged to submit issues and pull requests directly on the software repository. When doing so, please tag https://github.com/openjournals/joss-reviews/issues/7314 in the issue to create a link to this thread, enabling easy tracking. Please feel free to post comments, questions, and suggestions as they arise, rather than waiting until the entire package is reviewed.

We target completing reviews within 4-6 weeks, but please initiate your review well in advance. JOSS reviews are iterative, and your early feedback will help us stay on schedule.

giswqs commented 2 weeks ago

Review checklist for @giswqs

Conflict of interest

[x] 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

[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 https://github.com/iosefa/PyForestScan?
[x] 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 (@iosefa) 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?

npucino commented 5 days ago

Review checklist for @npucino

Conflict of interest

[x] 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

[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 https://github.com/iosefa/PyForestScan?
[x] 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 (@iosefa) 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?

openjournals / joss-reviews