[PRE REVIEW]: WEPPCLIFF: A command-line tool to process climate inputs for soil loss models

[whedon]

Submitting author: @ryanpmcg (Ryan McGehee) Repository: https://github.com/ryanpmcg/WEPPCLIFF Version: 1.4 Editor: @kbarnhart Reviewers: @frengers, @stoor001, @khaors

Author instructions

Thanks for submitting your paper to JOSS @ryanpmcg. The JOSS editor @lheagy, will work with you on this issue to find a reviewer for your submission before creating the main review issue.

@ryanpmcg if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

Editor instructions

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

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[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @lheagy it looks like you're currently assigned as the editor for this paper :tada:

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What happens now?

This submission is currently in a pre-review state which means we are waiting for the assigned editor (@lheagy) to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience :smile_cat:

You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here.

[whedon]

Attempting to check references...

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.2489/jswc.74.4.334 may be missing for title: Updated climate database and impacts on WEPP model predictions
- https://doi.org/10.13031/2013.27921 may be missing for title: Erosivity index values for northern Mississippi
- https://doi.org/10.2489/jswc.73.4.363 may be missing for title: Benchmarking reliable erosion indices from quarter-hour station data for climate studies in the Southeastern United States

INVALID DOIs

- None

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[danielskatz]

👋 @lheagy - sorry, I didn't mean to assign this to you as editor - Since I don't think @whedon will let me unassign it, I'm going to assign it to me for the minute while I find an appropriate editor

[danielskatz]

@whedon assign @danielskatz as editor

[whedon]

OK, the editor is @danielskatz

[danielskatz]

👋 @kbarnhart - would you be willing to edit this submission?

[ooo[bot]]

:wave: Hey @danielskatz...

Letting you know, @kbarnhart is currently OOO until Wednesday, December 4th 2019. :heart:

[danielskatz]

@whedon remind @danielskatz in 2 days

[whedon]

Sorry, I can't set reminders on PRE-REVIEW issues.

[danielskatz]

@whedon - what are you good for?

[danielskatz]

👋 @kbarnhart - would you be willing to edit this submission?

[kbarnhart]

Yes. I can do it

[kbarnhart]

@whedon assign @kbarnhart as editor

[whedon]

OK, the editor is @kbarnhart

[kbarnhart]

@ryanpmcg if you have recommendations for reviewers please tag them on this thread.

This here is a pre-review issue. Once I've attracted sufficient reviewers I'll open a dedicated review issue where check-boxes guide you through the review process.

Let me know if you have questions.

[ryanpmcg]

Thank you @kbarnhart, I am working on that, but I am new to the community and have not yet built up a network of potential reviewers on GitHub. Am I correct that they should have a GitHub account to be considered as a potential reviewer?

[ryanpmcg]

There are two post-docs who have now used WEPPCLIFF, and I can ask them to join and review. Otherwise, I saw two persons in the list of people who agreed to be reviewers for the journal (one with climate background and one with soil background).

[kbarnhart]

@ryanpmcg I think that its most important that the reviewers are well suited to reviewing the software.

If there are people who you think would be good, but who are not yet on GitHub, I can reach out to them via email, see if they are interested in reviewing, and if they are willing, they would make a GitHub account in order to submit the review.

[kbarnhart]

@ryanpmcg while we are working to find suitable reviewers, I wanted to follow up with an additional comment. Based on looking over the contents of the submission, I would consider adding instructions describing how a user might test that the software has been installed correctly and is working as expected.

Some more information about testing can be found in this part of the JOSS docs.

Given the tutorials you have provided, one possible approach might be a script that when run, executes the tutorial steps, asserts that known outputs are produced, and prints a success message when testing completes successfully.

[ryanpmcg]

@kbarnhart I have uploaded automated testing scripts for OSX and Windows. All changes have been added to an AUTOTEST folder in the repository. I tested both on my two machines, and verified the outputs. I will update the Readme.md with instructions soon; it will be exactly the same as the AutoTutorial shell and batch scripts for consistency.

[ryanpmcg]

@kbarnhart how should R packages used in WEPPCLIFF be given credit? Right now they are listed in the WEPPCLIFF documentation (acknowledgements). Should they also be listed in the paper somewhere?

[kbarnhart]

@ryanpmcg

1. I think your approach to adding a testing component to this repository is a good one. Thanks for adding that. Now the repository will be prepared for the reviewers to test the ability to test WEPPCLIFF.

2. If it is possible to cite those packages, I would recommend citing them in the paper. If not, I suspect that your approach thus far is good.

3. I've found one reviewer for this package but want one or two more. If you have recommendations, please let me know.

[kbarnhart]

@whedon assign @frengers as reviewer

[whedon]

OK, the reviewer is @frengers

[kbarnhart]

@frengers. Thanks for agreeing to review this. The review process is a bit different than other academic journals. The streamlined review process takes place on GitHub and focuses on the software and a very short paper.

This here is a pre-review issue. Once I've attracted sufficient reviewers I'll open a dedicated review issue where check-boxes guide you through the review process.

Once that has occurred, we generally request that reviewers try and complete their review in 2-3 weeks. Obviously many of us are at AGU right now, so I expect that the timeline for getting reviewers and getting reviews may be slightly stretched.

Let me know if you have questions.

[ryanpmcg]

@kbarnhart in response to your three points:

1. Thank you. The tests are different for each system, and I do not know enough to make them identical for each. The OSX test is the better one (and the system I use most often). The Windows check does not use checksums because there are slight differences in the binary files produced in windows versus OSX from the same R code. So I just check the main output (.cli file) for any text differences with FC. If you or reviewers have suggestions to improve this, I would be glad to hear them.

2. I did not see examples in the 8-10 JOSS papers I read of dependencies being cited in the paper. That is what I based my decision on. I can always add a dependency section to the paper and discuss briefly how each package supports the tool.

3. WEPPCLIFF is the project that linked me to the two potential reviewers, so they may not be impartial in their reviews. Unfortunately, the few people I know that could be suitable reviewers all work with me on various projects. I am sorry that I am not able to help much on this.

[kbarnhart]

@ryanpmcg Thanks for the update. I've asked around for some review recommendations and have gotten some good ones. I'll be sending out review requests today and hope to get a total of three reviewers (two additional reviewers).

[kbarnhart]

:wave: @dvalters @tcoulthard would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

This is a pre-review issue that I use to coordinate reviewers. Once there are sufficient reviewers (usually 2-3), I will open a new issue where the review will take place.

If you are not able, please let me know if you have recommendations for other reviewers. Please recommend without mentioning a handle (e.g., you would refer to me as @ kbarnhart instead of @kbarnhart). This way we attempt to reduce the number of people who are subscribed to this thread.

[kbarnhart]

@ryanpmcg I wanted to touch base. I'm having a hard time finding additional reviewers who are able to review this. I suspect that this is in part because AGU was last week, most universities are ending their semester this week or last week, and the end of the year holidays are approaching. I've found one person who is appropriate and willing to review, and at minimum I'll need one more (ideally I try and get 3 reviewers, though sometimes this is not possible).

I want to propose that I take a break from looking for reviewers and restart in early January after people return from vacation/not-working time.

Is this OK with you?

In the meantime, can you look through this list of people to see if there are any people who look appropriate? Mention them here and put a space between the @ and their GitHub handle (e.g., you'd refer to me as @ kbarnhart).

[ryanpmcg]

@kbarnhart of course that is no problem, I expected things to be put on hold during the holidays. I am sorry for not replying sooner myself.

As for a second reviewer, you may try contacting Andrew.Fullhart@ars.usda.gov (he told me that he would be willing to review the software).

[kbarnhart]

@ryanpmcg thanks for the recommendation.

[kbarnhart]

@ryanpmcg I just wanted to touch base again and let you know that I am still actively seeking out reviewers for this submission. Unfortunately Andrew Fullhart has a conflict of interest for this submission, so I still need additional reviewers.

[ryanpmcg]

@kbarnhart thanks for the update. From the list of people, I have identified a few potentials with justification next to their names below:

@ KristinaRiemer -- lists R as preferred and interest in agriculture @ dlebauer -- same as above @ wjakethompson -- R preferred and interest in data management/workflow tools @ khaors -- R preferred and interest in environmental modeling/hydrogeology @ ha0ye -- R preferred and interest in time series analysis

WEPPCLIFF is a tool to process general time series climate inputs for agricultural/soil loss models like WEPP. Do you think any of these matches may work?

[kbarnhart]

@whedon add @stoor001 as reviewer

[whedon]

OK, @stoor001 is now a reviewer

[kbarnhart]

:wave: @KristinaRiemer @dlebauer @khaors would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

This is a pre-review issue that I use to coordinate reviewers. I'm looking for one more reviewer for this submission.

[kbarnhart]

:wave: @KristinaRiemer @dlebauer @khaors would you be willing to review this submission for JOSS?

[khaors]

Dear Katy:

Yes, I am available to review the paper. Please let me know how can I start the review process.

Thank & Regards,

Oscar

On Fri, Jan 17, 2020, 2:06 PM Katy Barnhart notifications@github.com wrote:

👋 @KristinaRiemer https://github.com/KristinaRiemer @dlebauer https://github.com/dlebauer @khaors https://github.com/khaors would you be willing to review this submission for JOSS?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1930?email_source=notifications&email_token=AFVHXLHEBEA5FCW5MKKL34DQ6H6UNA5CNFSM4JUJRDAKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEJIVJEQ#issuecomment-575755410, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFVHXLDK7NEDARGMKCJIPLLQ6H6UNANCNFSM4JUJRDAA .

[kbarnhart]

@khaors thanks for your willingness to review! @ryanpmcg thank you for your patience as I found suitable reviewers.

I will now start the official review issue which will provide additional instructions to @frengers, @stoor001 and @khaors for undertaking the review.

[kbarnhart]

@whedon add @khaors as reviewer

[whedon]

OK, @khaors is now a reviewer

[kbarnhart]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2029. Feel free to close this issue now!