[REVIEW]: experDesign: helping performing experiments on batches

whedon commented 3 years ago

Submitting author: @llrs (Lluís Revilla Sancho) Repository: https://github.com/llrs/experDesign Version: v0.1.1 Editor: @lpantano Reviewer: @abartlett004, @stemangiola Archive: 10.5281/zenodo.5718051

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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

@abartlett004 & @stemangiola, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @lpantano 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 ✨

Review checklist for @abartlett004

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 repository url?
[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 (@llrs) 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 and who the target audience is?
[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?

Review checklist for @stemangiola

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 repository url?
[ ] 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 (@llrs) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[ ] 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.
[ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[ ] 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?
[ ] 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 and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[ ] 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?

llrs commented 3 years ago

Sorry for all the notifications, I think that now it is ready for publication. @lpantano I removed all the code and left only two plots and the scheme, the page length is still 5 pages though.

lpantano commented 2 years ago

Thank you, I think we can do a final edit. I would remove figure 1 and add the text under each tool section together with the bullet points you have there. I think that would leave a good structure to the paper, with enough information for the reader to go to other tools. You can leave a description in the text what is the difference with figure 1 without having the figure. Let me know if this makes sense to you, and after that I will accept it, whatever is the number of pages. Thanks!

llrs commented 2 years ago

@whedon generate pdf from branch paper

whedon commented 2 years ago

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

whedon 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:

llrs commented 2 years ago

@whedon generate pdf from branch paper

whedon commented 2 years ago

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

whedon 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:

llrs commented 2 years ago

@lpantano I agree with the changes, they makes sense and simplify the manuscript. I made a couple more of minor changes: adding links to my own software and thanking the reviewers and you for your time: Thanks!!

lpantano commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago

No archive DOI set. Exiting...

lpantano commented 2 years ago

Thank you! almost there, I forgot the last step :)

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.

I can then move forward with accepting the submission. Almost there!

llrs commented 2 years ago

After merging the paper branch with the main branch of the software I made a tagged release with version: 0.1.1. I updated archive on Zenodo at: https://doi.org/10.5281/zenodo.5718051 (I copied the title and author's data copied from the manuscript). I haven't submitted the new version of the package to CRAN, let me know if this is also needed.

lpantano commented 2 years ago

@whedon set 10.5281/zenodo.5718051 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5718051 is the archive.

lpantano commented 2 years ago

@whedon set v0.1.1 as version

whedon commented 2 years ago

OK. v0.1.1 is the version.

lpantano commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago

Attempting dry run of processing paper acceptance...

whedon commented 2 years ago

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

OK DOIs

- 10.1038/nrg2825 is OK
- 10.15252/embj.201592958 is OK
- 10.1371/journal.pone.0017238 is OK
- 10.1186/1471-2164-13-689 is OK
- 10.1093/bioinformatics/btab159 is OK
- 10.1038/nmeth.3091 is OK
- 10.1037/met0000301 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2768

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2768, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

llrs commented 2 years ago

@whedon generate pdf

whedon 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:

llrs commented 2 years ago

Hi, many thanks for accepting the manuscript. I noticed that when merging the branches the flow chart has disappeared from the pdf. Not sure how to proceed as the preview shows the figure and I haven't modified that (till latest commit after releasing 0.1.1)

Kevin-Mattheus-Moerman commented 2 years ago

@llrs @lpantano I have proofread the paper and have inspected the archived software on ZENODO and found all to be in order. I will now proceed to accept this work in JOSS.

Kevin-Mattheus-Moerman commented 2 years ago

@whedon accept deposit=true

whedon commented 2 years ago

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

whedon commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 2 years 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/2771
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03358
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 2 years ago

@llrs congratulations on getting this work published in JOSS!

Thank you @abartlett004 and @stemangiola for your review efforts, and thank you @lpantano for editing this work!

whedon commented 2 years 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:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03358/status.svg)](https://doi.org/10.21105/joss.03358)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03358">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03358/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03358/status.svg
   :target: https://doi.org/10.21105/joss.03358

This is how it will look in your documentation:

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