editorialbot commented 1 year ago

Submitting author: !--author-handle-->@sebastien-plutniak@oliviaguest<!--end-editor-- Reviewers: @bischrob, @nevrome, @joeroe Archive: 10.5281/zenodo.10200892

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/ec7d14809161bb21d0e258742e64f131/status.svg)](https://joss.theoj.org/papers/ec7d14809161bb21d0e258742e64f131)

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

@bischrob & @nevrome & @joeroe, 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 @oliviaguest 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 @bischrob

📝 Checklist for @joeroe

📝 Checklist for @nevrome

editorialbot commented 1 year 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 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (1425.5 files/s, 308391.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               46            664            317           6621
Markdown                         5            510              0           2117
TeX                              1             29              0            182
Rmd                              3            569           1050            141
YAML                             2              6             13            112
-------------------------------------------------------------------------------
SUM:                            57           1778           1380           9173
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1386

editorialbot commented 1 year ago

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

OK DOIs

- 10.1201/9780429447273 is OK
- 10.3406/bspf.2019.14988 is OK
- 10.1007/s12520-022-01667-3 is OK
- 10.14434/sdh.v2i2.24446 is OK
- 10.1109/DigitalHeritage.2015.7419505 is OK
- 10.5281/zenodo.8092474 is OK
- 10.5334/jcaa.81 is OK
- 10.1201/9781315370279 is OK
- 10.1007/978-3-319-24277-4 is OK
- 10.5281/zenodo.7674698 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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:

joeroe commented 1 year ago

Review checklist for @joeroe

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://github.com/sebastien-plutniak/archeoviz?
[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 (@sebastien-plutniak) 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?

oliviaguest commented 1 year ago

:wave: Hi @bischrob, @nevrome, @joeroe, thank you so much for helping out at JOSS. If you need any pointers, please feel free to look at previous reviews (which can be found by looking at published papers) and the documentation. If you need to comment on the code itself, opening an issue at the repo and then linking to it from here (to help me/others keep track) is the way to go. For comments on the paper, you can also open issues or PRs (say for typos), but those can be directly posted as replies in this issue. Thanks, and feel free to reach out if you need me. :relaxed:

bischrob commented 1 year ago

Review checklist for @bischrob

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://github.com/sebastien-plutniak/archeoviz?
[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 (@sebastien-plutniak) 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?

bischrob commented 1 year ago

@oliviaguest -- the submitting author was a visiting scholar at my institution (Arizona State University) last summer. We met for lunch to discuss our similar interests but worked in different organizations and have not collaborated. I do not consider this a conflict of interest. Can you confirm?

oliviaguest commented 1 year ago

@bischrob sorry for taking so long to get back to you. Meeting for lunch is not a CoI, indeed.

bischrob commented 1 year ago

@oliviaguest No worries, thanks!

nevrome commented 1 year ago

Review checklist for @nevrome

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://github.com/sebastien-plutniak/archeoviz?
[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 (@sebastien-plutniak) 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?

bischrob commented 1 year ago

@oliviaguest My review is complete. The paper and software are of excellent quality. There were just a couple of minor revisions with a reference and some typos I noted here https://github.com/sebastien-plutniak/archeoviz/pull/13.

oliviaguest commented 1 year ago

@sebastien-plutniak let us know when you want the reviewers or me to have a look at any edits you have made.

sebastien-plutniak commented 1 year ago

Thank you very much @bischrob for the review, I have merged your edits. @oliviaguest , I have just edited the text and figures with some updates about changes in the software made since the first version of the paper. I hope I have not introduced new grammar errors!

oliviaguest commented 1 year ago

@sebastien-plutniak feel free to use the bot to compile and check your paper.

sebastien-plutniak 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:

sebastien-plutniak 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:

sebastien-plutniak 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:

sebastien-plutniak commented 1 year ago

@oliviaguest , I've checked the proofs, it looks fine to me!

joeroe commented 1 year ago

I've also completed my review, sorry for the delay. I didn't find any major issues and I think it the software is a great fit for JOSS. I'll certainly be looking into it as a way to publish my own site data in the future.

Some minor notes:

[ ] Given that the software has already been translated into six languages, I thought I might find some instructions for translating it into others in the contribution guidelines. Something to consider.
[ ] The formatting of inline citations in the latest proof doesn't look right to me.

oliviaguest commented 1 year ago

@joeroe thank you so much! I will let the authors enact their changes and we can come back to this when they have. Great stuff.

sebastien-plutniak commented 1 year ago

Thank you very much @joeroe for your review and suggestion, I will make these change and update the file. I have a question about:

* [ ]  The formatting of inline citations in the latest proof doesn't look right to me.

Sorry, but I do not see where there is an issue, can you be more specific please? (which line(s) number(s)? Thanks!

joeroe commented 12 months ago

In https://raw.githubusercontent.com/openjournals/joss-papers/joss.05811/joss.05811/10.21105.joss.05811.pdf, on line 8, the first set of citations read:

[...] communication of archaeological spatial data (Plutniak et al., 2023), (Plutniak, 2023).

Where I'd expect:

[...] communication of archaeological spatial data (Plutniak et al., 2023, Plutniak, 2023).

All the multiple citations are like this. But maybe it's just JOSS' style?

sebastien-plutniak commented 12 months ago

@editorialbot generate pdf

editorialbot commented 12 months ago

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

sebastien-plutniak commented 12 months ago

@editorialbot generate pdf

editorialbot commented 12 months ago

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

sebastien-plutniak commented 12 months ago

In https://raw.githubusercontent.com/openjournals/joss-papers/joss.05811/joss.05811/10.21105.joss.05811.pdf, on line 8, the first set of citations read:

[...] communication of archaeological spatial data (Plutniak et al., 2023), (Plutniak, 2023).

Where I'd expect:

[...] communication of archaeological spatial data (Plutniak et al., 2023, Plutniak, 2023).

All the multiple citations are like this. But maybe it's just JOSS' style?

@joeroe Yes, I agree, the formatting you suggest would be better, but it seems impossible in the JOSS style (I've checked the doc). Any suggestion @oliviaguest ?

Besides this formatting issue, I think the paper is ready for publication!

sebastien-plutniak commented 12 months ago

I've also completed my review, sorry for the delay. I didn't find any major issues and I think it the software is a great fit for JOSS. I'll certainly be looking into it as a way to publish my own site data in the future.

Some minor notes:
* [ ]  Given that the software has already been translated into six languages, I thought I might find some instructions for translating it into others in the contribution guidelines. Something to consider.

* [ ]  The formatting of inline citations in the latest proof doesn't look right to me.

@joeroe The guidelines now include a “Translation” section, thanks for the suggestion!

joeroe commented 12 months ago

@joeroe Yes, I agree, the formatting you suggest would be better, but it seems impossible in the JOSS style (I've checked the doc).

Have you tried e.g. [@Plutniak2023archeoviz1.3.2; @Plutniak2023bspf]?

sebastien-plutniak commented 12 months ago

@editorialbot generate pdf

editorialbot commented 12 months ago

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

sebastien-plutniak commented 12 months ago

@editorialbot generate pdf

editorialbot commented 12 months ago

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

sebastien-plutniak commented 12 months ago

@joeroe Yes, I agree, the formatting you suggest would be better, but it seems impossible in the JOSS style (I've checked the doc).

Have you tried e.g. [@Plutniak2023archeoviz1.3.2; @Plutniak2023bspf]?

No! I tried [@Plutniak2023archeoviz1.3.2, @Plutniak2023bspf] and the result was even worst. But with “;” it works well, thanks for the trick! Now it looks fine!

oliviaguest commented 11 months ago

@sebastien-plutniak is it looking better now? I think yes, but wanted to check with you. :relaxed:

sebastien-plutniak commented 11 months ago

@sebastien-plutniak is it looking better now? I think yes, but wanted to check with you. ☺️

Yes it looks fine!

oliviaguest commented 11 months ago

@sebastien-plutniak is there anything you need to change or change? Please feel free to do that and archive the code on zenodo or similar. And post the DOI here. 😊

sebastien-plutniak commented 11 months ago

@oliviaguest the paper is ready, I do not want to to do more change! The code is already archived on Zenodo, DOI: 10.5281/zenodo.7460193, or do you want me to create a new release related to the JOSS submission?

oliviaguest commented 11 months ago

@sebastien-plutniak it should be the version that was the result of the JOSS review process, does that make sense? Because the publication at JOSS is the result of the review at JOSS (not a previous, or of course future, version).

oliviaguest commented 11 months ago

If it is, then fine. 😊 And if not, I think you can make it be this version (or link to this version), right?

oliviaguest commented 11 months ago

This list can help:

[ ] 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.
[x] Please list the DOI of the archived version here.

I can then move forward with recommending acceptance of the submission. 🥳

oliviaguest commented 11 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[ ] Double check authors and affiliations (including ORCIDs)
[ ] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here.
[ ] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[ ] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
[x] Check the references in the paper for corrections (e.g. capitalization)
[ ] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[ ] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

sebastien-plutniak commented 11 months ago

thanks @oliviaguest for the guidance. I agree, it makes sense to link the paper to a specific version of the code. Consequently, I've just created a new record, with this specific DOI : https://doi.org/10.5281/zenodo.10200892.

oliviaguest commented 11 months ago

@sebastien-plutniak thank you. Can you ping me when these are all checked off?

sebastien-plutniak commented 11 months ago

@oliviaguest

the release version is v1.3.3 (doi: https://doi.org/10.5281/zenodo.10200892)
about: Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper. actually, different roles are distinguished:
in the CRAN taxinomy, I am the 'author' and 'creator'; 5 other people are mentioned as 'contributors' (they translated the app into other languages)
in the Zenodo archive, I am role = 'project leader' and the 5 other persons are included as role = 'other'
however, I am the only author of the JOSS paper. What do you think? Is it fine like it is?

openjournals / joss-reviews

[REVIEW]: archeoViz: an R package for the Visualisation, Exploration, and Web Communication of Archaeological Spatial Data #5811

Status

Reviewer instructions & questions

Checklists

Review checklist for @joeroe

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @bischrob

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @nevrome

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance