@AoifeHughes I finished my checklist. All the comments have been well addressed. I would recommend accepting it for publication.

@tomelse Thanks for your contributions to the community!

from joss-reviews.

@tomelse could you assist with the above author tasks, DOI etc.

from joss-reviews.

@editorialbot set 10.5281/zenodo.10255220 as archive

from joss-reviews.

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

from joss-reviews.

@tomelse congratulations on this JOSS publiction

Thanks for editing this one @AoifeHughes.

And a special thank you to the reviewers: @MengjieSHI, @ASK-DataScience !!!!

from joss-reviews.

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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.05686/status.svg)](https://doi.org/10.21105/joss.05686)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05686">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05686/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05686/status.svg
   :target: https://doi.org/10.21105/joss.05686

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

from joss-reviews.

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

from joss-reviews.

Software report:

github.com/AlDanial/cloc v 1.88  T=0.15 s (1114.9 files/s, 181381.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          92           1851           1425           6291
XML                              4              0              0           3682
SVG                              4             21              4           2465
Jupyter Notebook                12              0           7470            702
TeX                              2             27              0            348
C++                              2             58             80            312
CUDA                             2             50             46            311
JSON                            19              1              0            261
YAML                             5             19              9            201
reStructuredText                13            121            196            143
Markdown                         3             56              0            136
TOML                             1             11              2             75
OpenCL                           2              8              9             71
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           163           2235           9249          15033
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

from joss-reviews.

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

OK DOIs

- 10.1158/0008-5472.CAN-18-1033 is OK
- 10.1109/TMI.2021.3090857 is OK
- 10.3390/s130607345 is OK
- 10.48550/ARXIV.2206.08612 is OK
- 10.1038/s41598-021-97726-1 is OK
- 10.1088/1361-6463/ABC37D is OK
- 10.2967/jnumed.116.182311 is OK

MISSING DOIs

- None

INVALID DOIs

- None

from joss-reviews.

Wordcount for paper.md is 1079

from joss-reviews.

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

from joss-reviews.

Review checklist for @MengjieSHI

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/BohndiekLab/patato?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@tomelse) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

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

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• 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

• 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, who the target audience is, and its relation to other work?
• 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)?
• 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?

from joss-reviews.

Review checklist for @ASK-DataScience

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/BohndiekLab/patato?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@tomelse) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

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

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• 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

• 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, who the target audience is, and its relation to other work?
• 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)?
• 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?

from joss-reviews.

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

from joss-reviews.

Hello @tomelse, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

from joss-reviews.

@AoifeHughes it looks like the paper PDF is an old version of the paper. Do you know why that would be? If you look at the current version, which is how I intended to submit it (https://github.com/BohndiekLab/patato/blob/main/paper/paper.md), the figures have been updated compared to the proof above. Would you be able to help fix this please?

from joss-reviews.

@editorialbot generate pdf

from joss-reviews.

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

from joss-reviews.

Still looks like the wrong version? Not sure why...

Note, the GitHub action compiles with the correct version on the repo: https://github.com/BohndiekLab/patato/actions/runs/5671505993

from joss-reviews.

Done! branch is now main

from joss-reviews.

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

from joss-reviews.

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

from joss-reviews.

@editorialbot check repository

from joss-reviews.

Software report:

github.com/AlDanial/cloc v 1.88  T=0.14 s (1105.4 files/s, 180453.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          92           1851           1425           6291
XML                              2              0              0           2494
SVG                              4             21              4           2465
Jupyter Notebook                12              0           8295            702
C++                              2             58             80            312
CUDA                             2             50             46            311
JSON                            19              1              0            261
TeX                              1             14              0            235
YAML                             5             19              9            201
reStructuredText                13            121            199            143
Markdown                         2             37              0             81
TOML                             1             11              2             75
OpenCL                           2              8              9             71
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           159           2203          10077          13677
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

from joss-reviews.

Wordcount for paper.md is 1607

from joss-reviews.

@editorialbot generate pdf

from joss-reviews.

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

from joss-reviews.

@AoifeHughes @ASK-DataScience @MengjieSHI
Apologies for all the spam above. Please find the correct PDF for the article in the comment directly above this one. For some reason it was compiling a very old version previously. Thanks!

from joss-reviews.

Hmm, strange. Sorry about that @tomelse. Glad it's resolved now, let me know if any other issues!

from joss-reviews.

Hi @ASK-DataScience, @MengjieSHI , could I just check in and see how the reviews are going?

from joss-reviews.

@ASK-DataScience, @MengjieSHI ?

from joss-reviews.

Hi Aoife. Sorry for missing your message. I was back from the leave and will proceed in the following week.

from joss-reviews.

Hi @tomelse I created an issue regarding the errors when running the tests. Thanks!

from joss-reviews.

@ASK-DataScience ?

from joss-reviews.

No worries @MengjieSHI 😄 thanks for your updates!

from joss-reviews.

@AoifeHughes so sorry for the delay, I was very sick. Will resume working on the review this week.

from joss-reviews.

@ASK-DataScience no worries. Thanks for letting me know. Prioritise your own health please. Reviews can always wait, there is no pressure from our end on this. Just let me know if I can support you in anyway.

from joss-reviews.

@AoifeHughes thank you so much. I really appreciate it.

from joss-reviews.

Likewise @ASK-DataScience glad to hear you're doing okay, and thanks for taking the time to review the paper!

from joss-reviews.

Thanks so much for your time and for your helpful comments, @MengjieSHI!

from joss-reviews.

Hi @ASK-DataScience, how are you doing?

from joss-reviews.

Sorry to ping again @ASK-DataScience, do let me know if you'd like me to find another reviewer.

from joss-reviews.

@AoifeHughes I apologize for this delay. A lot of health issues lately. I will do my best to finish the review this week. Again, I am so sorry for the delay.

from joss-reviews.

@ASK-DataScience it's no problem, please make yourself the priority and if you'd like to step-down from reviewing that is completely fine, just let me know and I'll sort everything out. Again, just to reiterate, look after your own wellbeing and don't feel pressured to complete your review.

Please let me know if I can support you in anyway, or if you want to have a private conversation then feel free to email me directly.

from joss-reviews.

@AoifeHughes thank you so much for your understanding. I am working on my checklist and will continue to work throughout the weekend as well. Will keep you updated!
@tomelse so sorry for the delay.

from joss-reviews.

Hi @tomelse, I created an issue regarding running the speed of sound command on the command line. Thanks!

from joss-reviews.

Hi @tomelse, I created another issue regarding the unit tests. Thanks!

from joss-reviews.

Thanks for the progress @ASK-DataScience, @tomelse is addressing these points going okay?

from joss-reviews.

Thanks yes I've addressed the issues - I'm just waiting for a reply to diagnose an issue on Windows.

from joss-reviews.

Thank you @AoifeHughes and thank you @tomelse for your help with the last issue. I will be running examples next.

from joss-reviews.

@ASK-DataScience please let me know if you have any issues running the examples and I can try and debug.

from joss-reviews.

@ASK-DataScience @AoifeHughes do you think we could try and push this forward? I think it's only one more checkbox to complete 😅

from joss-reviews.

@AoifeHughes I finished my checklist. I would recommend accepting it for publication.
@tomelse I ran the examples without issues. Thank you for your help and patience.

from joss-reviews.

@editorialbot generate pdf

from joss-reviews.

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

from joss-reviews.

Thanks everyone :)

from joss-reviews.

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

• Read the text of the paper and offer comments/corrections (as either a list or a PR)
• 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
• Set archive DOI with @editorialbot set <DOI here> as archive
• Set version with @editorialbot set <version here> as version
• Double check rendering of paper with @editorialbot generate pdf
• Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• Recommend acceptance with @editorialbot recommend-accept

from joss-reviews.

@editorialbot check references

from joss-reviews.

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

OK DOIs

- 10.1098/rsfs.2011.0028 is OK
- 10.1242/dmm.039636 is OK
- 10.17863/CAM.93181 is OK
- 10.1038/s41598-021-83405-8 is OK
- 10.1117/1.JBO.27.8.083010 is OK
- 10.1117/1.JBO.24.12.121914 is OK
- 10.1117/1.JBO.26.8.085001 is OK
- 10.1038/s41598-021-97726-1 is OK
- 10.3390/biomedicines9050483 is OK
- 10.1088/1361-6463/ABC37D is OK
- 10.1016/j.pacs.2019.05.001 is OK
- 10.1158/0008-5472.CAN-18-1033 is OK
- 10.1126/science.1216210 is OK
- 10.1103/PhysRevE.71.016706 is OK

MISSING DOIs

- None

INVALID DOIs

- None

from joss-reviews.

Here is the release: https://github.com/BohndiekLab/patato/releases/tag/0.5.13 (version 0.5.13). I will look at the rest of the tasks today. Thanks!

from joss-reviews.

@editorialbot generate pdf

from joss-reviews.

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

from joss-reviews.

Here is the DOI for the code archive: 10.5281/zenodo.10255220

I can confirm that all of my checklist is complete. Thanks!

from joss-reviews.

Done! archive is now 10.5281/zenodo.10255220

from joss-reviews.

@AoifeHughes is there anything else I need to do for this? I'm going to be on holiday soon and it would be nice to get everything done before the new year.

from joss-reviews.

Hello, sorry to pester you again, but it seems there isn't very much less to complete the review for this paper. Would you be able to look at this in the next few days?
Thanks

from joss-reviews.

@Kevin-Mattheus-Moerman @AoifeHughes I'm sorry to keep bothering you, but it's now been over a month since I last heard anything regarding the review process for this paper. It seems that almost everything is complete. Please again let me know if there is anything I can do to help. Thank you.

from joss-reviews.

@tomelse sorry for the delays encountered here. I'll inquire to see why @AoifeHughes hasn't responded to date.

For the moment, since the review is finalised and steps were taken towards acceptance, I will assign myself as editor now, and take over to speed things along. Once again, our apologies for the delay.

from joss-reviews.

@editorialbot assign me as editor

from joss-reviews.

Assigned! @Kevin-Mattheus-Moerman is now the editor

from joss-reviews.

@editorialbot set 0.5.13 as version

from joss-reviews.

Done! version is now 0.5.13

from joss-reviews.

@editorialbot recommend-accept

from joss-reviews.

Attempting dry run of processing paper acceptance...

from joss-reviews.

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

OK DOIs

- 10.1098/rsfs.2011.0028 is OK
- 10.1242/dmm.039636 is OK
- 10.17863/CAM.93181 is OK
- 10.1038/s41598-021-83405-8 is OK
- 10.1117/1.JBO.27.8.083010 is OK
- 10.1117/1.JBO.24.12.121914 is OK
- 10.1117/1.JBO.26.8.085001 is OK
- 10.1038/s41598-021-97726-1 is OK
- 10.3390/biomedicines9050483 is OK
- 10.1088/1361-6463/ABC37D is OK
- 10.1016/j.pacs.2019.05.001 is OK
- 10.1158/0008-5472.CAN-18-1033 is OK
- 10.1126/science.1216210 is OK
- 10.1103/PhysRevE.71.016706 is OK

MISSING DOIs

- None

INVALID DOIs

- None

from joss-reviews.

👋 @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4918, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

from joss-reviews.

@tomelse As AEiC I will now help to process this work for acceptance. I have checked your repository, the paper, this review, and the archive link. Most seems in order. I only have the below minor point that requires your attention:

• Please spell out UK as United Kingdom in your affiliations.

from joss-reviews.

Thank you for responding so quickly, I have updated the affiliation as requested in the main branch of the repository.

from joss-reviews.

@editorialbot generate pdf

from joss-reviews.

Looks good to me :)

from joss-reviews.

@tomelse yes. All looks good to proceed now. Sorry again for the delay. I myself was out for a long break over the holidays, so perhaps @AoifeHughes was too. And a lot of us are battling the start of a new semester. Having said that we should have checked in at least to respond, so apologies for that. Either way, good to see we were able to wrap this us in a smooth fashion now.

from joss-reviews.

@editorialbot accept

from joss-reviews.

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

from joss-reviews.

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:

cff-version: "1.2.0"
authors:
- family-names: Else
  given-names: Thomas R.
  orcid: "https://orcid.org/0000-0002-2652-4190"
- family-names: Gröhl
  given-names: Janek
  orcid: "https://orcid.org/0000-0002-5332-4856"
- family-names: Hacker
  given-names: Lina
  orcid: "https://orcid.org/0000-0001-5160-0952"
- family-names: Bohndiek
  given-names: Sarah E.
  orcid: "https://orcid.org/0000-0003-0371-8635"
contact:
- family-names: Bohndiek
  given-names: Sarah E.
  orcid: "https://orcid.org/0000-0003-0371-8635"
doi: 10.5281/zenodo.10255220
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Else
    given-names: Thomas R.
    orcid: "https://orcid.org/0000-0002-2652-4190"
  - family-names: Gröhl
    given-names: Janek
    orcid: "https://orcid.org/0000-0002-5332-4856"
  - family-names: Hacker
    given-names: Lina
    orcid: "https://orcid.org/0000-0001-5160-0952"
  - family-names: Bohndiek
    given-names: Sarah E.
    orcid: "https://orcid.org/0000-0003-0371-8635"
  date-published: 2024-01-19
  doi: 10.21105/joss.05686
  issn: 2475-9066
  issue: 93
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5686
  title: "PATATO: a Python photoacoustic tomography analysis toolkit"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05686"
  volume: 9
title: "PATATO: a Python photoacoustic tomography analysis toolkit"

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.

from joss-reviews.

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

from joss-reviews.

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#4928
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05686
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

from joss-reviews.

@editorialbot set @AoifeHughes as editor

from joss-reviews.

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

@editorialbot commands

from joss-reviews.

Just setting @AoifeHughes back as editor, as she did most of editorial work and should be the one listed on the paper.

from joss-reviews.

@editorialbot assign @AoifeHughes as editor

from joss-reviews.

Assigned! @AoifeHughes is now the editor

from joss-reviews.

@editorialbot re-accept

from joss-reviews.

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

@editorialbot commands

from joss-reviews.

@editorialbot reaccept

from joss-reviews.

Rebuilding paper!

from joss-reviews.

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#4933

from joss-reviews.