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[REVIEW]: SonoUno development: a User Centred Sonification software for data analysis #5819

Closed editorialbot closed 9 months ago

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@johicasado<!--end-author-handle-- (Johanna Casado) Repository: https://github.com/sonoUnoTeam/sonoUno-desktop Branch with paper.md (empty if default branch): master Version: 4.1.1 Editor: !--editor-->@ivastar<!--end-editor-- Reviewers: @ceb8, @james-trayford Archive: 10.5281/zenodo.10303871

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Markdown: [![status](https://joss.theoj.org/papers/3de1d3d23f457171356cb8b87fab8e8d/status.svg)](https://joss.theoj.org/papers/3de1d3d23f457171356cb8b87fab8e8d)

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

@ceb8 & @james-trayford, 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 @ivastar 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 @ceb8

📝 Checklist for @james-trayford

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:

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editorialbot commented 1 year ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.14 s (102.1 files/s, 68931.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          10            882           1853           6279
TeX                              1             20              0            184
Markdown                         2             66              0            144
YAML                             1              1              5             19
-------------------------------------------------------------------------------
SUM:                            14            969           1858           6626
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 1 year ago

Wordcount for paper.md is 1903

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1017/S1743921321000272 is OK
- 10.1007/978-3-030-77411-0_12 is OK
- 10.4018/jitr.2014010105 is OK
- 10.4018/IJCICG.2021010102 is OK
- 10.4018/978-1-5225-8539-8.ch002 is OK
- 10.21785/icad2021.031 is OK
- 10.1145/3136755.3136783 is OK
- 10.1051/epjconf/201920001013 is OK
- 10.4018/IJSKD.299048 is OK
- 10.11648/j.ajaa.20210904.11 is OK
- 10.1038/s41550-022-01721-z is OK
- 10.22201/ia.14052059p.2022.54.01 is OK
- 10.1093/astrogeo/atac027 is OK
- 10.1017/S174392132100079X 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:

ivastar commented 1 year ago

@ceb8, @james-trayford thank you for agreeing to review this submission! Check out the comment above for instructions on how to generate your checklist. We are looking for reviews to be completed ~ the end of September. Don't hesitate to contact me if you have any issues.

ceb8 commented 1 year ago

Review checklist for @ceb8

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

james-trayford commented 1 year ago

Review checklist for @james-trayford

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

ivastar commented 1 year ago

@ceb8 @james-trayford could we please look at wrapping the review in the next week or so? Let me know if there's anything I can help with.

james-trayford commented 1 year ago

@ivastar Yes definitely reasonable I think - I had to defer reviewing until this week due to unforeseen circumstances (hopefully you received my email)

ivastar commented 1 year ago

@james-trayford yes, I did, thank you for the heads up! Just pinging everyone here for visibility of the authors as well.

james-trayford commented 1 year ago

@johicasado I enjoyed exploring sonoUno and it's functionality, and think it represents a valuable tool in providing accessible sonification of 1D data (in the pitch-mapping tradition) for research applications. I congratulate the developers on their work and hope that the comments are constructive towards the future development of the code! I think the code works as represented in the submission and there are a few relatively minor things to complete the checklist.

I opened a related Issue here: https://github.com/sonoUnoTeam/sonoUno-desktop/issues/11

With some small code suggestions in the PR https://github.com/sonoUnoTeam/sonoUno-desktop/pull/10

My checklist quoted below with some explanations (@ivastar I was unsure if the check means that I have considered that aspect or that aspect has been deemed to already be met by the submission, have assumed the latter)

Review checklist for @james-trayford

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

General checks

I noticed that the current MIT license includes some extra text, I've included that in the PR https://github.com/sonoUnoTeam/sonoUno-desktop/pull/10

  • [x] Contribution and authorship: Has the submitting author (@johicasado) 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).

it would be good to package the SDSS example data with the code - I had problems with the SDSS server while going through instructions which meant I couldn't proceed. If this is included in the sample data, that could make things more convenient

  • [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?

The User guide document could use some proofreading, but is fully comprehensible. Perhaps some more extension on the Octave functionality or pointing to external relevant octave documentation would be helpful.

  • [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

I think more or less covered, but it might be good to make these three more explicit in e.g. the README

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?
  • [ ] 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?

The paper is clear and addresses all of these points in my opinion. One thing I think could be improved is mentioning some other codes that have emerged for sonification (e.g. astronify, strauss, starsound, and Desmos sonification capabilities) explicitly to better clarify how it fits into the software landscape and emphasise the unique aspects of sonoUno. I would think a unique aspect of sonoUno is the combination of being a dedicated GUI-based FOSS and platform independent python code, with the user centered design mentioned already.

ivastar commented 1 year ago

My checklist quoted below with some explanations (@ivastar I was unsure if the check means that I have considered that aspect or that aspect has been deemed to already be met by the submission, have assumed the latter)

@james-trayford, yes, this assumption is correct: a check means that the submission meets the requirements

johicasado commented 1 year ago

@james-trayford thank you very much for all your comments! I will go through the GitHub Issues shortly, thank you!

ivastar commented 1 year ago

@ceb8 a gentle reminder to complete the review. Thanks!

ceb8 commented 1 year ago

@johicasado This is clearly represents substantial effort and is a valuable contribution to the sonification landscape.

I have only minor comments which I intersperse with the relevant checklist items below.

Review checklist for @ceb8

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

General checks

  • [x] Repository: Is the source code for this software available at the https://github.com/sonoUnoTeam/sonoUno-desktop?

  • [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 (@johicasado) 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?

I first installed sonoUno from pip, however that version threw an error, so instead I installed from source which worked perfectly well. Perhaps this means a new pip release is in order.

  • [x] Functionality: Have the functional claims of the software been confirmed?

A few things I noticed:

  • [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).

While everything (installation instructions, user manual, github repo) is nicely linked from the sonoUno website, the website is not mentioned in the GitHub repo. I would be good to include that prominently, right at the top of the README file. Similarly after the installation instructions in the README it would be good to have a link to the user manual before diving into the bash mode instructions.

Also when the website is mentioned in the user manual itself the URL is not included (or at least in the English version, which was the one I looked at), and should be.

  • [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?

I don't know what this statement means:

“In the files to import the first column must have continuous values, it is used as a coordinate dependent axis.”

I think it means that the first column needs to be monotonically increasing or decreasing, but it could do with clarification. And if it does mean what I think then either the file(s) that do not conform to this format in the sample_data directory should be removed (sinsoidal_copia is the one I found), or there should be some explanation of the purpose of those example files.

  • [ ] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?

The user manual provides much of this functionality, but there are a few holes:

  • [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

In the documentation it indicates that users should communicate any issues to the development team (start of section 2), it would be good to include specific instructions on how.

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?

ivastar commented 1 year ago

@ceb8 thank you for the detailed review! @johicasado please let me know when you have been able to address the comments.

johicasado commented 1 year ago

@ceb8 Thank you very much for all your comments! I'll try to implement most of them shortly!

@ivastar Thank you very much for all!

johicasado commented 1 year ago

@ivastar How will we continue the review process? I have already started with the documentation to implement the recommendations. Do I have to indicate here the updates that solve the recommendations? or do I have to open an issue on GitHub?

ivastar commented 1 year ago

@johicasado you can make all changes to the library, documentation and paper and commit them to the repository. This will allow us to generate a new manuscript here. You don't have to open a new issue. Once the changes are made, please let us know here. The reviewers and I will check the changes.

johicasado commented 1 year ago

@ivastar Thank you very much! I will let you know shortly!

johicasado commented 11 months ago

I will explane the updates following the @james-trayford list:

@johicasado I enjoyed exploring sonoUno and it's functionality, and think it represents a valuable tool in providing accessible sonification of 1D data (in the pitch-mapping tradition) for research applications. I congratulate the developers on their work and hope that the comments are constructive towards the future development of the code! I think the code works as represented in the submission and there are a few relatively minor things to complete the checklist.

I opened a related Issue here: sonoUnoTeam/sonoUno-desktop#11

With some small code suggestions in the PR sonoUnoTeam/sonoUno-desktop#10 I attend this issue, merg the code suggestion and implement the issue as much as I can sonoUnoTeam/sonoUno-desktop#11

My checklist quoted below with some explanations (@ivastar I was unsure if the check means that I have considered that aspect or that aspect has been deemed to already be met by the submission, have assumed the latter)

Review checklist for @james-trayford

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

General checks

I noticed that the current MIT license includes some extra text, I've included that in the PR sonoUnoTeam/sonoUno-desktop#10

This was implemented.

  • [x] Contribution and authorship: Has the submitting author (@johicasado) 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).

it would be good to package the SDSS example data with the code - I had problems with the SDSS server while going through instructions which meant I couldn't proceed. If this is included in the sample data, that could make things more convenient

The SDSS file used on the User Manual was included on the data_sample folder.

  • [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?

The User guide document could use some proofreading, but is fully comprehensible. Perhaps some more extension on the Octave functionality or pointing to external relevant octave documentation would be helpful.

The link to Octave documentation was included inside the Octave section in the User Manual

  • [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

I think more or less covered, but it might be good to make these three more explicit in e.g. the README

Items included in the README.

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?
  • [ ] 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?

The paper is clear and addresses all of these points in my opinion. One thing I think could be improved is mentioning some other codes that have emerged for sonification (e.g. astronify, strauss, starsound, and Desmos sonification capabilities) explicitly to better clarify how it fits into the software landscape and emphasise the unique aspects of sonoUno. I would think a unique aspect of sonoUno is the combination of being a dedicated GUI-based FOSS and platform independent python code, with the user centered design mentioned already.

I update the paper taking into accound this recommendation on the next commit: https://github.com/sonoUnoTeam/sonoUno-desktop/commit/99d8196883b23bf134c3170c573492fd0a545558

Thank you very much for all your time and suggestions! If there is anything else, or if any issue is badly addressed, let me know, please.

johicasado commented 11 months ago

I will explane the updates following the @ceb8 list:

@johicasado This is clearly represents substantial effort and is a valuable contribution to the sonification landscape.

I have only minor comments which I intersperse with the relevant checklist items below.

Review checklist for @ceb8

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

General checks

  • [x] Repository: Is the source code for this software available at the https://github.com/sonoUnoTeam/sonoUno-desktop?
  • [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 (@johicasado) 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?

I first installed sonoUno from pip, however that version threw an error, so instead I installed from source which worked perfectly well. Perhaps this means a new pip release is in order.

I update the README to advice the problem with the pip installation, and don't recommend anymore in the README the pip installation.

  • [x] Functionality: Have the functional claims of the software been confirmed?

A few things I noticed:

  • I couldn't really detect a difference between the discrete and continuous sound options, perhaps the continuous notes were a little longer.

Yes, at the moment we are unable to found a better aproximation, if we allows loger notes the sound turns waired and it does not accurately represent the data.

  • For large data files even the fastest tempo went through the data quite slowly

Yes, the principal goal of sonoUno was allows data exploration, visual in conjuction to sound, so we prioratize the relation between the position red bar and the sound, that made us depend on the speed with which each frame is updated by the GUI, so we could't perform at the moment faster reproductions.

  • When you make a bunch of panels visible it sometimes causes the layout to do strange things and overlap panels

Yes, I include the posibility to go up and down inside the pannels, it makes complex the display to visual users, but makes accessible the tool to screen readers. The pop-up windows with interactions inside produce loss of focus with the use of screen readers and makes navigation with said tool more complex.

  • Two things that might be because I fed in bad data (see discussion of the requirements on the x-axis below)

    • When you switch the x/y columns weird things can happen, i.e for sinsoidal_copia it plays about 3/4 of the way through, then stops playing sounds while the plot x-axis continually expands to the left
    • The abscissa position goes weird when the data is not sorted on the x-axis column

I erase the sinsoidal_copia; the data file was wrong and I include the expected data type in the User Manual.

  • [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).

While everything (installation instructions, user manual, github repo) is nicely linked from the sonoUno website, the website is not mentioned in the GitHub repo. I would be good to include that prominently, right at the top of the README file. Similarly after the installation instructions in the README it would be good to have a link to the user manual before diving into the bash mode instructions.

Also when the website is mentioned in the user manual itself the URL is not included (or at least in the English version, which was the one I looked at), and should be.

The website was mentioned now on the README and the User Manual was update following the recommendation on the next issue: https://github.com/sonoUnoTeam/sonoUno-desktop/commit/5f6c398b9994fa9fe7d97445cbd0cfb202bf374e

  • [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?

I don't know what this statement means:

“In the files to import the first column must have continuous values, it is used as a coordinate dependent axis.”

I think it means that the first column needs to be monotonically increasing or decreasing, but it could do with clarification. And if it does mean what I think then either the file(s) that do not conform to this format in the sample_data directory should be removed (sinsoidal_copia is the one I found), or there should be some explanation of the purpose of those example files.

This means what you understand; I take off the bad data from the data-sample, and explain better how the data are opened by the software.

  • [ ] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?

The user manual provides much of this functionality, but there are a few holes:

  • The average mathematical function is not sufficiently explained, it seems to map the data onto the 0-1 range, and is clearly not a rolling average, but how exactly it is implemented is not clear.

I include a better explanation about the function on the manual (issue https://github.com/sonoUnoTeam/sonoUno-desktop/commit/5f6c398b9994fa9fe7d97445cbd0cfb202bf374e). I include the following text: Finally, the average function or smooth uses the number of points entered by the user for group the data and calculate the average on the original data. For example, if number of points is 6, the algorithm groups the first 6 values, calculate the average between them and replace all the 6 point by the new value; then, continue with the next 6 values and do the same.

  • It's not entirely clear what should happen when bad data is fed into the software

When the data could be detected as numbers in two or more different columns, it will be plotted with matplotlib, and it will take the x-axis as time for the sound; if the data are text, for example, and the software couldn't detect any number, through an error explaining the problem found. I clarify that in the user manual, section 2, the text I added was: "One aspect to take in mind is that sonoUno works with numerical data in table format, that’s means that sonoUno try to store in a DataFrame variable the columns with numbers so: if it could detected numbers in two or more different columns, it will be stored, and it will be plotted with matplotlib (first column as x-axis; second column as y-axis; it could be changed later), the x-axis was consider for the time variation in the sonification; if the data are text, for example, and the software couldn't detect any number, through an error explaining the problem found."

  • [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

In the documentation it indicates that users should communicate any issues to the development team (start of section 2), it would be good to include specific instructions on how.

The email and link to GitHub was added to the User Manual as methods of communication, and I add it to the README too.

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?

Thank you very much for all your time and suggestions! If there is anything else, or if any issue is badly addressed, let me know, please.

johicasado commented 11 months ago

@ivastar Sorry for the delay. I answered the recommendations by replaying them; I found it easier to follow. I also mention this issue in some comments about solving the problems. I mentioned each reviewer on each replay. Let me know how we proceed, please. Thank you very much!

james-trayford commented 11 months ago

@ivastar @johicasado Great, this all looks good to me, as far as I'm concerned all my pre-publication comments were addressed, and the current code version seems ready to go!

ceb8 commented 11 months ago

@johicasado @ivastar I too feel like all of my comments have been addressed and that everything looks good.

ivastar commented 11 months ago

@johicasado @ceb8 @james-trayford Thank you all for the prompt review and responses! This is one of the smoothest review processes I've had.

I am moving forward with the publications process.

ivastar commented 11 months ago

@editorialbot commands

editorialbot commented 11 months ago

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


# List all available commands
@editorialbot commands

# Add to this issue's reviewers list
@editorialbot add @username as reviewer

# Remove from this issue's reviewers list
@editorialbot remove @username from reviewers

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

# Assign a user as the editor of this submission
@editorialbot assign @username as editor

# Remove the editor assigned to this submission
@editorialbot remove editor

# Remind an author, a reviewer or the editor to return to a review after a 
# certain period of time (supported units days and weeks)
@editorialbot remind @reviewer in 2 weeks

# 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 version
@editorialbot set v1.0.0 as version

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

# Set a value for repository
@editorialbot set https://github.com/organization/repo as repository

# Set a value for the archive DOI
@editorialbot set set 10.5281/zenodo.6861996 as archive

# Mention the EiCs for the correct track
@editorialbot ping track-eic

# Generates the pdf paper
@editorialbot generate pdf

# Recommends the submission for acceptance
@editorialbot recommend-accept

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Flag submission with questionable scope
@editorialbot query scope

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

# Creates a post-review checklist with editor and authors tasks
@editorialbot create post-review checklist

# Open the review issue
@editorialbot start review
ivastar commented 11 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

ivastar 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:

ivastar commented 11 months ago

@editorialbot check references

editorialbot commented 11 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1017/S1743921321000272 is OK
- 10.1007/978-3-030-77411-0_12 is OK
- 10.4018/jitr.2014010105 is OK
- 10.4018/IJCICG.2021010102 is OK
- 10.4018/978-1-5225-8539-8.ch002 is OK
- 10.21785/icad2021.031 is OK
- 10.1145/3136755.3136783 is OK
- 10.1051/epjconf/201920001013 is OK
- 10.4018/IJSKD.299048 is OK
- 10.11648/j.ajaa.20210904.11 is OK
- 10.1038/s41550-022-01721-z is OK
- 10.22201/ia.14052059p.2022.54.01 is OK
- 10.1093/astrogeo/atac027 is OK
- 10.1017/S174392132100079X is OK

MISSING DOIs

- None

INVALID DOIs

- None
ivastar commented 11 months ago

@johicasado I will read the paper throughout and might make some small editorial suggestions by the end of the week. I'll post the suggested edits here. Following that we can proceed with the checklist above.

johicasado commented 11 months ago

@ivastar Thank you very much!

ivastar commented 11 months ago

@johicasado here are some editorial comments, just improving the readability and fixing a couple of citations. Sorry it ended being long! Let me know if you have questions.

johicasado commented 11 months ago

Thanks @ivastar, I add some comments between lines.

@johicasado here are some editorial comments, just improving the readability and fixing a couple of citations. Sorry it ended being long! Let me know if you have questions.

  • Lines 11-13: The phrase "Even when it's challenging to think of a method to understand astrophysics through other sensorial inputs" is a bit out of pace. I suggest deleting it or paraphrasing the sentence, for example: "Sonification is a technique that uses non-speach audio to translate data into sound and it is a commonly-used approach to exploring astrophysical data through sensory inputs. "

Done

  • Line 14: "since 1992 with the International..." --> "since 1992 with the start of the International", my understanding is that conferences started in 1992 and continue since, this phrasing makes it seem that there ware only conferences in 1992.

Done

  • Line 15: ICAD as an abbreviation should be in parenthesis: "International Community for Auditory Display (ICAD) conferences"

Done

  • Line 17: "The differences between the present development from others are:" I would suggest paraphrasing to "The main distinguishing features of the development presented here are:"

Done

  • Line 19: "functional diverse users" - do you mean "functionally-diverse" or maybe just "diverse users" I mean "functionally-diverse" referring to people with and without disabilities.

Done.

  • Line 35: Remove "furthermore". The sentence will read better the following way: "After an international sound workshop held in August of 2021, Zanella et al (2022) created a repository (or maybe a list?) of existing software as of December 2021 which contained 92 projects developed since 1962. Unfortunately many of them were no longer actively developed, lacked documentation and had no evidence of science applications."

Done

  • Line 39: Replace "until" with "as of"

Done

  • Line 42: Remove "nevertheless"

Done

  • Line 44: "intended" --> "intend"; "conference"-->"conferences"? and "this field" --> "the field"

Done

  • Line 45: Remove "since its creation in 1992", repeats from page 1

Done

  • Line 46: List the categories outside the parenthesis: "six categories: sonification methods, ...."

Done

  • Line 52: Is there a reference you can cite for the Lorentz Center workshop recommentations?

Includded

  • Line 74: The reference to Harrison et al. (2021) should be out of parenthesis.

Done

  • Lines 77-79: The first 2 sentences: "It is evident that ... software update" I recommend deleting this text. The information about centering the users is later in the paragraph.

Done

  • Line 84: "To reach that goal we follow three main actions. First, the ISO.... Second, a theoretical.... And finally, a focus group...."

Done

  • Line 95: "remark" --> "feature"

Done

  • Line 98: "installing" - do you mean running? It was not clear to me in the installation instructions on GitHub which parts were optional for the module if you only want the scripting functionality.

I replace it by: "without installing the graphic user interface library 'wxPython'"; I think this is important because wxPython presents problems with the software updates sometimes, and it is hard to install. In addition, it's a big library to be installed if you only want to produce sonification without a GUI.

  • Line 99: "point" --> "feature", "was" --> "is"

Done

  • Line 110: "make science" --> "carry out reasearch"?

Done

  • Line 111: I recommend splitting this sentence in 2: sonoUno has three main functionalities: .... During our user tests it was observed that the tool allows for (a) deployment of data sets, (b) sonification .... and (c) application of math functions.

Done

  • Line 113: "in the same way that recommend the data owners" - not sure I understand the meaning, can you clarify?

I erased that part following your recommendation above, but that intent to explain that sonoUno produces the same graph obtained from the database, for example.

  • Line 117: the phrase "graphs, sounds, marks and data plotted" should be in parenthesis.

Done

  • Line 118: "Furthermore" --> "Finally"?

Done

  • Line 122: the listing of 2 citations in line like this is odd, maybe "the work of Casado et al. (2019, 2022)..."

I don't know how to cite it in the correct form, so I modify a little the text to use the traditional citation style.

  • Lines 127-142: The bullet points should start with a capital letter and finish with a period

Done

  • Line 132: There is a reference after Harvard that is not correct. Maybe Wanda et al., 2019?

The reference was correct, I don't know why itemize don't allows citation, so I put the items in different paragraphs. What do you think?

  • Line 134: "Fork" --> "fork"

Done

  • Line 137: "this user wrote to us" or "contacted us"

Done

  • Line 139: "short future" --> "near future"

Done

  • Line 157: "expect" --> "hope"?

Done

  • Footnote 7: "?cn-reloaded=1&cn-reloaded=1" is not part of the URL, delete it

Done

I think I addressed all the recommendations. Maybe at the end I missed some citation; I hope not. Thank you very much for your patience!

ivastar 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:

ivastar commented 11 months ago

@editorialbot check references

editorialbot commented 11 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1017/S1743921321000272 is OK
- 10.1007/978-3-030-77411-0_12 is OK
- 10.4018/jitr.2014010105 is OK
- 10.4018/IJCICG.2021010102 is OK
- 10.4018/978-1-5225-8539-8.ch002 is OK
- 10.21785/icad2021.031 is OK
- 10.1145/3136755.3136783 is OK
- 10.1051/epjconf/201920001013 is OK
- 10.4018/IJSKD.299048 is OK
- 10.11648/j.ajaa.20210904.11 is OK
- 10.1038/s41550-022-01721-z is OK
- 10.22201/ia.14052059p.2022.54.01 is OK
- 10.1093/astrogeo/atac027 is OK
- 10.1017/S174392132100079X is OK

MISSING DOIs

- 10.21785/icad2023.2124 may be a valid DOI for title: The Audible Universe Workshop: an Interdisciplinary Approach to the Design and Evaluation of Tools for Astronomical Data Sonification

INVALID DOIs

- None
johicasado commented 11 months ago

@ivastar I added the missing reference to bib file

ivastar commented 11 months ago

@johicasado great! Can you please go through the checkout list above? Generate tag, archive and DOI, etc.? Please post the version and DOI here.

johicasado commented 11 months ago

@editorialbot check references

editorialbot commented 11 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1017/S1743921321000272 is OK
- 10.1007/978-3-030-77411-0_12 is OK
- 10.4018/jitr.2014010105 is OK
- 10.21785/icad2023.2124 is OK
- 10.4018/IJCICG.2021010102 is OK
- 10.4018/978-1-5225-8539-8.ch002 is OK
- 10.21785/icad2021.031 is OK
- 10.1145/3136755.3136783 is OK
- 10.1051/epjconf/201920001013 is OK
- 10.4018/IJSKD.299048 is OK
- 10.11648/j.ajaa.20210904.11 is OK
- 10.1038/s41550-022-01721-z is OK
- 10.22201/ia.14052059p.2022.54.01 is OK
- 10.1093/astrogeo/atac027 is OK
- 10.1017/S174392132100079X is OK

MISSING DOIs

- None

INVALID DOIs

- None
johicasado commented 11 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

  • [x] Double check authors and affiliations (including ORCIDs)
  • [x] 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.

Name of the release: JOSS paper review Version number: 4.1

  • [x] Archive the release on Zenodo/figshare/etc and post the DOI here.

I don't understand what means 'figshare/etc'; I used the Zenodo account that we previously had to sonoUno repositories. Is that ok? [DOI: 10.5281/zenodo.10303871] (https://doi.org/10.5281/zenodo.10303871)

  • [x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
  • [x] 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
  • [x] 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
ivastar commented 11 months ago

@editorialbot set 10.5281/zenodo.10303871 as archive

editorialbot commented 11 months ago

Done! archive is now 10.5281/zenodo.10303871

ivastar commented 11 months ago

@editorialbot set 4.1 as version