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[REVIEW]: A Python Tool for Predicting and Assessing Unconventional Rare-Earth and Critical Mineral Resources #5500

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editorialbot opened this issue May 30, 2023 · 116 comments
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[REVIEW]: A Python Tool for Predicting and Assessing Unconventional Rare-Earth and Critical Mineral Resources #5500

editorialbot opened this issue May 30, 2023 · 116 comments
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accepted Makefile published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 6 (ESE) Earth Sciences and Ecology waitlisted Submissions in the JOSS backlog due to reduced service mode.

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editorialbot commented May 30, 2023 •
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Submitting author: @justaPCWingo (Patrick Wingo)
Repository: https://github.com/NETL-RIC/URC-Assessment-Method
Branch with paper.md (empty if default branch): joss-submit
Version: v1.0.1
Editor: @elbeejay
Reviewers: @jeinsle, @jameshgrn, @FrancescoPerrone
Archive: 10.5281/zenodo.8319843

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/08aaa53d1f620dec132d7ef5807af16c"><img src="https://joss.theoj.org/papers/08aaa53d1f620dec132d7ef5807af16c/status.svg"></a>
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:

@editorialbot generate my checklist

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 editorialbot added Makefile Python review TeX Track: 6 (ESE) Earth Sciences and Ecology waitlisted Submissions in the JOSS backlog due to reduced service mode. labels May 30, 2023
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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

@editorialbot editorialbot mentioned this issue May 30, 2023
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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", "="]

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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

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Wordcount for paper.md is 1203

@elbeejay
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@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

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@editorialbot remind @jeinsle in three weeks

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Reminder set for @jeinsle in three weeks

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@editorialbot remind @jameshgrn in three weeks

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

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Reminder set for @jameshgrn in three weeks

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jeinsle commented May 30, 2023 •
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Review checklist for @jeinsle

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/NETL-RIC/URC-Assessment-Method?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • 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?
  • 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?

@elbeejay
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@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
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jeinsle commented May 30, 2023 via email

@elbeejay
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@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.

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FrancescoPerrone commented Jun 1, 2023 via email

@jeinsle
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jeinsle commented Jun 1, 2023 via email

@jameshgrn
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@editorialbot generate my checklist

@elbeejay
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elbeejay commented Jun 6, 2023

@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
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FrancescoPerrone commented Jun 7, 2023 •
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Review checklist for @FrancescoPerrone

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/NETL-RIC/URC-Assessment-Method?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • 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?
  • 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?

@jameshgrn
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jameshgrn commented Jun 7, 2023 •
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Review checklist for @jameshgrn

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/NETL-RIC/URC-Assessment-Method?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • 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?
  • 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?

@FrancescoPerrone
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fp_comments.md

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jameshgrn commented Jun 7, 2023 •
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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.

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elbeejay commented Sep 3, 2023

@editorialbot check references

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.5884351 is OK
- 10.18141/1503876 is OK
- 10.18141/1614852 is OK
- 10.1190/INT-2019-0019.1 is OK
- 10.1016/j.coal.2011.11.001 is OK
- 10.1016/j.gsf.2018.12.005 is OK
- 10.1007/s11053-023-10163-x is OK
- 10.18141/1891489 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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elbeejay commented Sep 3, 2023

Thanks to your responses, I think I know the best course of action here. Zenodo is the way to go in this case. I need to get permission to upload to Zenodo, but since this is just a snapshot of existing publically released code, I don't foresee an issue, just some CYA.

This sounds good, let me know when you've been able to do this @justaPCWingo - thanks for being understanding and flexible.

@justaPCWingo
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Hi @elbeejay ,

the tagged version is v1.0.1.
the zenodo DOI is 10.5281/zenodo.8319843

Please let me know if there is anything else you need me to do.

@kthyng
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kthyng commented Sep 6, 2023

Sounds like you all went with Zenodo, let me know if you still have questions.

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elbeejay commented Sep 8, 2023

@editorialbot set v1.0.1

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I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

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elbeejay commented Sep 8, 2023

@editorialbot set v1.0.1 as version

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Done! version is now v1.0.1

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elbeejay commented Sep 8, 2023

@editorialbot set 10.5281/zenodo.8319843 as archive

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Done! archive is now 10.5281/zenodo.8319843

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elbeejay commented Sep 8, 2023

@editorialbot recommend-accept

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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

- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.5884351 is OK
- 10.18141/1503876 is OK
- 10.18141/1614852 is OK
- 10.1190/INT-2019-0019.1 is OK
- 10.1016/j.coal.2011.11.001 is OK
- 10.1016/j.gsf.2018.12.005 is OK
- 10.1007/s11053-023-10163-x is OK
- 10.18141/1891489 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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elbeejay commented Sep 8, 2023

Nothing else you have to do @justaPCWingo - thanks!

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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#4538, 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 Sep 8, 2023
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kthyng commented Sep 8, 2023 •
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Ok next steps on my end:

  • Check that version was updated
  • Check that software archive exists, has been input to JOSS, and title and author list look good
  • Check paper

@kthyng
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kthyng commented Sep 8, 2023

Looks great!

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kthyng commented Sep 8, 2023

@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: Wingo
  given-names: Patrick
  orcid: "https://orcid.org/0000-0003-3934-7733"
- family-names: Justman
  given-names: Devin
- family-names: Creason
  given-names: C. Gabriel
  orcid: "https://orcid.org/0000-0002-3440-1174"
- family-names: Mark-Moser
  given-names: Mackenzie
  orcid: "https://orcid.org/0000-0001-5138-5527"
- family-names: Montross
  given-names: Scott
  orcid: "https://orcid.org/0000-0002-6551-7700"
- family-names: Rose
  given-names: Kelly
  orcid: "https://orcid.org/0000-0001-6130-4727"
contact:
- family-names: Wingo
  given-names: Patrick
  orcid: "https://orcid.org/0000-0003-3934-7733"
doi: 10.5281/zenodo.8319843
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Wingo
    given-names: Patrick
    orcid: "https://orcid.org/0000-0003-3934-7733"
  - family-names: Justman
    given-names: Devin
  - family-names: Creason
    given-names: C. Gabriel
    orcid: "https://orcid.org/0000-0002-3440-1174"
  - family-names: Mark-Moser
    given-names: Mackenzie
    orcid: "https://orcid.org/0000-0001-5138-5527"
  - family-names: Montross
    given-names: Scott
    orcid: "https://orcid.org/0000-0002-6551-7700"
  - family-names: Rose
    given-names: Kelly
    orcid: "https://orcid.org/0000-0001-6130-4727"
  date-published: 2023-09-08
  doi: 10.21105/joss.05500
  issn: 2475-9066
  issue: 89
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5500
  title: A Python Tool for Predicting and Assessing Unconventional
    Rare-Earth and Critical Mineral Resources
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05500"
  volume: 8
title: A Python Tool for Predicting and Assessing Unconventional
  Rare-Earth and Critical Mineral Resources

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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🚨🚨🚨 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.05500 joss-papers#4539
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05500
  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 Sep 8, 2023
@kthyng
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kthyng commented Sep 8, 2023

Congrats on your new publication @justaPCWingo!! Many thanks to editor @elbeejay and reviewers @jeinsle, @jameshgrn, and @FrancescoPerrone for your time, hard work, and expertise!!

(I will close this issue once the DOI resolves)

@kthyng kthyng closed this as completed Sep 9, 2023
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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.05500/status.svg)](https://doi.org/10.21105/joss.05500)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05500">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05500/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05500/status.svg
   :target: https://doi.org/10.21105/joss.05500

This is how it will look in your documentation:

DOI

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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