Closed editorialbot closed 1 year ago
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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", "="]
Software report:
github.com/AlDanial/cloc v 1.88 T=0.41 s (224.7 files/s, 149354.1 lines/s)
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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 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
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SUM: 93 5037 6582 50210
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 1203
@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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:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
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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?
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?
β 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: @.***>
@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.
Hi there, apologies for not getting back sooner than now. Iβm just acknowledging your email; Iβll 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.
β 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: @.***>
@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
Status badge code:
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.
β¨ 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 β¨
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
β 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: @.***>
@editorialbot generate my checklist
@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!
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
PAPER COMMENTS
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!
@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.
@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
@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.
:wave: @jeinsle, please update us on how your review is going (this is an automated reminder).
:wave: @jameshgrn, please update us on how your review is going (this is an automated reminder).
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
Sent from Outlook for iOShttps://aka.ms/o0ukef
From: The Open Journals editorial robot @.> Sent: Tuesday, June 20, 2023 1:40:29 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)
π @jeinslehttps://github.com/jeinsle, please update us on how your review is going (this is an automated reminder).
β Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/5500#issuecomment-1598695798, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADVMCU5M4GQDOFRVJ4GMCA3XMGK33ANCNFSM6AAAAAAYT6NQU4. You are receiving this because you were mentioned.Message ID: @.***>
@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!
That all sounds good, thank you for the update @justaPCWingo
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!
No problem, thanks for keeping us in the loop @justaPCWingo
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!
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.
@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.
Howdy. I am at a conference this week. So will dig into it next week
Sent from Outlook for iOShttps://aka.ms/o0ukef
From: J. Hariharan @.> Sent: Wednesday, July 12, 2023 2:13:30 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, @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.
β Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/5500#issuecomment-1632419465, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADVMCU3BJJXYD7XNIZVJFDDXP2IGVANCNFSM6AAAAAAYT6NQU4. You are receiving this because you were mentioned.Message ID: @.***>
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.
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.
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)!
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.
Dear all apologies for being slow with this. I did not forget it just being truly snowed under workβ¦ Iβll 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.
β 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: @.***>
Let me echo @FrancescoPerrone , did not forget... slammed
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
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:
will follow up soon
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.
β 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: @.***>
Great, thanks for the updates all.
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!
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:
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.
Submitting author: !--author-handle-->@justaPCWingo<!--end-author-handle-- (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: !--editor-->@elbeejay<!--end-editor-- Reviewers: @jeinsle, @jameshgrn, @FrancescoPerrone Archive: 10.5281/zenodo.8319843
Status
Status badge code:
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:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @elbeejay know.
β¨ 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 β¨
Checklists
π Checklist for @jeinsle
π Checklist for @FrancescoPerrone
π Checklist for @jameshgrn