[REVIEW]: A Python Tool for Predicting and Assessing Unconventional Rare-Earth and Critical Mineral Resources

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@justaPCWingo@elbeejay<!--end-editor-- Reviewers: @jeinsle, @jameshgrn, @FrancescoPerrone Archive: 10.5281/zenodo.8319843

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Markdown: [![status](https://joss.theoj.org/papers/08aaa53d1f620dec132d7ef5807af16c/status.svg)](https://joss.theoj.org/papers/08aaa53d1f620dec132d7ef5807af16c)

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

@jeinsle & @jameshgrn, 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:

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @elbeejay 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 @jeinsle

📝 Checklist for @FrancescoPerrone

📝 Checklist for @jameshgrn

editorialbot commented 1 year ago

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editorialbot commented 1 year ago

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "," (COMMA) [#<BibTeX::Bibliography data=[15]>, "@", #<BibTeX::Entry >, {:title=>["Unlocking the Potential of Unconventional Critical Mineral Resources Story Map"], :author=>["Yesenchak, Rachel and Justman, Devin and Bauer, Sophia and Creason, C Gabriel and Gordon, Andrew and Montross, Scott N and Sabbatino, Michael and Rose, Kelly"], :abstractnote=>["An ArcGIS Story Map that provides context and understanding of unconventional critical mineral resource potential."], :doi=>["10.18141/1891489"], :url=>["https://www.osti.gov/biblio/1891489"], :journal=>[""]}, ",", "number", "="]

editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.41 s (224.7 files/s, 149354.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          61           4728           6528          42582
SVG                              4              2              0           4152
Qt                               4              0              0           2506
Markdown                        12            247              0            585
TeX                              2             23              0            264
YAML                             4             10             13             75
DOS Batch                        1              8              1             26
reStructuredText                 4             15             33             11
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            93           5037           6582          50210
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1203

elbeejay commented 1 year ago

@jeinsle and @jameshgrn thanks for agreeing to review this submission. This is the "official" review issue, instructions for creating your reviewer checklist and conducting the review should be in the top comment of this issue, but please do not hesitate to reach out to me with any questions or to ask for any clarification.

Ideally we'd like to ask that you complete your reviews within 6 weeks, and I will set up reminder so the bot prods us all in 3 weeks.

Thanks, Jay

elbeejay commented 1 year ago

@editorialbot remind @jeinsle in three weeks

editorialbot commented 1 year ago

Reminder set for @jeinsle in three weeks

elbeejay commented 1 year ago

@editorialbot remind @jameshgrn in three weeks

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

Reminder set for @jameshgrn in three weeks

jeinsle commented 1 year ago

Review checklist for @jeinsle

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/NETL-RIC/URC-Assessment-Method?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@justaPCWingo) 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.
[x] 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?
[x] 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).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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?

elbeejay commented 1 year ago

@jeinsle per your comment in the pre-review issue:

Hi Jay

as noted my post-doc Francesco Perrone will be helping on my end. His GitHub info is: FrancescoPerrone

We will get started on the checklist from tomorrow.

Cheers

josh

Would you and Francesco prefer that he be added as a separate reviewer?

jeinsle commented 1 year ago

for him it may be better for profile to be separate, but not clear how you want to handle.

Sometimes I work outside of standard hours, but I do not expect replies during these times.

Joshua F. Einsle Lord Kelvin Adam Smith Research Fellow in Data Science School of Geographical and Earth Sciences University of Glasgow

https://www.gla.ac.uk/schools/ges/staff/joshuafranzeinsle/

From: J. Hariharan @.> Sent: Tuesday, May 30, 2023 4:05 PM To: openjournals/joss-reviews @.> Cc: Joshua Franz Einsle @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [REVIEW]: A Python Tool for Predicting and Assessing Unconventional Rare-Earth and Critical Mineral Resources (Issue #5500)

@jeinslehttps://github.com/jeinsle per your comment in the pre-review issue:

Hi Jay

as noted my post-doc Francesco Perrone will be helping on my end. His GitHub info is: FrancescoPerrone

We will get started on the checklist from tomorrow.

Cheers

josh

Would you and Francesco prefer that he be added as a separate reviewer?

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/5500#issuecomment-1568605705, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADVMCUZXN5N2JMULCLVMVBLXIYEDDANCNFSM6AAAAAAYT6NQU4. You are receiving this because you were mentioned.Message ID: @.***>

elbeejay commented 1 year ago

@FrancescoPerrone I've added you to the list of reviewers so you should be able to generate your own review checklist and fill it out / edit it. Please let me know if this does not work properly.

FrancescoPerrone commented 1 year ago

Hi there, apologies for not getting back sooner than now. I’m just acknowledging your email; I’ll be in touch if any additional question/help will be required.

Thanks a lot! With kind regards, Francesco

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From: J. Hariharan @.> Sent: Tuesday, May 30, 2023 4:15:15 PM To: openjournals/joss-reviews @.> Cc: Francesco Perrone @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [REVIEW]: A Python Tool for Predicting and Assessing Unconventional Rare-Earth and Critical Mineral Resources (Issue #5500)

@FrancescoPerronehttps://github.com/FrancescoPerrone I've added you to the list of reviewers so you should be able to generate your own review checklist and fill it out / edit it. Please let me know if this does not work properly.

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/5500#issuecomment-1568622141, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AALXCV7JCDEQWLSOPYN6CZDXIYFIHANCNFSM6AAAAAAYT6NQU4. You are receiving this because you were mentioned.Message ID: @.***>

jeinsle commented 1 year ago

@editorialbot generate my checklist

Sometimes I work outside of standard hours, but I do not expect replies during these times.

Joshua F. Einsle Lord Kelvin Adam Smith Research Fellow in Data Science School of Geographical and Earth Sciences University of Glasgow

https://www.gla.ac.uk/schools/ges/staff/joshuafranzeinsle/

From: The Open Journals editorial robot @.> Sent: Tuesday, May 30, 2023 1:39 PM To: openjournals/joss-reviews @.> Cc: Joshua Franz Einsle @.>; Mention @.> Subject: [openjournals/joss-reviews] [REVIEW]: A Python Tool for Predicting and Assessing Unconventional Rare-Earth and Critical Mineral Resources (Issue #5500)

Submitting author: @justaPCWingohttps://github.com/justaPCWingo (Patrick Wingohttp://orcid.org/0000-0003-3934-7733) Repository: https://github.com/NETL-RIC/URC-Assessment-Method Branch with paper.md (empty if default branch): joss-submit Version: v1.0.0 Editor: @elbeejayhttps://github.com/elbeejay Reviewers: @jeinslehttps://github.com/jeinsle, @jameshgrnhttps://github.com/jameshgrn Archive: Pending

Status

[status]https://joss.theoj.org/papers/08aaa53d1f620dec132d7ef5807af16c

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repositoryhttps://github.com/NETL-RIC/URC-Assessment-Method 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

@jeinslehttps://github.com/jeinsle & @jameshgrnhttps://github.com/jameshgrn, 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 @elbeejayhttps://github.com/elbeejay 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

@jeinslehttps://github.com/jeinsle, please create your checklist typing: @editorialbot generate my checklist

@jameshgrnhttps://github.com/jameshgrn, please create your checklist typing: @editorialbot generate my checklist

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/5500, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADVMCU26FQIDBPTRQNDTHJ3XIXS7FANCNFSM6AAAAAAYT6NQU4. You are receiving this because you were mentioned.Message ID: @.***>

jameshgrn commented 1 year ago

@editorialbot generate my checklist

elbeejay commented 1 year ago

@jameshgrn I don't know what happened there, maybe the bot was down for a bit. I'd say try once more to get it to generate checklist, and if that is unsuccessful we can find you the raw markdown to create a comment with your reviewer checklist manually.

Thanks!

FrancescoPerrone commented 1 year ago

Review checklist for @FrancescoPerrone

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/NETL-RIC/URC-Assessment-Method?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@justaPCWingo) 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.
[x] 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?
[x] 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).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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?

jameshgrn commented 1 year ago

Review checklist for @jameshgrn

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/NETL-RIC/URC-Assessment-Method?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@justaPCWingo) 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.
[x] 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?
[x] 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).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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?

FrancescoPerrone commented 1 year ago

fp_comments.md

jameshgrn commented 1 year ago

Adding my thoughts in here. I agree with everything @FrancescoPerrone said so consider that a +1 for their recommendations. I think this is certainly a package that meets JOSS standards of content and substantial effort, but there are several changes to the repository that need to happen before it meets FAIR standards.

I tried to solve a conda environment for this package this morning and gave up after a little while of no success. Once an environment management system is implemented (requirements.txt or preferably an environment.yml file for conda) I will test out the package. below are some comments for the repository in general and the paper itself.

REPOSITORY COMMENTS

Please include detailed installation instructions and a requirements.txt or an environment.yml file. This is crucial. I realize it is also in the readme, but id rather have pip or conda build the env for me as opposed to building it myself especially when GDAL is in play.
Please include instructions to perform tests or implement a formal system for automated testing as discussed by @FrancescoPerrone
The authors are encouraged to rename the COPYING file to 'LICENSE' to make it easier to find.
"Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?" I dont see the API reference in the documentation. This should be easy to compile with sphinx and function docstrings..

PAPER COMMENTS

Authors are encouraged to add detail to figure captions, hard to understand with the current captions.
I think the paragraph that outlines the use of the equations needs to be expanded. It is currently hard to follow and some of the details are glossed over. If it is detailed in the sister paper to this one, just refer to that paper and dont include them.
Authors are encouraged to add more to their manuscript, particularly a section after the statement of need. Maybe an example and more detailed description of what the package does / use cases, and where it fits into the open source landscape.

elbeejay commented 1 year ago

Thank you @FrancescoPerrone and @jameshgrn for taking a look at the repository and providing your feedback. Those comments all look reasonable and important to me. I agree with @jameshgrn and suggest that all reviewers wait until revisions are made before attempting to test the code and review the submission.

@justaPCWingo please read over and address these comments and notify us all here once changes have been made. Thanks!

justaPCWingo commented 1 year ago

@FrancescoPerrone and @jameshgrn Thanks for the feedback and comments. The requests seem reasonable to me. I'll dig in a bit and speak with my fellow authors.

@jameshgrn I hear you when it comes to GDAL; getting it installed is the bane of my existence. I can't tell you how many versions, platforms, and build configurations I've wrestled with over the years; its one of the biggest reason I push for PyInstaller bundles for distribution. I'll see what I can do with environment/requirement files. I should probably look into a proper pypi installation if time permits.

@elbeejay I'll shoot to address the Reviewer comments over the next two weeks. I have some other work obligations I need to balance with this, but I think that's a reasonable timeframe.

jameshgrn commented 1 year ago

@justaPCWingo Totally hear you. I've had success with some clever conda environment settings. I'll do some more thinking on my end as well. Cheers

elbeejay commented 1 year ago

@justaPCWingo please update us with your progress, and provide a timeline for when you might expect to get those revisions taken care of so that our reviewers will have an idea of when they'll need to put this item back on their to-do lists.

Re: the geospatial/GDAL dependency question, my 2-cents are to use conda as pip is less capable of resolving dependency conflicts in non-python codebases (e.g., the underlying C/C++ powering GDAL). Another option to improve reproducibility of the environment could be creating some sort of container (e.g., using Docker) with the necessary libraries.

editorialbot commented 1 year ago

:wave: @jeinsle, please update us on how your review is going (this is an automated reminder).

editorialbot commented 1 year ago

:wave: @jameshgrn, please update us on how your review is going (this is an automated reminder).

jeinsle commented 1 year ago

Sorry have not really made much progress. I was wondering if I was superfluous after @fperone had reviewed. I will attack some of the items tomorrow

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justaPCWingo commented 1 year ago

@elbeejay I'm shooting to have addressed existing issues and to provide review responses by Monday, June 26th. I believe that is doable with my schedule and timeline. I have already begun making changes based on the feedback from @FrancescoPerrone and @jameshgrn. If it looks like that date will slip, I'll post an update here.

@elbeejay unfortunately, docker is essentially a nonstarter here; our cyber policy keeps the command set for such virtualization solutions disabled (it blocks the use of Microsoft's WSL as well, which would be useful for cross-platform development). Generally, I use conda on windows precisely for the reason you mentioned: binary DLLs underpinning so many of the libraries. When on a Linux or Mac system, I don't find it as necessary and generally stick with pip for simplicity.

Thanks!

elbeejay commented 1 year ago

That all sounds good, thank you for the update @justaPCWingo

justaPCWingo commented 1 year ago

Hi @elbeejay I hate to do this, but I think I'll have to revise my response date to Friday, July 1st. I've had a few delays on my end. I'm almost done with my pass, but I want to make sure my co-authors have a chance to look over my changes before I respond.

Thanks!

elbeejay commented 1 year ago

No problem, thanks for keeping us in the loop @justaPCWingo

justaPCWingo commented 1 year ago

Hi @elbeejay , @FrancescoPerrone , and @jameshgrn , I've posted a new draft of paper.md to the joss-submit branch of the repository. I've also uploaded a response to @FrancescoPerrone and a response to @jameshgrn to the repo with my answers in red text.

Thanks!

elbeejay commented 1 year ago

Great, thanks for the update @justaPCWingo.

@jeinsle, @jameshgrn, @FrancescoPerrone please revisit this submission sometime in the next few weeks when you get a chance. I'll just request that if you don't think you can get to this in July, please let us know here so everyone is on the same page.

elbeejay commented 1 year ago

@jeinsle, @jameshgrn, @FrancescoPerrone I'm just checking in here, please reach out if there are any outstanding questions or comments about the process. It'd be great to get @justaPCWingo estimates about when you'll each be able to take a look at the revised package, thanks.

jeinsle commented 1 year ago

Howdy. I am at a conference this week. So will dig into it next week

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@jeinslehttps://github.com/jeinsle, @jameshgrnhttps://github.com/jameshgrn, @FrancescoPerronehttps://github.com/FrancescoPerrone I'm just checking in here, please reach out if there are any outstanding questions or comments about the process. It'd be great to get @justaPCWingohttps://github.com/justaPCWingo estimates about when you'll each be able to take a look at the revised package, thanks.

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FrancescoPerrone commented 1 year ago

Apologies for being out of touch. I should be able to look into this next week. I will keep you updated is anything changes in my schedule.

jameshgrn commented 1 year ago

Hi all, was at a conference last week and at one next week. Going to get this done in the next 7-8 days. thanks.

elbeejay commented 1 year ago

Awesome, thanks all for the updates. No problem if you need more time, please just let us know - sounds like there is a lot of conference going and other activities (which is great to hear)!

elbeejay commented 1 year ago

Hi @jeinsle, @jameshgrn, @FrancescoPerrone it has been a couple weeks so I just wanted to ping everyone and keep this on your collective to-do lists.

FrancescoPerrone commented 1 year ago

Dear all apologies for being slow with this. I did not forget it just being truly snowed under work… I’ll get it done!

Sent from Outlook for iOShttps://aka.ms/o0ukef

From: J. Hariharan @.> Sent: Tuesday, July 25, 2023 1:20:40 PM To: openjournals/joss-reviews @.> Cc: Francesco Perrone @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [REVIEW]: A Python Tool for Predicting and Assessing Unconventional Rare-Earth and Critical Mineral Resources (Issue #5500)

Hi @jeinslehttps://github.com/jeinsle, @jameshgrnhttps://github.com/jameshgrn, @FrancescoPerronehttps://github.com/FrancescoPerrone it has been a couple weeks so I just wanted to ping everyone and keep this on your collective to-do lists.

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/5500#issuecomment-1649733044, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AALXCVZ4LTCTLIFLPG3H7MTXR62ZRANCNFSM6AAAAAAYT6NQU4. You are receiving this because you were mentioned.Message ID: @.***>

jameshgrn commented 1 year ago

Let me echo @FrancescoPerrone , did not forget... slammed

jameshgrn commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

jameshgrn commented 1 year ago

cheers to the authors for a well-done revision, pretty much everything looks good to me. I cant test it right now, but the paper as well as the new readme look good. a couple things now:

Link to CONTRIBUTING and LICENSE in the original README.md
add a sentence to check this box: "State of the field: Do the authors describe how this software compares to other commonly-used packages?"
include installation guidelines in the readme

will follow up soon

jeinsle commented 1 year ago

Echoing both @jameshgrnhttps://github.com/jameshgrn, and @FrancescoPerronehttps://github.com/FrancescoPerrone I have been slammed with deadlines since I returned from holidays. I have made some progress but need to write things down / comment on Git.

j

Sometimes I work outside of standard hours, but I do not expect replies during these times.

Joshua F. Einsle Lord Kelvin Adam Smith Research Fellow in Data Science School of Geographical and Earth Sciences University of Glasgow

https://www.gla.ac.uk/schools/ges/staff/joshuafranzeinsle/

From: J. Hariharan @.> Sent: Tuesday, July 25, 2023 1:20 PM To: openjournals/joss-reviews @.> Cc: Joshua Franz Einsle @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [REVIEW]: A Python Tool for Predicting and Assessing Unconventional Rare-Earth and Critical Mineral Resources (Issue #5500)

Hi @jeinslehttps://github.com/jeinsle, @jameshgrnhttps://github.com/jameshgrn, @FrancescoPerronehttps://github.com/FrancescoPerrone it has been a couple weeks so I just wanted to ping everyone and keep this on your collective to-do lists.

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/5500#issuecomment-1649733044, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADVMCU2WXYVIE3PPJWFZHKTXR62ZRANCNFSM6AAAAAAYT6NQU4. You are receiving this because you were mentioned.Message ID: @.***>

elbeejay commented 1 year ago

Great, thanks for the updates all.

justaPCWingo commented 1 year ago

Just a quick update from my end: I've made some changes in response to @jameshgrn 's suggestions above. I figure I can address additional feedback as it comes in. Thanks!

FrancescoPerrone commented 1 year ago

Dear all,

I appreciate your prompt and detailed responses to my initial review comments. I have reviewed the modifications made in response to my initial feedback, and here are my follow-up comments:

Authors' contributions: Thank you for detailing the contributions made by each author in your response. While this information is not strictly required in the JOSS submission documentation, it adds value to the review process and helps ensure that each individual's contributions are appropriately credited.
Manuscript detail: I am satisfied with the addition of the "Implementation Details" section in your manuscript, and the expansion of the example tutorial in your documentation. This does improve the reproducibility of the methods employed by the URC Resource Assessment Tool, and I appreciate your attention to this point.
License file: The renaming of your license file to "LICENSE" aligns with best practices for open-source software projects and enhances the clarity of your project's legal framework.
Version information: Thank you for including version information in the README, user documentation, and making it available through the __version__ variable in urclib. This is a positive addition that aids in reproducibility and usage of your software.
Testing instructions: I appreciate your adding instructions for running tests using pytest to the documentation. This addition is helpful for users and contributors who wish to verify the software's functionality.
Community Guidelines: The inclusion of a CONTRIBUTING.md file in your repository enhances your project's openness to contributions, which is a critical aspect of open-source software.

Regarding the manuscript:

Title: While it may be a bit long, I understand your concern about introducing undefined acronyms. Retaining the current title is acceptable given this consideration.
Summary: The breaking down of sentences has indeed improved readability. Thank you for your attention to this detail.
Methodology: I understand your concerns about reproducing large amounts of detail from the Creason 2023 paper. Directing the reader to this paper for additional information is a reasonable solution.
Support Libraries: Thank you for specifying the versions of the libraries used. This enhances the reproducibility of your software.

On the basis of these modifications, I am satisfied that you have addressed all the major points raised in my initial review. I appreciate the constructive manner in which you engaged with my comments, and your commitment to improving both your manuscript and your software is clear.

Recommendation: Based on these changes, I recommend that the manuscript and software are accepted for publication in the Journal of Open Source Software (JOSS), pending any final checks by the editor.

Once again, congratulations on developing this valuable tool and for producing a clear and informative paper to accompany it.

Best regards,

Francesco

Additional comments

While I trust that you have made the changes you mentioned, I unfortunately was not able to run the tool again due to time constraints. However, I would like to provide the following general recommendations to further enhance the tool and its documentation:

Continuous Integration (CI): If it is not already in place, consider adding a CI workflow to automatically run tests when changes are pushed to the repository. This would add an additional layer of assurance that the software is working as intended.
Software Tutorial: If time permits, consider developing a video tutorial or webinar for users. This can be especially helpful for complex software like yours, as it can help users visualize the process and better understand how to use the tool.
Use Cases: Continue to add real-world use cases or examples to the documentation as they become available. These can serve as valuable guides for users to understand how the tool can be applied to their specific needs.
Active Community Engagement: Aim to maintain an active presence in the repository to address questions, issues, or suggestions that users may post. This will encourage users to contribute and engage more with your project.

Again, these are suggestions for potential improvements and may be considered as the project evolves and grows.

On the basis of your responses and modifications, I am satisfied that you have addressed all the major points raised in my initial review. I appreciate the constructive manner in which you engaged with my comments, and your commitment to improving both your manuscript and your software is clear.

Recommendation: Given my inability to run the tool a second time due to time constraints, my recommendation is made based on the changes as stated by the authors. I recommend that the manuscript and software are accepted for publication in the Journal of Open Source Software (JOSS), pending any final checks by the editor and, if possible, a final verification by someone able to run the tool.

Once again, congratulations on developing this valuable tool and for producing a clear and informative paper to accompany it.

openjournals / joss-reviews