Submitting author: @benjaminbolling (Benjamin Edward Bolling)
Repository: https://github.com/benjaminbolling/DynaGUI
Version: v1.0.0
Editor: @majensen
Reviewer: @Chilipp, @pythonpanda2
Archive: Pending
Status badge code:
HTML: <a href="https://joss.theoj.org/papers/eede632738a83ce2b21bd85fe039ed45"><img src="https://joss.theoj.org/papers/eede632738a83ce2b21bd85fe039ed45/status.svg"></a>
Markdown: [](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.)
@Chilipp & @pythonpanda2, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
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 ✨
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Attempting to check references...
Attempting PDF compilation. Reticulating splines etc...
```Reference check summary:
OK DOIs
MISSING DOIs
INVALID DOIs
Hi @Chilipp - just wanted to ping you and ask if you are still willing to review this submission around 20 Jan. Thanks!
Yes @majensen, I will do so.
Hi @pythonpanda2 and @Chilipp -- looking forward to your reviews. Thank you very much for your time on this!
@majensen
Looking forward to the response to the queries.
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.
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
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.
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.
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.
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.
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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!
@benjaminbolling please remember also to review @pythonpanda2 's questions that were created as issues on the DynaGUI repo. thanks!
Hi @benjaminbolling - how are things proceeding?
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?
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Thanks for the update @benjaminbolling -- no worries
👋 @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.
@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.
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.
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._
@whedon remind @majensen in 2 weeks
Reminder set for @majensen in 2 weeks
@majensen - looks like Whedon forgot to remind you :-)
Well that's a data point @arfon !
@benjaminbolling just want to check in here with you. Let me know how it's going.
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.
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Sounds good @benjaminbolling - I will unpause us.
@whedon generate pdf
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
@whedon generate pdf
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
@whedon generate pdf
@whedon generate pdf
@whedon generate pdf
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.
@whedon generate pdf
@Chilipp @pythonpanda2 - Hope to see your comments within the next week or so. Thank @benjaminbolling for all this work.
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.
@majensen @benjaminbolling
I have started a new job this week. Hopefully i would try to get back to this sometime next week.
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
@majensen Apologies. I will be try to complete the review over the weekend.
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.
@Chilipp - no problem; thanks for the heads up. Will touch base next week-
@whedon remind @Chilipp in 7 days
Reminder set for @Chilipp in 7 days
There are already some very well rounded points raised by @Chilipp in the last round . I would wait to see if some of those points have been addresses to their satisfaction (To avoid repetitions) and i will stick to the one issue I have raised.
In addition, the funding sources should be duly acknowledged.
:wave: @Chilipp, please update us on how your review is going.
Hi @benjaminbolling,
my apologies for the delay and thank you very much @benjaminbolling for your ongoing work on this!
I have the feeling that most of my points from my comment above have not been addressed (or at least I could not find them). As it takes me quite a while to go through everything, please address the individual issues in the future that I reference down below, or cite my comments and answer within this thread.
I apologize if I just did not find the information on some of the issues mentioned below. If so, please point me individually to the correct place where this is answered from your perspective or ask if there is need for clarification.
Contribution and authorship:
Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
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
State of the field: Do the authors describe how this software compares to other commonly-used packages?
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?
@Chilipp thanks for this summary - @benjaminbolling can you address these issues? Just let me know an approximate timeline here. Thanks!
Thank you @Chilipp, I will be addressing these issues in the coming two weeks in the evenings. @majensen Thus, we can set a deadline for next Friday, July 17th.
@whedon remind @majensen in 10 days
Reminder set for @majensen in 10 days
@Chilipp : I have updated the code a bit to address issue#4: To decrease the dependency of PyTango. All codes now enables user to select between the packages "Tango" (using PyTango), "EPICS" (using PyEPICS), "Finance" (using Pandas Datareader) and "Randomizer" (for testing and demonstration purposes using random values). Other packages used for obtaining values from sources can be added in later stages with ease. I will address each issue in their own reference.
As for "Contribution and authorship", I did all of the code except for the original code for the "2D Spectrogram" part which I referenced in both the paper.md and the documentation file under Acknowledgements. If this is incorrect or if you need me to change something there, let me know.
Again, thanks for the patience!
I have now addressed issues 3, 4, 5, 7, 8 and 9.
Installation instructions: Added to the README file.
State of the field: I am unaware of currently existing Python-based package for constructing dynamic GUI:s (without any programming), and I have added this also to the README file.
Left to do:
The API documentation might sadly take a little bit longer time, but I am working on it (doing in-code comments).
@Chilipp @pythonpanda2 @majensen : I have written a test procedure (see test.txt), let me know if you find it sufficient or not. The API documentation will, as stated before, take a little while (ca. a week). You can start testing it anyways if you'd want to, as it seems to me as if all other issues and comments have now been addressed. Thank you all for the patience and the comments, and have a nice weekend!
@benjaminbolling thanks for this work. A tip, if you rename your test.txt to test.md, then GitHub will render it in a nice form.
@pythonpanda2 - based on the work done, can you check off the items in your review that are satisfied?
thanks everyone
thanks @majensen, I have renamed test.txt to test.md as you suggested.
@pythonpanda2 please let us know here if you are still able to review this work. Thanks --@majensen
@majensen Sorry for the delay. In between the peak review season now. I will have a looking this week.
thanks @benjaminbolling! I'll have a look at it within this week
@majensen @benjaminbolling I have closed this issue . https://github.com/benjaminbolling/DynaGUI/issues/4
@majensen @benjaminbolling . Thanks a lot for your patience. It would be good to see if we can resolve this : https://github.com/benjaminbolling/DynaGUI/issues/3
@benjaminbolling Have you been able to take care of benjaminbolling/DynaGUI#3 per @pythonpanda2 ?
I have just opened the issue, sorry for taking time to replying (I recently came back to work from vacation). I have replied to the issue, but I am not sure on how to proceed with it. PyTango is only essential for the package at for facilities/users utilising TANGO Controls.
I will have a look at this soon. I think there should be a simple way to describe this.
Looks like https://github.com/benjaminbolling/DynaGUI/issues/3#issuecomment-679137058 is taking care of it.
@Chilipp @pythonpanda2 @benjaminbolling I would like to take stock of where we are in this review. Could reviewers please make sure that the items they are satisfied with are checked off in their reviewer forms? What are the next steps @benjaminbolling for finishing with reviewer suggestions? Thank you all-
Could reviewers please make sure that the items they are satisfied with are checked off in their reviewer forms?
Everything's up-to-date from my side @majensen
@Chilipp and @pythonpanda2 Hi! I am the rotating associate editor in chief here this week trying to help ping stale issues. @Chilipp I see you said just above that you are satisfied with the submission, but you have a lot of unchecked boxes above. Could you either check the boxes or state what are the next issues?
@pythonpanda2 How is your review coming along?
Thanks all!
Hello @kthyng! There seems to be a misunderstanding. No, the items are not yet resolved. My last comment just states that the open points I mentioned are still open. @benjaminbolling just made some changes yesterday and I'll review them as soon as possible
@Chilipp Ok excellent! Thanks for your response and glad things are working out ok.
@kthyng thanks for checking in. Things have started to proceed over at https://github.com/benjaminbolling/DynaGUI/issues/3#issuecomment-704386598
@benjaminbolling any progress to report? thanks
@majensen Sorry for the delay in my reply, I have a lot of work nowadays during the pandemic.
I have replied to Issue #3.
I will deal with Issue #7 this evening.
I am close to finished with the API documentation for Issue #8, and will post here when it is finished.
Again, thanks for all patience and all your efforts put into this!
@benjaminbolling @Chilipp @pythonpanda2 - as we're coming up on the one year anniversary of the submission, I thought I would see if we're still on track. I think @benjaminbolling is making some progress. @Chilipp I think you are still with us. @pythonpanda2 can you ping back on this thread as to whether you are still following this review and able to pick it up again?
thanks all
Good morning all, and thanks again. Can you confirm what is left to be done? I think I am ready to push the changes in terms of the last part of the API documentation, Issue #8.
Let me know what else is left to do. Thanks again all, and sorry for taking so much time.
Thanks for your work on this @benjaminbolling! @majensen I will go through it again by the end of this week. My apologies for the delay as my workload is pretty high at the moment and it takes some time for me to get into this again.
@benjaminbolling @Chilipp @pythonpanda2 - as we're coming up on the one year anniversary of the submission, I thought I would see if we're still on track. I think @benjaminbolling is making some progress. @Chilipp I think you are still with us. @pythonpanda2 can you ping back on this thread as to whether you are still following this review and able to pick it up again?
thanks all
So i have already closed this issue . But i will go through the checklist once more by early next week.
Thanks a lot everybody- we are closing in!
Most helpful comment
Hi @benjaminbolling,
my apologies for the delay and thank you very much @benjaminbolling for your ongoing work on this!
I have the feeling that most of my points from my comment above have not been addressed (or at least I could not find them). As it takes me quite a while to go through everything, please address the individual issues in the future that I reference down below, or cite my comments and answer within this thread.
I apologize if I just did not find the information on some of the issues mentioned below. If so, please point me individually to the correct place where this is answered from your perspective or ask if there is need for clarification.
General checks
Functionality
Documentation
Software paper