[REVIEW]: tsp ("Teaspoon"): A library for ground temperature data

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@nicholas512@kbarnhart<!--end-editor-- Reviewers: @Elchin, @mdpiper Archive: 10.5281/zenodo.7121289

Status

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Markdown: [![status](https://joss.theoj.org/papers/4c4a5818941114c3814810634032cee5/status.svg)](https://joss.theoj.org/papers/4c4a5818941114c3814810634032cee5)

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

@Elchin & @mdpiper, 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 @kbarnhart 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 @mdpiper

📝 Checklist for @Elchin

editorialbot commented 2 years ago

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 commented 2 years ago

Software report:

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gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 1334

editorialbot commented 2 years ago

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

OK DOIs

- 10.5194/gmd-11-2475-2018 is OK
- 10.5334/dsj-2020-006 is OK
- 10.22215/pn/10120001 is OK
- 10.5194/essd-7-245-2015 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.5281/zenodo.3509134 is OK
- 10.1073/pnas.2100163118 is OK
- 10.5194/gmd-12-4443-2019 is OK
- 10.1038/s43017-021-00247-8 is OK
- 10.1016/S1366-7017(01)00066-6 is OK
- 10.1038/sdata.2016.18 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

kbarnhart commented 2 years ago

👋🏼 @Elchin and @mdpiper this is the review thread for the paper. All of our communications about this review will happen here from now on.

At the top of the thread is https://github.com/openjournals/joss-reviews/issues/4704#issue-1348227281 a comment with key information about the review process. Please read it carefully. If you have issues as you go about your review, let me know, and I'll provide guidance and assistance.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository https://gitlab.com/permafrostnet/teaspoon. When doing so, please mention openjournals/joss-reviews/issues/4704 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

I'll set an automatic reminder for four weeks from now.

Please feel free to ping me (@krbarnhart or krbarnhart@usgs.gov) if you have any questions/concerns.

Thank you for contributing a review to JOSS.

kbarnhart commented 2 years ago

@editorialbot remind @Elchin in four weeks

editorialbot commented 2 years ago

Reminder set for @Elchin in four weeks

kbarnhart commented 2 years ago

@editorialbot remind @mdpiper in four weeks

editorialbot commented 2 years ago

Reminder set for @mdpiper in four weeks

mdpiper commented 2 years ago

Review checklist for @mdpiper

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://gitlab.com/permafrostnet/teaspoon?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@nicholas512) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

Elchin commented 2 years ago

Review checklist for @Elchin

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://gitlab.com/permafrostnet/teaspoon?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@nicholas512) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

mdpiper commented 2 years ago

Opened issues #7, #8, and #9 in the target repository, which @nicholas512 has resolved and closed.

editorialbot commented 2 years ago

:wave: @Elchin, please update us on how your review is going (this is an automated reminder).

editorialbot commented 2 years ago

:wave: @mdpiper, please update us on how your review is going (this is an automated reminder).

kbarnhart commented 2 years ago

@Elchin and @mdpiper - I see you have both started your reviews, and have also started opening issues in the main repository. Thank you!

If you could write a quick update here indicating when you anticipate completing your review, that would be excellent. Completing your review doesn't mean you need to have checked off every checkbox in the above lists... If there are checkboxes that you do not think can be checked yet, make an issue in the source repository indicating why, or make a comment here.

Let me know if you have any questions.

mdpiper commented 2 years ago

👋 @kbarnhart One last issue (#13) in the manuscript repo. Once it's addressed by the author, my review will be complete.

mdpiper commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

nicholas512 commented 2 years ago

I just noticed a small error in the inline citations. This has been fixed.

@editorialbot generate pdf

danielskatz commented 2 years ago

@editorialbot generate pdf

a command needs to be the first thing in a comment...

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mdpiper commented 2 years ago

@kbarnhart My review is complete. A summary note: this is a tidy, well-focused package, perfect for JOSS. Years ago, I worked with snow temperature profile data from Campbell Scientific CR-10 dataloggers. This package would have been helpful!

nicholas512 commented 2 years ago

Thanks for the review @mdpiper!

Elchin commented 2 years ago

Hi @nicholas512, I am almost done with my reviews, just waiting for you to address my comments.

nicholas512 commented 2 years ago

Thanks for letting me know @Elchin - I didn't get notified on github. I'll take a look at those.

arfon commented 2 years ago

Thanks for the feedback in this issue @Elchin (https://github.com/openjournals/joss-papers/issues/3518). We ideally would like review comments to be posted either here and/or on the software repo directly (https://gitlab.com/permafrostnet/teaspoon).

I'm going to close https://github.com/openjournals/joss-papers/issues/3518 but just wanted to reinforce that I'm grateful for the review but am simply cleaning upon the joss-papers issues.

kbarnhart commented 2 years ago

@Elchin and @mdpiper thank you for these reviews. Sorry that I also missed your review comment @Elchin. I'll paste the contents in the tsp repository shortly.

@nicholas512 - when you have completed addressing all reviewer comments, please ping me. I'll review the changes and then ask the reviewers to revisit their reviews.

kbarnhart commented 2 years ago

I've placed @Elchin 's comments here: https://gitlab.com/permafrostnet/teaspoon/-/issues/14

Elchin commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Elchin commented 2 years ago

@kbarnhart my review is done. I will be leaving it up to @nicholas512 if he wants to include gap-filling and QA/QC process discussion in the paper. @nicholas512 please copy-paste your responses here https://gitlab.com/permafrostnet/teaspoon/-/issues/14. Thank you!

nicholas512 commented 2 years ago

Thanks everyone. I've copied the responses and added an abridged version of the discussion in this commit.

@kbarnhart - I'm ready for you to review the changes and confirm the changes with the reviewers

kbarnhart commented 2 years ago

@editorialbot check references

kbarnhart commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

OK DOIs

- 10.5194/gmd-11-2475-2018 is OK
- 10.5334/dsj-2020-006 is OK
- 10.22215/pn/10120001 is OK
- 10.5194/essd-7-245-2015 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.5281/zenodo.3509134 is OK
- 10.1073/pnas.2100163118 is OK
- 10.5194/gmd-12-4443-2019 is OK
- 10.1038/s43017-021-00247-8 is OK
- 10.1016/S1366-7017(01)00066-6 is OK
- 10.1038/sdata.2016.18 is OK
- 10.5194/gmd-13-2825-2020 is OK
- 10.5194/gmd-7-2831-2014 is OK
- 10.5194/essd-10-2311-2018 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

kbarnhart commented 2 years ago

@Elchin and @mdpiper , thank you for your reviews. I have looked at the reviews, @nicholas512's responses, and the changes to the code base and paper. I've concluded that @nicholas512 has responded sufficiently. Please revisit your review, check any remaining checkboxes (@mdpiper you have one remaining) and make a comment on this thread confirming that you think this submission can move forward to the final steps before publication.

I do want to clarify a comment from you @Elchin. When you wrote

Overall, it is a timely and important software that still requires a lot of work due heterogeneity of the permafrost datasets. However, this is the first substantial attempt in the right direction. Standardization of the data collection and processing procedures are required to make this software universal.

Do you mean that the software requires a lot of work to publish in JOSS or to fully realize the goal of standardizing permafrost data collection and processing procedures. I think that you mean the later because you indicate that this is "the first substantial attempt" and also indicated in the checklist that this submission met the substantial scholarly effort criterion.

@nicholas512, at the same time that the reviewers are revisiting their reviews, I have a few minor editorial comments to address.

L48. Comma around "indeed" and misspelling of "heterogeneity"
L90. I think "In the case" should be "For"
L94 and 103. "which" should be "that"
L109&10. Consider "of ground temperature time series from both sensor data and model output."

mdpiper commented 2 years ago

@kbarnhart This submission can move forward.

nicholas512 commented 2 years ago

@kbarnhart : Thanks for catching those issues; I've made the changes in commit cd74fb9a

Elchin commented 2 years ago

@kbarnhart I mean the latter. As I mentioned in my comments, the permafrost data are not ground temperatures only. It is more diverse and requires acknowledgment of this fact. That said it would be nice to think about how the current product could be possibly extended to address a more diverse data spectrum.

kbarnhart commented 2 years ago

@Elchin thanks for the clarification. Much appreciated.

kbarnhart commented 2 years ago

@nicholas512 at this point could you:

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here.

At that point I will update the paper metadata and recommend the submission be accepted. At that point one of the JOSS EIC's will handle final processing.

nicholas512 commented 2 years ago

@kbarnhart

Tagged release created (version 1.3.1)
Reviewed software archived on Zenodo
Metadata is correct
- title: tsp ("Teaspoon"): A library for ground temperature data
- author: Nicholas Brown
- ORCID: 0000-0002-2719-0671
DOI of archived version is https://doi.org/10.5281/zenodo.7121289

kbarnhart commented 2 years ago

@editorialbot check references

kbarnhart commented 2 years ago

@editorialbot generate pdf

kbarnhart commented 2 years ago

@editorialbot set 10.5281/zenodo.7121289 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.7121289

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

kbarnhart commented 2 years ago

@editorialbot set v1.3.1 as version

openjournals / joss-reviews