[REVIEW]: GRISView: A Python package for visualization of GRIS spectro-polarimetric data

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@tyakobchuk@adonath<!--end-editor-- Reviewers: @dstansby, @wtbarnes Archive: Pending

Status

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Markdown: [![status](https://joss.theoj.org/papers/de67b4f27164c9505f06af13830243d6/status.svg)](https://joss.theoj.org/papers/de67b4f27164c9505f06af13830243d6)

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

@dstansby & @wtbarnes, 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 @adonath 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 @dstansby

📝 Checklist for @wtbarnes

editorialbot commented 1 year ago

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For a list of things I can do to help you, just type:

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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=0.19 s (280.0 files/s, 155684.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Qt                               5              0              0          14714
Python                          21            925            952          12174
Markdown                        24            127              0            478
TeX                              1              4              0             36
YAML                             1              8             28             19
Bourne Shell                     1              0              0              5
-------------------------------------------------------------------------------
SUM:                            53           1064            980          27426
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 768

editorialbot commented 1 year ago

:warning: An error happened when generating the pdf.

dstansby commented 1 year ago

Review checklist for @dstansby

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://gitlab.leibniz-kis.de/sdc/gris/grisview?
[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 (@tyakobchuk) 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? https://gitlab.com/sdc-gitlab/grisview/-/issues/3
[ ] Functionality: Have the functional claims of the software been confirmed? https://gitlab.com/sdc-gitlab/grisview/-/issues/11
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems). https://gitlab.com/sdc-gitlab/grisview/-/issues/4, https://gitlab.com/sdc-gitlab/grisview/-/issues/8
[ ] 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? https://gitlab.com/sdc-gitlab/grisview/-/issues/5
[ ] 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 https://gitlab.com/sdc-gitlab/grisview/-/issues/9

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?
[ ] 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?

adonath commented 1 year ago

@tyakobchuck @dstansby @wtbarnes this is the review thread for the paper. All of our communications will happen here from now on. Thanks again for the submission and for agreeing to review!

A short reminder for @dstansby and @wtbarnes on the review process:

You can create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread. You also find general instructions for the review here in the issue in the top comment as well as in the JOSS documentation here: https://joss.readthedocs.io/en/latest/review_criteria.html

The checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#REVIEW_NUMBER so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@adonath) if you have any questions/concerns.

dstansby commented 1 year ago

@adonath it looks like the paper failed to compile above - is this something you can help fix?

dstansby commented 1 year ago

👋 @tyakobchuk, I'm just starting to review your package. One of the review criteria is:

Are there clear guidelines for third parties wishing to ... 2) Report issues or problems with the software ...

I have tried signing in to open an issue on the project repository, but I can't find a way to create an account on the sign in page of your GitLab instance. Before I go further with the review, could you fix this so it's possible for anyone to create an account and open issues on the repository?

adonath commented 1 year ago

In https://github.com/openjournals/joss-reviews/issues/5307 @tyakobchuk mentioned that the public repo could be found at https://gitlab.com/sdc-gitlab/grisview instead. I thought we updated the link in the issue description here, but we did not. Sorry for that, I just corrected for that.

@dstansby and @wtbarnes please use https://gitlab.com/sdc-gitlab/grisview to open issues. Thanks!

@tyakobchuk can you please double check the paper build? From a quick look it seemed that there is some additional whitespace before closing the meta section using ---. I can help with debugging if that is not successful.

dstansby commented 1 year ago

Hi all, a quick update on the review. It seems like the software package doesn't have any tests (https://gitlab.com/sdc-gitlab/grisview/-/issues/5), examples of usage (https://gitlab.com/sdc-gitlab/grisview/-/issues/4), and I cannot successfully install the package (https://gitlab.com/sdc-gitlab/grisview/-/issues/3). Because these are major items on the JOSS review criteria, I've stopped reviewing any futher to wait for these to be addressed.

adonath commented 1 year ago

Thanks @dstansby! Please address the comments @tyakobschuk and report on the progress, such that we continue the review as soon as possible.

adonath commented 1 year ago

What is the status here @tyakobchuk?

tyakobchuk commented 1 year ago

@adonath I have addressed most concerns, except the one about the tests. Basically, I have never done them, especially with GUI (this is my first Python GUI program), and I was busy with my other tasks in the institute. Anyway, I plan to finish the tests in the coming weeks.

adonath commented 12 months ago

Ok, thanks @tyakobchuk. We can keep the review going as long as there is continuous progress.

adonath commented 11 months ago

What is the status @tyakobchuk?

adonath commented 11 months ago

Please comment on the status here @tyakobchuk, otherwise we would need to close the submission at some point.

adonath commented 11 months ago

@tyakobchuk Please provide an update until Oct 31st. Otherwise I will close the review for now. However you are welcome to re-submit once the paper is ready for a new review.

tyakobchuk commented 10 months ago

@adonath I have added tests. I could not make them run automatically on the server or using headless mode, but I hope this can be also enough.

adonath commented 10 months ago

@tyakobchuk Yes, I think running tests manually is fine, as long as the procedure is documented. If not please do so. Please also proceed and address the other issues open by @dstansby. Thanks!

tyakobchuk commented 10 months ago

@adonath, I closed/replied to all issues opened by @dstansby.

tyakobchuk commented 8 months ago

It's been a while. Any updates @adonath @dstansby ?

adonath commented 8 months ago

Apologies for the unresponsiveness! @dstansby are you willing to resume the review process after @tyakobchuk addressed your comments?

dstansby commented 8 months ago

Hi all, I'm afraid I'm on medium term medical leave at the moment, so I could only get back to this in ~two months. Sorry about that, and feel free to replace me with another reviewer if that's too long to wait.

adonath commented 8 months ago

Thanks @dstansby, get well soon!

@tyakobchuk I'll find a second reviewer asap. Meanwhile @wtbarnes, please start your review.

wtbarnes commented 8 months ago

@adonath Thanks for the reminder! Yes, I'll complete my review shortly

wtbarnes commented 8 months ago

Review checklist for @wtbarnes

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://gitlab.com/sdc-gitlab/grisview?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[ ] Contribution and authorship: Has the submitting author (@tyakobchuk) 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

[ ] Installation: Does installation proceed as outlined in the documentation?
[ ] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[ ] 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

[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?

wtbarnes commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

:warning: An error happened when generating the pdf.

wtbarnes commented 8 months ago

@tyakobchuk As David noted above, there is an issue with the PDF that is preventing it from being compiled. Could you please fix that? I will still continue the review of the software in the meantime. Thanks!

tyakobchuk commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

:warning: An error happened when generating the pdf.

tyakobchuk commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

:warning: An error happened when generating the pdf.

tyakobchuk commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

:warning: An error happened when generating the pdf.

tyakobchuk commented 7 months ago

Sorry, @wtbarnes @adonath I checked the error description, tried several fixes and don't quite understand what can be wrong in the paper in line 38 (or around it).

wtbarnes commented 7 months ago

I'm not sure either and the error is a bit cryptic. Maybe it is because the - marks denoting the end of the heading material are indented?

dfm commented 7 months ago

@tyakobchuk — I believe that the issue is that the --- line at the bottom of the metadata block (line 19 in https://gitlab.com/sdc-gitlab/grisview/-/raw/paper/paper/paper.md?ref_type=heads) needs to be left justified (i.e. remove the spaces at the beginning of the line). You might also add another newline before # Summary, but I'm not sure that's necessary.

tyakobchuk commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

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

tyakobchuk commented 7 months ago

@dfm Perfect, thank you!

adonath commented 7 months ago

Is there anything else you require @wtbarnes and @dstansby to finish the review? Please continue as soon as possible.

adonath commented 6 months ago

@wtbarnes and @dstansby please finish the review as soon as possible. Thanks!

dstansby commented 6 months ago

As I said in https://github.com/openjournals/joss-reviews/issues/5470#issuecomment-1883227575, I'm not able to continue with this review at the moment. I might be able to in ~ a months time, but can't guarentee anything.

adonath commented 6 months ago

Thanks @dstansby, for reminding me again! I was not sure about the ~2 months time scale and I haven't been successful with finding another reviewer yet. I'll keep you assigned as long as no other reviewer has agreed to finishing the task. Best wishes again for a speedy recovery!

wtbarnes commented 6 months ago

I have to apologize once again for my tardiness here. I've almost finished my review.

wtbarnes commented 6 months ago

@adonath @tyakobchuk I've finished my review and I greatly apologize for the extended delay in completing this. Unfortunately at this time, I am not able to accept this paper for publication in JOSS as I was forced to leave several items unchecked in each section of my reviewer checklist above. I have outlined my full reasoning for leaving each item unchecked in the comments below, but the main issue I have with the software as it stands is my inability to run even a simple example. This is primarily due to the lack of a clear example workflow as part the documentation or the manuscript as well as the difficulty in searching for and downloading data from the web interface listed in the manuscript.

As part of my review, I have created or commented on several issues on the grisview repository that, if addressed, will resolve many of my major concerns listed below. I am happy to work with the author to get the package to a state where it can be accepted into JOSS.

Major Concerns

Functionality: The installation instructions on the README and in the manual do not work. One must use pip install . rather than python setup.py install. In particular, the code does not install in Python 3.11 when running python setup.py install, but running pip install -e . does work, presumably due to an issue of available wheels. This is the reason I did not check the "Installation" box. See sdc-gitlab/grisview#6 for additional details.
Functionality: I was not able to verify the functionality claims of this software and thus could not check the "Functionality" box in this section. This is for two primary reasons:
1. As pointed out by @dstansby in this issue sdc-gitlab/grisview#4, while the manual is extensive, it does not provide a clear example workflow. Thus, it is difficult to know where to start or whether my installation is working as expected.
2. I was not able to get data from the data source listed in the manuscript. For most of the queries I tried through the web interface, I got an internal server error. This is of course not related to the software that is being reviewed, but this, combined with my first concern made it impossible to verify the functionality claims of this software.
Documentation: While there are a set of tests provided that can be run with pytest, they are not run on any sort of continuous integration system. Furthermore, when I try to run the tests on my machine, they fail. This is the reason I did not check the "Automated tests" box. See sdc-gitlab/grisview#7.
Documentation: The "Contributing" section of the README does not provide instructions for how to set up a development environment so that someone could make a pull request fixing a bug or adding a feature. This is the reason I did not check the "Community guidelines" box.

Minor Comments

Authorship: From the GitLab contributor information, I see there is one additional contributor. Is there a reason they are not listed in the author list as well? This is the reason I've not checked the "Contribution and Authorship" box.
Functionality: The installation is complicated by the fact that the software is not available on any of the standard Python package indices. I would suggest making the package available on the Python Package Index (PyPI).
Documentation: I was initially confused by the fact that the manual only exists within the GUI application itself. I would encourage the authors to provide a rendered HTML version as well as is standard within the scientific Python ecosystem (e.g. using Read the Docs).
Documentation: There is no API or method documentation. This is not a major concern given that this is a GUI application. This is why I did not check the "Functionality documentation" box.
Paper: In the manuscript, it states that the package is using PyQT5, but it appears that the package is now using PyQT6, e.g. this line of code.
Paper: Some of the material giving context for what GREGOR is and what kind of observations of the Sun it makes would be better placed in the Summary section rather than the Statement of Need section.

adonath commented 6 months ago

Thanks a lot @wtbarnes for the thorough review! Opening issues is good way to provide feedback and comments.

@tyakobchuk, please address the comments and iterate with @wtbarnes if needed in the GitLab issues. Please ping me, if further feedback is required or the points are all resolved. Thanks!

tyakobchuk commented 6 months ago

Thank you very much @wtbarnes for the review. I appreciate your comments and will address them as far as I can.

@adonath I would like to change the reviewer(s) for the next round, please, if that is possible. We may agree/disagree on certain issues, but I am sorry I cannot accept the fact that the reviewer could not even download the data from the data source listed in the manuscript, which was available world-wide approximately 99% (maybe 97%) of the time that the reviewer spent on the review. Thank you. Can I answer in more detail to the points that I disagree with here or in the GitLab issues?

adonath commented 6 months ago

Thanks for the comment @tyakobchuk! I understand that getting a series of review comments to address, means additional work and creates frustration in first place. However please bear in mind this is part of the open review process and eventually leads to an improvement of your software and project. Thanks again @wtbarnes and @dstansby for the thorough review!

I double checked and compared the last comments raised by @wtbarnes against the JOSS guidelines and I concluded they are fair and well argued. I think he clearly and in detail described the points to work on. I also think the comments can be addressed in a reasonable amount of time. Please acknowledge that both reviewers agreed on multiple points. Thus right now I see no justification of exchanging the reviewers (I'll comment on the unavailability of @dstansby again later).

Please let me comment on some issues raised by @wtbarnes, where I think some clarification is helpful:

Automated tests (CI system) are not required by JOSS. Running tests manually is sufficient as long as the procedure is documented. However @wtbarnes clearly mentioned that running the tests locally failed. This is needs to be addressed.
While there is no requirement on the availability of example data, it might be needed to verify the functionality of the software. I cannot comment on the reliability of the specific web service that provides the data, however I can recommend to provide a small independent example dataset for testing as well as for users on an independent server for download. You can consider for example https://zenodo.org. Both reviewers agreed that such an example and a documented example workflow using it would be helpful. Right now I have no reason to "overrule" this comment.
The installation and contributing guidelines need to be updated.

My impression is that some of disagreement comes from the general question on how to verify and establish functionality for GUIs. I will consult again the JOSS editor team and see whether there any additional recommendations.

I would recommend to keep the discussion for specific issues (those that have an issue thread) in the GitLab, anything else (especially related to paper content) can be discussed here.

openjournals / joss-reviews