[REVIEW]: PyGMI - a python package for geoscience modelling and interpretation

[editorialbot]

Submitting author: @Patrick-Cole (Patrick Cole)
Repository: https://github.com/Patrick-Cole/pygmi
Branch with paper.md (empty if default branch):
Version: v3.2.8.0
Editor: @boisgera
Reviewers: @AnkitBarik, @jmtemmos
Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b5e69e8e0d634e313e7b0037cadc950f"><img src="https://joss.theoj.org/papers/b5e69e8e0d634e313e7b0037cadc950f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b5e69e8e0d634e313e7b0037cadc950f/status.svg)](https://joss.theoj.org/papers/b5e69e8e0d634e313e7b0037cadc950f)

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

@AnkitBarik & @AlexanderJuestel, 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 @boisgera 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 @AnkitBarik

📝 Checklist for @jmtemmos

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.33 s (455.6 files/s, 200786.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          96          13105          16139          34787
reStructuredText                 2            111              0           1049
HTML                            45              3              0            921
TeX                              1             17              0            208
TOML                             1              6              0             71
Markdown                         1              9              0             34
CSV                              1              0              0             27
DOS Batch                        1              1              0             22
YAML                             1              1              4             18
XML                              2              0              0             16
-------------------------------------------------------------------------------
SUM:                           151          13253          16143          37153
-------------------------------------------------------------------------------

Commit count by author:

   968	Patrick
    86	[email protected]
     6	Janine-Cole
     2	Patrick Cole
     1	Marinda

[editorialbot]

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

OK DOIs

- 10.1190/1.1439386 is OK
- 10.1016/j.cageo.2005.03.002 is OK
- 10.1016/j.cageo.2006.02.016 is OK
- 10.1186/s40623-015-0228-9 is OK
- 10.1109/36.3001 is OK
- 10.1190/1.1444531 is OK
- 10.1785/0220190313 is OK
- 10.2113/econgeo.107.2.209 is OK
- 10.1190/1.1988183 is OK
- 10.1190/1.1543203 is OK
- 10.1109/PROC.1981.11918 is OK
- 10.1071/EG08028 is OK
- 10.1190/1.1444942 is OK

MISSING DOIs

- No DOI given, and none found for title: Multiresolution Segmentation: An Optimization Appr...
- No DOI given, and none found for title: Potential Theory in Gravity and Magnetic Applicati...
- No DOI given, and none found for title: GDAL/OGR Geospatial Data Abstraction software Libr...
- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
- No DOI given, and none found for title: Joint modelling of gravity and magnetic fields - a...

INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 925

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[editorialbot]

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

[AlexanderJuestel]

Review checklist for @AlexanderJuestel

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/Patrick-Cole/pygmi?
• 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 (@Patrick-Cole) 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?

[AnkitBarik]

Review checklist for @AnkitBarik

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/Patrick-Cole/pygmi?
• 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 (@Patrick-Cole) 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?

[Patrick-Cole]

I have started making corrections and am responding directly to the comments on my repository above. I hope this is okay.

[boisgera]

Hello everyone,

Let me try to recap the state of the review and see how to proceed.

• wrt Installation issues: @AlexanderJuestel initially experienced some problems (the standard pip install pygmi on Windows was not enough) and after a discussion, @Patrick-Cole made some changes that should make it work. Can you confirm that @AlexanderJuestel? @AnkitBarik if by any chance you are a Windows user, could you give some feedback on this?

• I have made a quick check of the state of the Comments on the GitHub repo issue. Do we agree on this @AlexanderJuestel?

• wrt the paper issue. The latest changes have been made on Sept. 2 and I then mentioned that you still have a bit of wiggle room to make some changes. I have not check the latest version of the paper. @Patrick-Cole, did you manage to adress the comments made by @AlexanderJuestel? Otherwise could you say what's still in the works and if some extra discussions are needed on some points?

@AnkitBarik feel free to chime in of course, about those issues or any other feedback that you may have!

More generally, for everyone, do not hesitate to contact me if you need my help to push this review forward.

Best regards,

Sébastien

[Patrick-Cole]

I think I made most of the changes. I have the following comments:

Statement of Need: If you present so much of the capability of PyGMI, I would recommend using one or two more figures outlining the functionality. Maybe create different sections that outline the functionality.

I avoided adding sections given paper size limitations, and how much functionality PyGMI has. If you still prefer more sections, I can put them in and then get advice on paper length issues which result.

I see I missed adding a resources section, I will add that.

It is possible that I have not given enough detail on other corrections, and will fix that once I get some feedback.

Once again, I appreciate the feedback. I have definitely learned a lot from it.

[Patrick-Cole]

I have completed all changes to the paper, and posted a new version, thanks.

[AlexanderJuestel]

@boisgera, unfortunately, I cannot finish the review due to work conflicts. I hope you can quickly find a new reviewer for this manuscript. I hope that the comments I have already submitted were already a little helpful.

Sorry for the inconvenience
Alex

[boisgera]

Hi @AlexanderJuestel, sorry to hear that! Thank you for your investement in the review so far, the issues that you have opened have been really useful in my opinion.

[boisgera]

@editorialbot remove @AlexanderJuestel from reviewers

[editorialbot]

@AlexanderJuestel removed from the reviewers list!

[AnkitBarik]

Hi, I'm really sorry for taking this long. I'll try to finish part of my review by tomorrow.

[boisgera]

Hi @Patrick-Cole, @AnkitBarik,

For your information, I am in contact with potential replacements for Alexander (since the JOSS process mandates two reviewers or more). I'll keep you informed!

Best regards,

Sébastien

[Patrick-Cole]

No problem, and thanks for the update.

[boisgera]

@editorialbot add @jmtemmos as reviewer

Jean-Marc Temmos (of SEMANTIC TS) has kindly accepted to review the project.

Thanks! 🙏

[editorialbot]

@jmtemmos added to the reviewers list!

[boisgera]

@editorialbot generate pdf

[editorialbot]

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

[jmtemmos]

Review checklist for @jmtemmos

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/Patrick-Cole/pygmi?
• 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 (@Patrick-Cole) 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?

[boisgera]

Hi @AnkitBarik, @jmtemmos,

Do you identify some "low-hanging fruits" in your respective checklists? Some blockers?

Anything I can do to help move the process forward?

Best regards,

Sébastien