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[REVIEW]: The DynaGUI package #1942

Closed whedon closed 3 years ago

whedon commented 4 years ago

Submitting author: @benjaminbolling (Benjamin Edward Bolling) Repository: https://github.com/benjaminbolling/DynaGUI Version: v1.0.1 Editor: @majensen Reviewer: @Chilipp, @pythonpanda2 Archive: 10.5281/zenodo.4396227

Status

status

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Markdown: [![status](https://joss.theoj.org/papers/eede632738a83ce2b21bd85fe039ed45/status.svg)](https://joss.theoj.org/papers/eede632738a83ce2b21bd85fe039ed45)

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

@Chilipp & @pythonpanda2, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @Chilipp

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @pythonpanda2

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @Chilipp, @pythonpanda2 it looks like you're currently assigned to review this paper :tada:.

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whedon commented 4 years ago 
Attempting to check references...
whedon commented 4 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 4 years ago 

OK DOIs

- 10.1107/S1600577514011503 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

pythonpanda2 commented 4 years ago

https://github.com/benjaminbolling/DynaGUI/issues/2#issue-538141258

pythonpanda2 commented 4 years ago

https://github.com/benjaminbolling/DynaGUI/issues/3

pythonpanda2 commented 4 years ago

https://github.com/benjaminbolling/DynaGUI/issues/4

majensen commented 4 years ago

Hi @Chilipp - just wanted to ping you and ask if you are still willing to review this submission around 20 Jan. Thanks!

Chilipp commented 4 years ago

Yes @majensen, I will do so.

majensen commented 4 years ago

Hi @pythonpanda2 and @Chilipp -- looking forward to your reviews. Thank you very much for your time on this!

pythonpanda2 commented 4 years ago

@majensen

Looking forward to the response to the queries.

Chilipp commented 4 years ago

Dear @majensen and @benjaminbolling. My apologies for the delay and thank you very much for your patience! I am done with my review (so far) and note a high number of issues to work on concerning the DynaGUI package. As these are so many, I did not want to create an issue for each individual point, but rather want to give @benjaminbolling the chance to comment on each of these.

My general feeling is, that this repository is a collection of scripts that have a massive lack in documentation. There are no installation instructions, there is no quick start guide (not even a README in the repository), and there are only explanations about the GUI widgets, but not even about how to start the GUI. Please let me know @benjaminbolling and @majensen if you want me to open issues for the individual points listed below.

General checks

License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?

I recommend to rename GNU_Licence.txt to LICENSE, as this is common for software packages. But this is not a blocking issue, of course.

Contribution and authorship: Has the submitting author (@benjaminbolling) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

I cannot judge this @majensen as the commit history is not present in the repository. Don't know how to handle this, but from the paper itself it seems like some others have been involved from Tavares et. al

Functionality

Installation: Does installation proceed as outlined in the documentation?

I could not find any installation instructions. Please create a README.md and provide some guidance for the user.

Functionality: Have the functional claims of the software been confirmed?

I couldn't because I did not install it.

Documentation

There exists a PDF-Document in the repository (DynaGUI_documentation.pdf) which serves, I guess as the documentation. So I will judge based on this document.

Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.

There is a System Requirements section, but no installation instructions.

Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).

No, there is no example usage. There are some screenshots of the different widgets, but I could not find any executable code in the documentation to verify the functionality of the package.

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

As there are only explanations of the various images, no, it is not explained well enough. There should be a piece of code somewhere stating how to generate and open the different widgets. How to establish a connection to the server, etc. The code also contains almost no documentation/comments.

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

I could not find any tests associated with the repository.

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

No, there are no community guidelines.

Software paper

State of the field: Do the authors describe how this software compares to other commonly-used packages?

I could not find any comment on that in the paper.

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 package also depends on matplotlib and numpy, which need to be cited.

benjaminbolling commented 4 years ago

Dear Philipp,

Many thanks for your review. I will rewrite the code for the package shortly so that it does not consist solely “of a bunch of scripts” but instead of a whole package and I will include an installation method with instructions, and instructions / a README file with clear instructions.

I will be more clear in the list of contributors, which have been included in the acknowledgments section. I will cite MatPlotLib and NumPy, and compare with other similar software.

Thank you for your time and patience.

Kind regards Benjamin

23 jan. 2020 kl. 09:43 skrev Philipp S. Sommer notifications@github.com:

 Dear @majensen and @benjaminbolling. My apologies for the delay and thank you very much for your patience! I am done with my review (so far) and note a high number of issues to work on concerning the DynaGUI package. As these are so many, I did not want to create an issue for each individual point, but rather want to give @benjaminbolling the chance to comment on each of these.

My general feeling is, that this repository is a collection of scripts that have a massive lack in documentation. There are no installation instructions, there is no quick start guide (not even a README in the repository), and there are only explanations about the GUI widgets, but not even about how to start the GUI. Please let me know @benjaminbolling and @majensen if you want me to open issues for the individual points listed below.

General checks

License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?

I recommend to rename GNU_Licence.txt to LICENSE, as this is common for software packages. But this is not a blocking issue, of course.

Contribution and authorship: Has the submitting author (@benjaminbolling) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

I cannot judge this @majensen as the commit history is not present in the repository. Don't know how to handle this, but from the paper itself it seems like some others have been involved from Tavares et. al

Functionality

Installation: Does installation proceed as outlined in the documentation?

I could not find any installation instructions. Please create a README.md and provide some guidance for the user.

Functionality: Have the functional claims of the software been confirmed?

I couldn't because I did not install it.

Documentation

There exists a PDF-Document in the repository (DynaGUI_documentation.pdf) which serves, I guess as the documentation. So I will judge based on this document.

Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.

There is a System Requirements section, but no installation instructions.

Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).

No, there is no example usage. There are some screenshots of the different widgets, but I could not find any executable code in the documentation to verify the functionality of the package.

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

As there are only explanations of the various images, no, it is not explained well enough. There should be a piece of code somewhere stating how to generate and open the different widgets. How to establish a connection to the server, etc. The code also contains almost no documentation/comments.

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

I could not find any tests associated with the repository.

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

No, there are no community guidelines.

Software paper

State of the field: Do the authors describe how this software compares to other commonly-used packages?

I could not find any comment on that in the paper.

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 package also depends on matplotlib and numpy, which need to be cited.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

Chilipp commented 4 years ago

Great to hear @benjaminbolling, I am looking forward to it. Just tell me, when you are ready for another round of review or if there is anything else.

Thanks for your work on this!

majensen commented 4 years ago

@benjaminbolling please remember also to review @pythonpanda2 's questions that were created as issues on the DynaGUI repo. thanks!

majensen commented 4 years ago

Hi @benjaminbolling - how are things proceeding?

benjaminbolling commented 4 years ago

Hi,

I am rewriting some code and adding in-code explanations which can assist you during the reviewal. I am sorry for taking so much time, but I will let you know when it is ready together with a clear manual and installation routine such that the reviewal will go smoothly. I have also been busy with a lot of work, but I am working on this as much as I can.

Thanks for the patience!

On 31 Jan 2020, at 15:38, Mark Jensen notifications@github.com wrote:

Hi @benjaminbolling https://github.com/benjaminbolling - how are things proceeding?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1942?email_source=notifications&email_token=ANM6ZNTS5WVWO7LX7QQKKDTRAQZVTA5CNFSM4JZIGNJKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEKO245A#issuecomment-580759156, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANM6ZNR4QFUKNSA5TEAJQZ3RAQZVTANCNFSM4JZIGNJA.

majensen commented 4 years ago

Thanks for the update @benjaminbolling -- no worries

labarba commented 4 years ago

👋 @benjaminbolling — since it's been 3 weeks since your last comment here, would you like to tell us an estimated time for your work-in-progress? We can set a reminder and/or add the paused label.

majensen commented 4 years ago

@benjaminbolling can you give us an idea of your timeline, per @labarba 's comment? I will see if I can reach you via an alternative channel as well.

majensen commented 4 years ago

Thanks @benjaminbolling for touching base with me on the alternative channel. We'll add the "paused" label to this submission for now. Feel free to pick it back up with a post here.

arfon commented 4 years ago

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team.

majensen commented 4 years ago

@whedon remind @majensen in 2 weeks

whedon commented 4 years ago

Reminder set for @majensen in 2 weeks

arfon commented 4 years ago

@majensen - looks like Whedon forgot to remind you :-)

majensen commented 4 years ago

Well that's a data point @arfon !

majensen commented 4 years ago

@benjaminbolling just want to check in here with you. Let me know how it's going.

benjaminbolling commented 4 years ago

Dear all,

Thank you for being so patient! I am ensuring there are no bugs in the code now, finishing some additional features of it and expecting it to be ready with instructions and a short article before the end of this month.

Again, thank you for the patience!

Kind regards Benjamin

On 20 May 2020, at 19:14, Mark Jensen notifications@github.com wrote:

@benjaminbolling just want to check in here with you. Let me know how it's going.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

majensen commented 4 years ago

Sounds good @benjaminbolling - I will unpause us.

benjaminbolling commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

PDF failed to compile for issue #1942 with the following error:

Error reading bibliography ./paper.bib (line 31, column 1): unexpected "@" expecting space, ",", white space or "}" Error running filter pandoc-citeproc: Filter returned error status 1 Looks like we failed to compile the PDF

benjaminbolling commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

PDF failed to compile for issue #1942 with the following error:

Error reading bibliography ./paper.bib (line 32, column 14): unexpected "a" expecting white space, "#", "," or "}" Error running filter pandoc-citeproc: Filter returned error status 1 Looks like we failed to compile the PDF

benjaminbolling commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

benjaminbolling commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

benjaminbolling commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

benjaminbolling commented 4 years ago

Dear all, @majensen @Chilipp @arfon @pythonpanda2 thanks for the enormous patience. I have now updated the package, attached a README file with installation instructions and how to launch it, a documentation on how to use the applications in the package, and also updated the article itself.

benjaminbolling commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

majensen commented 4 years ago

@Chilipp @pythonpanda2 - Hope to see your comments within the next week or so. Thank @benjaminbolling for all this work.

Chilipp commented 4 years ago

Dear @majensen and @benjaminbolling, thank you for the update! I am looking forward to have another look at it, but I am on vacation until June 12th. I expect to finish the review by June 21st.

pythonpanda2 commented 4 years ago

@majensen @benjaminbolling

I have started a new job this week. Hopefully i would try to get back to this sometime next week.

majensen commented 4 years ago

Hi @pythonpanda2 - I hope the new job is going well. Do you have a sense of when you might have the opportunity to look at @benjaminbolling 's work? Thanks very much -- @majensen

pythonpanda2 commented 4 years ago

@majensen Apologies. I will be try to complete the review over the weekend.

pythonpanda2 commented 4 years ago

https://github.com/benjaminbolling/DynaGUI/issues/3#issuecomment-647886871

Chilipp commented 4 years ago

I expect to finish the review by June 21st.

Dear @majensen and @benjaminbolling. I have to apologize but something urgent forced me to change my plans and I won't have the possibility to review this within this week. I have to postpone it until next week and hope, this does not cause problems.