editorialbot commented 1 year ago

Submitting author: !--author-handle-->@jansim@crvernon<!--end-editor-- Reviewers: @welch16, @danielruss Archive: 10.5281/zenodo.8276813

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/17140f53558e06a06479539e9c1b8c59"><img src="https://joss.theoj.org/papers/17140f53558e06a06479539e9c1b8c59/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/17140f53558e06a06479539e9c1b8c59/status.svg)](https://joss.theoj.org/papers/17140f53558e06a06479539e9c1b8c59)

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

@welch16 & @danielruss, 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 @crvernon 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 @danielruss

📝 Checklist for @welch16

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=0.21 s (288.4 files/s, 45559.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               32            629           1960           4033
Markdown                         9            166              0           1236
Rmd                              6            209            343            236
TeX                              1             22              0            231
SVG                              3              0             41            225
YAML                             5             18              9            161
CSS                              1              8              0             45
Dockerfile                       2             11              9             26
Bourne Shell                     2              5              7              7
-------------------------------------------------------------------------------
SUM:                            61           1068           2369           6200
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1197

editorialbot commented 1 year ago

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

OK DOIs

- 10.1109/CBMS.2014.79 is OK
- 10.1093/ije/dyg080 is OK
- 10.1515/jos-2016-0003 is OK
- 10.2478/jos-2019-0008 is OK
- 10.1007/s11943-018-0231-2 is OK
- 10.2478/jos-2021-0042 is OK
- 10.1111/rssa.12297 is OK
- 10.1093/jssam/smaa023 is OK
- 10.1515/jos-2017-0006 is OK
- 10.1136/oemed-2015-103152 is OK
- 10.1145/135226.135228 is OK

MISSING DOIs

- None

INVALID DOIs

- None

crvernon commented 1 year ago

👋 @jansim , @welch16 , and @danielruss - This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

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. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/5505 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.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

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:

danielruss commented 1 year ago

Review checklist for @danielruss

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/occupationMeasurement/occupationMeasurement?
[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 (@jansim) 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?

crvernon commented 1 year ago

:mega: MIDWEEK RALLY :mega:

:wave: @welch16 and @danielruss

@danielruss it looks like you have your checklist rolling! Keep up the good work and post an update to your progress here when you have a minute. Thanks!

@welch16 I don't yet see your reviewer checklist. Let me know if you have any questions on how to get started. Thanks!

welch16 commented 1 year ago

Review checklist for @welch16

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/occupationMeasurement/occupationMeasurement?
[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 (@jansim) 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?

crvernon commented 1 year ago

:wave: @jansim, @welch16, @danielrussn it looks like your reviews and feedback have all been accounted for.

@welch16, @danielruss at this point are you both satisfied that the submission has addressed any concerns to be fit for publication?

@jansim do you have any other tasks left to complete?

danielruss commented 1 year ago

@crvernon good to go

jansim commented 1 year ago

Thanks for the update @crvernon, I'm not aware of any tasks left open, but am still happy to do any further updates as necessary, the reviews have already been very helpful in improving the software & paper 👍️

crvernon commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1109/CBMS.2014.79 is OK
- 10.1093/ije/dyg080 is OK
- 10.1515/jos-2016-0003 is OK
- 10.2478/jos-2019-0008 is OK
- 10.1007/s11943-018-0231-2 is OK
- 10.2478/jos-2021-0042 is OK
- 10.1111/rssa.12297 is OK
- 10.1093/jssam/smaa023 is OK
- 10.1515/jos-2017-0006 is OK
- 10.1136/oemed-2015-103152 is OK
- 10.1145/135226.135228 is OK

MISSING DOIs

- None

INVALID DOIs

- None

crvernon 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:

crvernon commented 1 year 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.
[ ] 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)
[x] 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
[x] 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

crvernon commented 1 year ago

:wave: @jansim - It's not often that I don't have any additional feedback; especially related to the paper. But your work is very well done. Thank you for your attention to detail!

I am going to move forward with getting this paper ready for acceptance.

We want to make sure the archival has the correct metadata that JOSS requires. This includes a title that matches the paper title and a correct author list.

So here is what we have left to do:

[ ] Conduct a GitHub release of the current reviewed version of the software you now have on the main and archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) to ensure it 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

I can then move forward with accepting the submission.

jansim commented 1 year ago

Thanks @crvernon ! It seems that the CRAN team is on vacation, so I will only be able to make a new release after August 3rd, but will get back to this then 😊

crvernon commented 1 year ago

👋 @jansim - just following up on the above. We you able to get the new release generated? Thanks!

jansim commented 1 year ago

Hey @crvernon, sorry for the delay! I'm currently waiting to hear back from CRAN, regarding the new release and will hopefully be able to get it through soon. Will let you know ASAP once we hear back from them 👍️

jansim commented 1 year ago

Hey @crvernon , so we heard back from CRAN and after some investigation, the issue seems to be related to a recent change in their test environment settings in regards to parallel processing. Since the code that does the parallel processing actually lies in other packages (which we only happen to be using), I would suggest to make a release of the current version of the package right now and use this for the paper and we will then upload that release (or a slightly updated one) to CRAN later on once these other packages had some time to deal with the issue.

I wrote a more detailed description of the situation in the issue we use to track the new CRAN release: https://github.com/occupationMeasurement/occupationMeasurement/issues/8.

If you're OK with this, I can get the new Zenodo release done any time 😊

crvernon commented 1 year ago

@jansim this sounds reasonable to me. Just send over the new Zenodo release here along with the new version number and we can move forward. Thanks!

jansim commented 1 year ago

Perfect, thanks! Here you go:

crvernon commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1109/CBMS.2014.79 is OK
- 10.1093/ije/dyg080 is OK
- 10.1515/jos-2016-0003 is OK
- 10.2478/jos-2019-0008 is OK
- 10.1007/s11943-018-0231-2 is OK
- 10.2478/jos-2021-0042 is OK
- 10.1111/rssa.12297 is OK
- 10.1093/jssam/smaa023 is OK
- 10.1515/jos-2017-0006 is OK
- 10.1136/oemed-2015-103152 is OK
- 10.1145/135226.135228 is OK

MISSING DOIs

- None

INVALID DOIs

- None

crvernon 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:

crvernon commented 1 year ago

@jansim the name and authors of the minted record on Zenodo has to match the name and authors of the paper exactly. Will you edit the name of your 10.5281/zenodo.8276813 archive?

jansim commented 1 year ago

Ahh so you're saying we can't rename the Zenodo archive?

crvernon commented 1 year ago

That's right, your Zenodo archive title should match that of your paper.

crvernon commented 1 year ago

So instead of:

occupationMeasurement/occupationMeasurement: occupationMeasurement 0.3.0 (not on CRAN): JOSS release

You would need:

occupationMeasurement: A Comprehensive Toolbox for Interactive Occupation Coding in Surveys

jansim commented 1 year ago

Done, I also updated the list of authors to match ✅

Thanks for the explanation!

crvernon commented 1 year ago

@editorialbot set 10.5281/zenodo.8276813 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.8276813

crvernon commented 1 year ago

@editorialbot v0.3.0 as version

editorialbot commented 1 year ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

crvernon commented 1 year ago

Thanks to @jansim for putting out a great software product and for @welch16 @danielruss submitting a timely and constructive review! I am now recommending that your submission be accepted for publication. An editor in chief will conduct a final pass shortly to finalize the process.

crvernon commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1109/CBMS.2014.79 is OK
- 10.1093/ije/dyg080 is OK
- 10.1515/jos-2016-0003 is OK
- 10.2478/jos-2019-0008 is OK
- 10.1007/s11943-018-0231-2 is OK
- 10.2478/jos-2021-0042 is OK
- 10.1111/rssa.12297 is OK
- 10.1093/jssam/smaa023 is OK
- 10.1515/jos-2017-0006 is OK
- 10.1136/oemed-2015-103152 is OK
- 10.1145/135226.135228 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/sbcs-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4503, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

jansim commented 1 year ago

Awesome, thank you for all your help @crvernon and the great reviews @welch16 @danielruss 🙏🙏

oliviaguest commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

Doing it live! Attempting automated processing of paper acceptance...

editorialbot commented 1 year ago

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Simson given-names: Jan orcid: "https://orcid.org/0000-0002-9406-7761" - family-names: Kononykhina given-names: Olga - family-names: Schierholz given-names: Malte orcid: "https://orcid.org/0000-0003-4058-1543" contact: - family-names: Simson given-names: Jan orcid: "https://orcid.org/0000-0002-9406-7761" doi: 10.5281/zenodo.8276813 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Simson given-names: Jan orcid: "https://orcid.org/0000-0002-9406-7761" - family-names: Kononykhina given-names: Olga - family-names: Schierholz given-names: Malte orcid: "https://orcid.org/0000-0003-4058-1543" date-published: 2023-08-24 doi: 10.21105/joss.05505 issn: 2475-9066 issue: 88 journal: Journal of Open Source Software publisher: name: Open Journals start: 5505 title: "occupationMeasurement: A Comprehensive Toolbox for Interactive Occupation Coding in Surveys" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05505" volume: 8 title: "occupationMeasurement: A Comprehensive Toolbox for Interactive Occupation Coding in Surveys" ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot commented 1 year ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 year ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/4507
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05505
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

oliviaguest commented 1 year ago

Congratulations and thank you, everybody! :blush:

editorialbot commented 1 year ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05505/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05505/status.svg
   :target: https://doi.org/10.21105/joss.05505

This is how it will look in your documentation:

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openjournals / joss-reviews

[REVIEW]: occupationMeasurement: A Comprehensive Toolbox for Interactive Occupation Coding in Surveys #5505

Status

Reviewer instructions & questions

Checklists

Review checklist for @danielruss

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @welch16

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