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[PRE REVIEW]: A Python Tool for Predicting and Assessing Unconventional Rare-Earth and Critical Mineral Resources #5316

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editorialbot opened this issue Mar 30, 2023 · 56 comments
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[PRE REVIEW]: A Python Tool for Predicting and Assessing Unconventional Rare-Earth and Critical Mineral Resources #5316

editorialbot opened this issue Mar 30, 2023 · 56 comments
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@elbeejay @jeinsle @jameshgrn
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Makefile pre-review Python 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 Mar 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: v1.0.0
Editor: @elbeejay
Reviewers: @jeinsle, @jameshgrn
Managing EiC: Kristen Thyng

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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)

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Thanks for submitting your paper to JOSS @justaPCWingo. Currently, there isn't a JOSS editor assigned to your paper.

@justaPCWingo if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

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@editorialbot editorialbot added pre-review Track: 6 (ESE) Earth Sciences and Ecology labels Mar 30, 2023
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Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.57 s (159.0 files/s, 107816.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          61           4728           6528          42582
SVG                              4              2              0           4152
Qt                               4              0              0           2506
Markdown                        11            211              0            530
TeX                              2             23              0            264
YAML                             3              7             13             65
DOS Batch                        1              8              1             26
make                             1              4              7              9
reStructuredText                 4             15             32              9
-------------------------------------------------------------------------------
SUM:                            91           4998           6581          50143
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1214

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⚠️ An error happened when generating the pdf.

@kthyng
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kthyng commented Mar 31, 2023

Hi @justaPCWingo and thanks for your submission. I think your comment at the top of the paper.md is messing up the paper generation. Can you remove that?

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kthyng commented Mar 31, 2023

Also I see there is a docs directory in your repo, but where can a person look at these docs?

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kthyng commented Apr 11, 2023

Hi @justaPCWingo — I am going to add the paused label while you work on these initial items.

@kthyng kthyng added the paused label Apr 11, 2023
@justaPCWingo
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Hi @kthyng - Apologies. I replied to the email message, but failed to notice that it was from an issues thread.

  • The comment at the head of paper.md has been removed from the document. It worked for me just prior to submission; perhaps I was using an older docker image?
  • The user-doc folder is the source code for the user documentation, but it can be built quite easily with Sphinx by running make.bat html or make.sh html in the user-doc folder. The user documentation is included as part of the PyInstaller bundle distribution of this product, which I last checked is still going through the approval process on EDX.

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Sorry I forgot to ask: is there any additional work on my end to request to the editorialbot to compile my paper submission?

@kthyng kthyng removed the paused label Apr 11, 2023
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kthyng commented Apr 11, 2023

@editorialbot generate pdf

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⚠️ An error happened when generating the pdf.

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kthyng commented Apr 11, 2023

The user-doc folder is the source code for the user documentation, but it can be built quite easily with Sphinx by running make.bat html or make.sh html in the user-doc folder. The user documentation is included as part of the PyInstaller bundle distribution of this product, which I last checked is still going through the approval process on EDX.

Usually a user doesn't have to compile the docs themselves though right? Or you expect that most users would use the bundle? You might consider something like ReadTheDocs to host your docs.

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kthyng commented Apr 11, 2023

I see this in the error for building your paper:

Problem with ORCID (Author Without ORCID) for Devin Justman. ORCID looks malformed (Theoj::Error)

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Hi @kthyng I have removed the orcid entry for Devin Justman, as he doesn't have one. That was a placeholder that I mistakenly left in. Still not sure why this wasn't flagged when I ran the docker container supplied by the JOSS website.

Our lab (NETL) is mostly concerned with product releases, and is in the process of understanding the licensing and releasing of Open Source code. So to answer your question, the expectation is that most people will be using the PyInstaller bundled version, with the documentation compiled.

I would be fine releasing the documentation on ReadTheDocs, but unfortunately that's not up to me. Anything published by our lab has to go through a Rights In Data (RID) process before it can be approved to go public. I can look into what would be involved to get approval, but it would take at minimum 30 days to go through the process.

However, we are already using the RTD theme for our documentation, so it would be a straight port.

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HI @kthyng , Just a followup to the comment above: I spoke with folks on my side and it seems like we can route through the existing approval process for the bundled version of the tool. This means I can have a RTD submission ready to go within a few days. I'll go ahead and get started on submitting that to both RTD and our process, and update here once its posted. Thanks for the suggestion!

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Hi @kthyng , I've added the user documentation for the URC Assessment Method to Read the Docs.

The PyInstaller bundled version of this software can be found on EDX.

Please let me know what other issues you encounter with this submission. I'll endeavor to address them as quickly as possible.

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kthyng commented Apr 18, 2023

@editorialbot generate pdf

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

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kthyng commented Apr 18, 2023

@justaPCWingo We're are at capacity for reviewers in this area of work, so I will add this submission to the waitlist. Thank you for your patience.

@kthyng kthyng added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Apr 18, 2023
@justaPCWingo
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Hi @kthyng ,
I totally understand. Thanks for being transparent and letting me know.

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kthyng commented Apr 19, 2023

@justaPCWingo thank you! And reading my message, I wrote it wrong; I meant to say "editors" instead of "reviewers"!

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kthyng commented May 8, 2023

@elbeejay One of your submissions is just wrapping up — might you be able to take this on?

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Quick update:

  • I've updated the default branch, as suggested by @elbeejay .
  • I've defined REE in the paper.md file as recommended by @elbeejay
  • The joss-reviewer script is crashing when configured according to the readme. I've submitted an issue outlining the conditions and output from the crash. I'm still contemplating if we have anyone we can recommend on our end.

Thanks.

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Thanks @justaPCWingo - there is also a more basic list of volunteer reviewers that you can search through. This falls outside of my direct field of expertise, so any recommendations for reviewers would be appreciated.

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kthyng commented May 12, 2023

You can also check out the new reviewer website! https://reviewers.joss.theoj.org/

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@justaPCWingo just as a check-in, I'm on travel this week so won't have time to do a proper search for reviewers until next week. If you get a chance and can recommend anyone that'd be appreciated too.

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Hi @elbeejay thanks for the heads up. I have a few from Joss' reviewers list, as well as someone who has been recommended to me as a review; once I reach out to them and get a response, I should have a list handy for you.

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elbeejay commented May 22, 2023 •
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@justaPCWingo thanks for providing the information about the hosted documentation. Can you link to it somewhere in the README or on the repository page itself? Without your comment above I would never have known there was hosted documentation or how to navigate to it.

As a related question, would it be possible to provide example data necessary to try out the tool somewhere? The input files and types of data required are (at least for me) not something I have on my computer or know where to grab.

Thanks!

@justaPCWingo
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hi @elbeejay and @kthyng , I've found a researcher who is willing to be a review for my submission. Should I direct them to the JOSS website to register as a reviewer, or is there another method that you prefer when inviting reviewers?

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If they have a GitHub account we can invite them here in the issue. The only requirement JOSS has is a GitHub account, one does not ned to be registered on the JOSS webpage to conduct a review.

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@sptennak, @kbevers, @dionhaefner and @jameshgrn I'm reaching out to ask if you'd be interested in reviewing this submission for JOSS describing the URC Analysis Tool: "A Python Tool for Predicting and Assessing Unconventional Rare-Earth and Critical Mineral Resources". You are all experienced in Python, and either geospatial, or geologic science; which is why I am asking if you'd be interested in getting involved in this review.

At JOSS we do open checklist-driven reviews; peer-review criteria can be viewed here. This issue is a "pre-review issue" which we use to find peer-reviewers. Once 3 reviewers are found, we will officially start the review in a dedicated GitHub issue. At present we are asking reviewers to complete reviews in 6 weeks, although this can be extended if needed. If you are not able to review but can recommend someone else, please mention them here (in this case please mention their GitHub handle without the "@" symbol).

If you are interested, please take a look at the journal's conflict of interest policy to ensure you do not have a conflict before agreeing to review this submission.

Thanks again for taking a moment to consider this, feel free to contact me if you have any questions about the JOSS review process. Please do not feel any pressure to accept this review request if you do not have the time or do not feel comfortable reviewing this software package, we appreciate and respect our peer-reviewers' time. If you cannot serve as a reviewer at this time but have a peer, collaborator, student, or colleague who might be available and would be a good fit for this submission, please let me know! If interested we can figure out how to set up a "co-review" for a colleague of yours that is a more junior or inexperienced member of the community. Note that for this submission in particular, the nature of the tool might make it a bit more difficult for someone with limited Python experience to review, as it involves a GUI, which can be difficult to manipulate and understand in Python.

Let me know, thanks.
Jay

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Thanks for the consideration, but I'll have to decline this time. Good luck with the review!

@justaPCWingo
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hi @elbeejay, Joshua Einsle has offered to be a reviewer for our submission. His github user name is jeinsle.

Thanks!

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kbevers commented May 24, 2023

I unfortunately wont be able to review this submission either.

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@jeinsle I'm reaching out to ask if you'd be interested in reviewing this submission for JOSS describing the URC Analysis Tool: "A Python Tool for Predicting and Assessing Unconventional Rare-Earth and Critical Mineral Resources". It sounds like @justaPCWingo has reached out to you and you've already expressed a willingness to conduct this review, which is great, would just like to get your confirmation here if possible.

At JOSS we do open checklist-driven reviews; peer-review criteria can be viewed here. This issue is a "pre-review issue" which we use to find peer-reviewers. Once 3 reviewers are found, we will officially start the review in a dedicated GitHub issue. At present we are asking reviewers to complete reviews in 6 weeks, although this can be extended if needed. If you are not able to review but can recommend someone else, please mention them here (in this case please mention their GitHub handle without the "@" symbol).

If you are interested, please take a look at the journal's conflict of interest policy to ensure you do not have a conflict before agreeing to review this submission.

Thanks again for taking a moment to consider this, feel free to contact me if you have any questions about the JOSS review process. Please do not feel any pressure to accept this review request if you do not have the time or do not feel comfortable reviewing this software package, we appreciate and respect our peer-reviewers' time. If you cannot serve as a reviewer at this time but have a peer, collaborator, student, or colleague who might be available and would be a good fit for this submission, please let me know! If interested we can figure out how to set up a "co-review" for a colleague of yours that is a more junior or inexperienced member of the community. Note that for this submission in particular, the nature of the tool might make it a bit more difficult for someone with limited Python experience to review, as it involves a GUI, which can be difficult to manipulate and understand in Python.

Let me know, thanks.
Jay

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Hi @elbeejay I missed your previous comments about Linking to the readthedocs in the readme, and requesting an example/test dataset. I've updated the readme to point to the documentation.

There are sample data provided as part of this EDX submission; specifically esm_3.zip. However, its not immediately obvious where/how to incorporate this data, so I'm writing a quick walkthrough/tutorial that will go through a complete run of the data with the tool. I hope to have it integrated with the user documentation by early next week.

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jeinsle commented May 26, 2023 via email

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@editorialbot add @jeinsle as reviewer

That sounds great @jeinsle!

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@jeinsle added to the reviewers list!

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quick update: I've added a quick example walkthrough to the documentation which can be found here.

Presently the CI action for testing is failing, but it appears to be from a bad GDAL installation in the ubuntu image rather than an issue with the code itself. I've had to change the .yml in the past to address this, but it seems to periodically crop up due to something outside of our control. I'm hoping to have that addressed soon as well.

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Quick followup: Fixed the CI testing by locking PIP to a specific version; I think the enforcement of some manifest rules broke how GDAL finds numpy, which caused my tests to fail!

Also thanks again @jeinsle for volunteering to review!

@jameshgrn
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@elbeejay hey Jay, was out for a few days, I can do this if still needed. Cheers

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That's be great @jameshgrn - thanks!

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@editorialbot add @jameshgrn as reviewer

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@jameshgrn added to the reviewers list!

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Will be starting the review in a separate issue now, thanks all for your responsiveness and communication here.

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@editorialbot start review

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OK, I've started the review over in #5500.

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jeinsle commented May 30, 2023 via email

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