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[REVIEW]: startinpy: A Python library for modelling and processing 2.5D triangulated terrains #7123

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editorialbot opened this issue Aug 20, 2024 · 61 comments
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accepted published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review Rust TeX Track: 6 (ESE) Earth Sciences and Ecology

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editorialbot commented Aug 20, 2024

Submitting author: @hugoledoux (Hugo Ledoux)
Repository: https://github.com/hugoledoux/startinpy
Branch with paper.md (empty if default branch):
Version: 0.12.0
Editor: @mikemahoney218
Reviewers: @weiji14, @kylemann16, @gadomski
Archive: 10.5281/zenodo.14001126

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/eae73ba0c3b646cc562a010e58c5b7a5"><img src="https://joss.theoj.org/papers/eae73ba0c3b646cc562a010e58c5b7a5/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/eae73ba0c3b646cc562a010e58c5b7a5/status.svg)](https://joss.theoj.org/papers/eae73ba0c3b646cc562a010e58c5b7a5)

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

@weiji14 & @kylemann16, 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 @mikemahoney218 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 @weiji14

📝 Checklist for @gadomski

📝 Checklist for @kylemann16

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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

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1703.6 files/s, 151548.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          26            182             93           1145
Rust                             1             62            418            901
Markdown                        13            265              0            774
YAML                             3             22              1            190
TeX                              1             27              0            117
TOML                             3             10              2             41
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            48            572            521           3177
-------------------------------------------------------------------------------

Commit count by author:

   402	Hugo Ledoux
    11	Ewout ter Hoeven
     1	Maarten Pronk

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

✅ OK DOIs

- 10.1007/BFb0014497 is OK
- 10.1038/s41597-024-03091-9 is OK
- 10.1016/S0098-3004(03)00017-7 is OK
- 10.1142/S0218195905001580 is OK
- 10.1145/237218.237337 is OK
- 10.1145/235815.235821 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Generation of a triangular grid with applications ...
- No DOI given, and none found for title: Spatial Height prediction of ICESat-2 data using r...
- No DOI given, and none found for title: Canopy gap fraction estimation from ICESat-2 ATL08...
- No DOI given, and none found for title: A brief description of natural neighbour interpola...
- No DOI given, and none found for title: The non-Sibsonian interpolation: A new method of i...
- No DOI given, and none found for title: Fast polygonal approximation of terrain and height...

❌ MISSING DOIs

- 10.1016/j.isprsjprs.2008.09.007 may be a valid DOI for title: Full-waveform topographic lidar: State-of-the-art

❌ INVALID DOIs

- http://dx.doi.org/10.1142/8685 is INVALID because of 'https://doi.org/' prefix

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Paper file info:

📄 Wordcount for paper.md is 930

✅ The paper includes a Statement of need section

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License info:

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

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

@mikemahoney218
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mikemahoney218 commented Aug 20, 2024

👋🏼 @hugoledoux @weiji14 @kylemann16 @gadomski this is the review thread for the paper. Just about of our communications will happen here from now on 😄

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#7123 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 4 weeks. Please let me know if you require some more time.

Please feel free to ping me (@mikemahoney218) if you have any questions/concerns. Thank you so much for reviewing for JOSS!

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@editorialbot add @gadomski as reviewer

👋 Pete, this is the review thread for startinpy. Hopefully my notes above make sense -- please feel free to reach out if you have any questions or anything comes up during your review. Thank you so much for reviewing for JOSS!

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@gadomski added to the reviewers list!

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gadomski commented Aug 21, 2024

Review checklist for @gadomski

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/hugoledoux/startinpy?
  • 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 (@hugoledoux) 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?

gadomski added a commit to gadomski/startinpy that referenced this issue Aug 21, 2024
These suggestions came out of an initial review of the JOSS paper as a part of
openjournals/joss-reviews#7123. These are merely
suggestions, and by no means are required to be taken up during the review
process. I just thought I'd do a quick-once over while reading through.
@hugoledoux
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hugoledoux commented Aug 22, 2024

btw @gadomski has already started and made 2 PR directly in the branch master of startinpy, which is fine.

My plan is to work directly on master (code+paper) during this review and at the end bump the version (0.12 or 1.0, depending on what you guys suggest also).

@hugoledoux
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hugoledoux commented Aug 22, 2024

@editorialbot generate pdf

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

@mikemahoney218
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Thank you so much for your speedy review, @gadomski !

@weiji14, @kylemann16 -- let me know if you have any questions or concerns with your reviews here 😄

@weiji14
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weiji14 commented Sep 15, 2024

Review checklist for @weiji14

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/hugoledoux/startinpy?
  • 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 (@hugoledoux) 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?
  • pip install startinpy worked for me on Linux (x86_64) with Python 3.12. I see support for Windows/macOS/Linux for Python 3.9-3.12 at https://pypi.org/project/startinpy/0.11.0/#files
  • Self-compiliation using maturin build --release and maturin develop works
  • 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).

Yes, many examples on how to read in and export data are listed under https://startinpy.readthedocs.io/0.11.0/examples.html

  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?

Yes, API docs are listed under https://startinpy.readthedocs.io/0.11.0/api.html, and the methods/attributes for the startinpy.DT class should be complete since docs are using Sphinx autoclass at https://github.com/hugoledoux/startinpy/blob/f1d9efc8e6353fc4d5c4adfc0610d6d197604e4a/docs/api.md?plain=1#L32-L35

  • 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

Yes. 1) Development installation instructions are available at https://startinpy.readthedocs.io/0.11.0/installation.html#development-to-debug-the-code. 2&3) Users looking at the docs at https://startinpy.readthedocs.io/0.11.0/issues.html are pointed to the GitHub issue page for issues/bugs/questions.

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?

@weiji14
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weiji14 commented Sep 15, 2024

Just quickly mentioning that I've done an initial round of reviewing the paper and repository code (#7123 (comment)), and have been pleased so far with the quality of the software and writing! So far, I have only two minor suggestions (reported at hugoledoux/startinpy#25 and hugoledoux/startinpy#26) for @hugoledoux to resolve, that can hopefully be addressed with a couple of small PRs/commits.

I do have two remaining items on my checklist in terms of verifying the Performance benchmarks and a more thorough Reproducibility check that will both take more time, but will try to get those done this or next week.

@mikemahoney218
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Thank you, @weiji14 !

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@editorialbot set 0.12.0 as version

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Done! version is now 0.12.0

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@editorialbot set 10.5281/zenodo.14001126 as archive

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Done! archive is now 10.5281/zenodo.14001126

@hugoledoux
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@mikemahoney218 is there anything I should do to finalise the acceptance?

@mikemahoney218
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Sorry @hugoledoux , I still haven't finished my checklist -- wound up being out most of last week due to a death in the family. Will get to this today.

@mikemahoney218
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@editorialbot recommend-accept

Think I can actually go ahead with this now -- paper looks great!

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Attempting dry run of processing paper acceptance...

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

✅ OK DOIs

- 10.1142/8685 is OK
- 10.1016/j.isprsjprs.2008.09.007 is OK
- 10.1016/0012-365X(72)90093-3 is OK
- 10.1007/BFb0014497 is OK
- 10.1038/s41597-024-03091-9 is OK
- 10.1016/S0098-3004(03)00017-7 is OK
- 10.1142/S0218195905001580 is OK
- 10.1145/237218.237337 is OK
- 10.1145/235815.235821 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Spatial Height prediction of ICESat-2 data using r...
- No DOI given, and none found for title: Canopy gap fraction estimation from ICESat-2 ATL08...
- No DOI given, and none found for title: A brief description of natural neighbour interpola...
- No DOI given, and none found for title: The non-Sibsonian interpolation: A new method of i...
- No DOI given, and none found for title: Fast polygonal approximation of terrain and height...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

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👋 @openjournals/ese-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#6110, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Nov 11, 2024
@mikemahoney218
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🎉 With everything looking good on my end, it's time for me to hand this back to the EiC for last steps. Thanks @hugoledoux for the submission, and thank you so much to @weiji14, @kylemann16, and @gadomski for reviewing!

@kthyng
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kthyng commented Nov 11, 2024

Hi! I'll take over now as Track Associate Editor in Chief to do some final submission editing checks. After these checks are complete, I will publish your submission!

  • Are checklists all checked off?
  • Check that version was updated and make sure the version from JOSS matches github and Zenodo.
  • Check that software archive exists, has been input to JOSS, and title and author list match JOSS paper (or purposefully do not).
  • Check paper.

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kthyng commented Nov 11, 2024

@hugoledoux
Please check the capitalization in your references. You can preserve capitalization by placing {} around characters/words in your .bib file. ("delaunay" is not capitalized, but please check other words too)

@hugoledoux
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done ✅

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kthyng commented Nov 12, 2024

@editorialbot generate pdf

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

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kthyng commented Nov 12, 2024

Excellent @hugoledoux! Looks good to go!

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kthyng commented Nov 12, 2024

@editorialbot accept

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Doing it live! Attempting automated processing of paper acceptance...

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Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Ledoux
  given-names: Hugo
  orcid: "https://orcid.org/0000-0002-1251-8654"
doi: 10.5281/zenodo.14001126
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Ledoux
    given-names: Hugo
    orcid: "https://orcid.org/0000-0002-1251-8654"
  date-published: 2024-11-12
  doi: 10.21105/joss.07123
  issn: 2475-9066
  issue: 103
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7123
  title: "startinpy: A Python library for modelling and processing 2.5D
    triangulated terrains"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07123"
  volume: 9
title: "startinpy: A Python library for modelling and processing 2.5D
  triangulated terrains"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🦋🦋🦋 👉 Bluesky post for this paper 👈 🦋🦋🦋

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🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.07123 joss-papers#6121
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07123
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Nov 12, 2024
@hugoledoux
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thanks everyone, the package is better because of you and the JOSS process

@kthyng
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kthyng commented Nov 12, 2024

Congratulations on your new publication @hugoledoux! Many thanks to editor @mikemahoney218 and to reviewers @weiji14, @kylemann16, and @gadomski for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

@kthyng kthyng closed this as completed Nov 12, 2024
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🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following

code snippets

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.07123/status.svg)](https://doi.org/10.21105/joss.07123)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.07123">
  <img src="https://joss.theoj.org/papers/10.21105/joss.07123/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.07123/status.svg
   :target: https://doi.org/10.21105/joss.07123

This is how it will look in your documentation:

DOI

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