[REVIEW]: pide: Petrophysical Interpretation tools for geoDynamic Exploration.

editorialbot commented 2 months ago

Submitting author: !--author-handle-->@sinanozaydin@kthyng<!--end-editor-- Reviewers: @kujaku11, @santisoler Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/13828c7227715f46aa96f343f1f544a3"><img src="https://joss.theoj.org/papers/13828c7227715f46aa96f343f1f544a3/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/13828c7227715f46aa96f343f1f544a3/status.svg)](https://joss.theoj.org/papers/13828c7227715f46aa96f343f1f544a3)

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

@kujaku11 & @santisoler, 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 @kthyng 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 @kujaku11

📝 Checklist for @santisoler

editorialbot commented 2 months ago

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editorialbot commented 2 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.10 s (1200.8 files/s, 200900.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          49           3290           1265           7300
Jupyter Notebook                11              0           3903           1329
TeX                              4              1              0           1095
JSON                             2              0              0           1046
CSV                             46              0              0            456
Markdown                         2             32              0             77
DOS Batch                        1              8              1             26
TOML                             1              1              0             21
make                             1              4              7              9
YAML                             1              4              7              7
reStructuredText                 1              6              7              7
-------------------------------------------------------------------------------
SUM:                           119           3346           5190          11373
-------------------------------------------------------------------------------

Commit count by author:

   235  Sinan Özaydın
     3  Lu Li
     1  Patrice Rey

editorialbot commented 2 months ago

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

OK DOIs

- 10.1029/2020gc009126 is OK
- 10.1002/2015GC006171 is OK
- 10.1016/j.cageo.2011.01.002 is OK
- 10.1016/j.cageo.2014.01.010 is OK
- 10.1093/gji/ggw290 is OK
- 10.1093/gji/ggz277 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 months ago

Paper file info:

📄 Wordcount for paper.md is 814

✅ The paper includes a Statement of need section

editorialbot commented 2 months ago

License info:

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

editorialbot commented 2 months ago

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

kthyng commented 2 months ago

@kujaku11, @santisoler This is where the review will take place, though as issues arise as you go through your review checklist, please open specific issues in the software repo itself, and link back to this issue to help keep things organized. Please let me know if you have any questions. Thank you!!

kujaku11 commented 2 months ago

Review checklist for @kujaku11

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/sinanozaydin/pide?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@sinanozaydin) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

kthyng commented 2 months ago

@kujaku11 and @santisoler Will you be able to get started on your reviews soon?

kujaku11 commented 2 months ago

@kthyng yes I was planning on have this done by Monday 8/12.

santisoler commented 2 months ago

I'll aim to start the review next week. Sorry for the delay.

kthyng commented 2 months ago

Thanks!

kujaku11 commented 2 months ago

@kthyng I have conducted my review and left an issue in the pide package repository.

Overall the package could be a great contribution to the geophysics community. Though there are some key components missing from the package. Namely, tests and documentation. Other issues include installation failed and some of the example notebooks don't run. Once these are implemented pide will be a strong contribution.

The manuscript was fine, just some minor grammatical suggestions and suggestions to add an example figure from outputs of the program.

Let me know if you need anything else or clarity.

kthyng commented 2 months ago

Thanks @kujaku11! @sinanozaydin Should address these comments when possible, and you may need to come back and see how it turns out or have some questions/comments, and for sure do a final check eventually

santisoler commented 1 month ago

Review checklist for @santisoler

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/sinanozaydin/pide?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@sinanozaydin) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] 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

[x] 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?

santisoler commented 1 month ago

Summary of first pass of my review

I think there's significant amount of work in pide that would make it a very useful tool for geophysical modelling and interpretation. I really appreciate the authors for the time they put into this project and that they made it available under an open-source license. Currently, there are a few minimum requirements that the submitted article doesn't meet in order to be accepted for publication by JOSS. My major comments are related to:

missing documentation for users and contributors to understand how pide is designed and find out what tools are available;
and missing tests to ensure that the code behaves as expected and to allow users to reproduce the tests results.

I provide more details about these and other topics that should be addressed through issues in the upstream repository.

Looking forward to continue the conversation and the review process.

Thanks again to authors for the effort put into this project, and thanks @kthyng for the invitation to review it.

kthyng commented 1 month ago

Thanks @santisoler!

When will you be able to start on this round of reviewer comments @sinanozaydin?

sinanozaydin commented 1 month ago

Hello @kthyng,

I am starting now. I am going to try to finish it in two weeks otherwise I have to wait a bit since I will be travelling for a while then.

Cheers,

Sinan

kthyng commented 1 month ago

@sinanozaydin Ok thanks! If you get enough done before you leave to pass it back to reviewers, that would be useful to communicate about so the process can continue on. Actually, good communication is useful regardless. Thank you!

kthyng commented 2 weeks ago

@sinanozaydin Can we have an update?

sinanozaydin commented 2 weeks ago

Hello @kthyng,

Just got back from travels, I will start working on this week and try to finish it.

sinanozaydin commented 1 week ago

Hello @kthyng

I have addressed all the opened issues in the repository.

All the best,

Sinan

santisoler commented 1 week ago

Thanks @kthyng for letting us know. I'll go through the replies to my issues and PRs in the next few days.

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