[PRE 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 Managing EiC: Kristen Thyng

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editorialbot commented 1 year ago

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editorialbot commented 1 year ago

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
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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
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SUM:                            91           4998           6581          50143
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gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1214

editorialbot commented 1 year ago

:warning: An error happened when generating the pdf.

kthyng commented 1 year ago

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?

kthyng commented 1 year ago

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

kthyng commented 1 year ago

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

justaPCWingo commented 1 year ago

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.

justaPCWingo commented 1 year ago

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

kthyng commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:warning: An error happened when generating the pdf.

kthyng commented 1 year ago

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.

kthyng commented 1 year ago

I see this in the error for building your paper:

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

justaPCWingo commented 1 year ago

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.

justaPCWingo commented 1 year ago

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!

justaPCWingo commented 1 year ago

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.

kthyng 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:

kthyng commented 1 year ago

@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.

justaPCWingo commented 1 year ago

Hi @kthyng , I totally understand. Thanks for being transparent and letting me know.

kthyng commented 1 year ago

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

kthyng commented 1 year ago

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

kthyng commented 1 year ago

@editorialbot invite @elbeejay as editor

editorialbot commented 1 year ago

Invitation to edit this submission sent!

elbeejay commented 1 year ago

@editorialbot add me as editor

editorialbot commented 1 year ago

Assigned! @elbeejay is now the editor

elbeejay commented 1 year ago

@justaPCWingo I'm going to take a closer look tomorrow and will probably have some questions and/or comments for you then

elbeejay commented 1 year ago

@justaPCWingo I've had a look and have the following questions and suggestions:

Consider setting the default branch back to "master", we can track the paper in the "joss-submit" branch for this process, but it looks like you plan to continue development on "master" so you don't want folks opening up the repository and looking at any stale code in "joss-submit"
While not a requirement for JOSS, it looks like there is sphinx documentation already written for this package. Have you considered building it and hosting it online somewhere (e.g., GitHub Pages)? That'd be significantly more accessible to users, developers, and reviewers, than asking them to build it locally
Line 20 of the PDF please define the acronym "REE" before using it in the text
Can you recommend any reviewers you think might be a good fit for this work? There is a reviewer application with volunteer reviewers, as well as a tool that might help.

justaPCWingo commented 1 year ago

Hi @elbeejay , Below are my responses to the bullets you provided above.

I can make this change; I must have unintentionally marked it as default. The joss-submit branch was created precisely for this reason.
I have! based on previous discussions in this thread I have posted the URC Assessment method on ReadTheDocs.io.
Ack! Good catch; I see what happened here; REE stands for Rare-Earth Elements, and are defined as part of URC; in a previous revision that acronym was REE-URC. I'll update line 20 to define that acronym.
Thanks for the link to the reviewer search tool; I'll start with that. One of my colleagues suggested a form mutual colleague who used to be with our lab, but has since moved on to the Department of Defense. I may reach out to him if needed.

I'll followup once I've carried out the tasks mentioned above. Thanks!

justaPCWingo commented 1 year ago

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.

elbeejay commented 1 year ago

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.

kthyng commented 1 year ago

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

elbeejay commented 1 year ago

@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.

justaPCWingo commented 1 year ago

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.

elbeejay commented 1 year ago

@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 commented 1 year ago

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?

elbeejay commented 1 year ago

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.

elbeejay commented 1 year ago

@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

dionhaefner commented 1 year ago

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

justaPCWingo commented 1 year ago

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

Thanks!

kbevers commented 1 year ago

I unfortunately wont be able to review this submission either.

elbeejay commented 1 year ago

@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

justaPCWingo commented 1 year ago

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.

jeinsle commented 1 year ago

Hi Jay

Happy to have a read go at reviewing. my firsttime doing a code review, but i am working with a CompSci PhD on a project that i can being in on this as well. He is building me a GUI so right up his alley.

Cheers

josh

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: Wednesday, May 24, 2023 7:16 PM To: openjournals/joss-reviews @.> Cc: Joshua Franz Einsle @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: A Python Tool for Predicting and Assessing Unconventional Rare-Earth and Critical Mineral Resources (Issue #5316)

@jeinslehttps://github.com/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 @justaPCWingohttps://github.com/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 herehttps://joss.readthedocs.io/en/latest/review_criteria.html. 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 policyhttps://joss.readthedocs.io/en/latest/reviewer_guidelines.html?#joss-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

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/5316#issuecomment-1561726208, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADVMCU53NIB5NSOQMKB7MRTXHZF7BANCNFSM6AAAAAAWNMHEHI. You are receiving this because you were mentioned.Message ID: @.***>

elbeejay commented 1 year ago

@editorialbot add @jeinsle as reviewer

That sounds great @jeinsle!

editorialbot commented 1 year ago

@jeinsle added to the reviewers list!

justaPCWingo commented 1 year ago

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.

justaPCWingo commented 1 year ago

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 commented 1 year ago

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

elbeejay commented 1 year ago

That's be great @jameshgrn - thanks!

openjournals / joss-reviews

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

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