[REVIEW]: PATATO: a Python photoacoustic tomography analysis toolkit

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@tomelse@AoifeHughes<!--end-editor-- Reviewers: @MengjieSHI, @ASK-DataScience Archive: 10.5281/zenodo.10255220

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/456eaf591244858915ad8730dcbc19d7"><img src="https://joss.theoj.org/papers/456eaf591244858915ad8730dcbc19d7/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/456eaf591244858915ad8730dcbc19d7/status.svg)](https://joss.theoj.org/papers/456eaf591244858915ad8730dcbc19d7)

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

@MengjieSHI & @ASK-DataScience, 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 @AoifeHughes 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 @MengjieSHI

📝 Checklist for @ASK-DataScience

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=0.15 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

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

Wordcount for paper.md is 1079

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:

MengjieSHI commented 1 year ago

Review checklist for @MengjieSHI

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/BohndiekLab/patato?
[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 (@tomelse) 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?

ASK-DataScience commented 1 year ago

Review checklist for @ASK-DataScience

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/BohndiekLab/patato?
[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 (@tomelse) 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?

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:

editorialbot commented 1 year ago

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

tomelse commented 1 year ago

@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?

AoifeHughes 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:

tomelse commented 1 year ago

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

editorialbot commented 1 year ago

Done! branch is now main

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:

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:

tomelse commented 1 year ago

@editorialbot check repository

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

Wordcount for paper.md is 1607

tomelse 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:

tomelse commented 1 year ago

@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!

AoifeHughes commented 1 year ago

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

AoifeHughes commented 1 year ago

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

AoifeHughes commented 1 year ago

@ASK-DataScience, @MengjieSHI ?

MengjieSHI commented 1 year ago

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

MengjieSHI commented 1 year ago

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

AoifeHughes commented 1 year ago

@ASK-DataScience ?

AoifeHughes commented 1 year ago

No worries @MengjieSHI 😄 thanks for your updates!

ASK-DataScience commented 1 year ago

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

AoifeHughes commented 1 year ago

@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.

ASK-DataScience commented 1 year ago

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

tomelse commented 1 year ago

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

MengjieSHI commented 1 year ago

@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!

tomelse commented 1 year ago

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

AoifeHughes commented 1 year ago

Hi @ASK-DataScience, how are you doing?

AoifeHughes commented 1 year ago

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

ASK-DataScience commented 1 year ago

@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.

AoifeHughes commented 1 year ago

@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.

ASK-DataScience commented 1 year ago

@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.

ASK-DataScience commented 1 year ago

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

ASK-DataScience commented 1 year ago

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

AoifeHughes commented 1 year ago

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

tomelse commented 1 year ago

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

ASK-DataScience commented 1 year ago

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

tomelse commented 1 year ago

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

tomelse commented 12 months ago

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

ASK-DataScience commented 11 months ago

@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.

AoifeHughes commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

openjournals / joss-reviews