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[REVIEW]: PyCS3: A Python toolbox for time-delay measurements in lensed quasars #2654
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Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @danhey, @coljac it looks like you're currently assigned to review this paper 🎉. Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post. ⭐ Important ⭐ If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿 To fix this do the following two things:
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@danhey, @coljac - This is the review thread for the paper. All of our communications will happen here from now on. Please read the "Reviewer instructions & questions" in the first comment above. Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also 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 #2654 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 Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time. |
@whedon generate pdf |
Hi all, I find the code to be well written and nicely documented. Great work! I have installed it without issue, and ran most of the example code. My only issue appears to be running the the code in Sec. 1.2. I am getting an attribute error which seems to be caused by misconfigured imports. I can get around this by replacing Otherwise, this is an excellent package and I recommend it for publication. |
Thanks @danhey for checking our code and thanks for spotting this problem in the documentation. |
Hi authors, I have a question about the multiprocessing. There are several methods that take a number of cores as an argument, for example
However, when I pass in a number > 1, I see this:
However, the documentation doesn't seem to mention this. Should the docs reflect that this feature isn't implemented, or did I miss something? |
Hi authors, Here's the rest of my review. Firstly, this is an excellent software package, and it serves a genuine scientific need, as time delay cosmology is only going to increase in the future and will be key in confirming or resolving the H0 tension. Congratulations on a great piece of work! It was also a pleasure to review, as everything is in great shape. Regarding the paper: I am satisfied with the paper and don't need to see any revisions. I would suggest fixing the citations so that the nested parentheses are removed - "(for instance, Wang 2010.)" This is a minor issue, as is the phrase "Since almost three decades" should probably be "for almost three decades". Regarding the software: I was able to successfully run the pytest tests in The notebooks were very good, all the examples ran for me (I had to install a latex package and dvipng; I don't think this was a deficiency on your end though). Otherwise, the package is well documented and rich in features, meeting a genuine scientific need. Subject to a note on pytest, I am satisfied with this submission. |
Thanks, @coljac and @danhey for your reviews and for helping us to improve this package. I have made the following changes :
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@whedon generate pdf |
Thanks for the update @martin-millon. I found one small typo in your paper which I corrected in https://gitlab.com/cosmograil/PyCS3/-/merge_requests/5 @coljac - assuming that @martin-millon's response addresses your concerns about testing, could you please check off the final item in your checklist? @martin-millon - At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:
I can then move forward with accepting the submission. |
@arfon - I have put an archive on Zenodo. Here is the DOI: http://doi.org/10.5281/zenodo.4046260 |
@whedon set 10.5281/zenodo.4046260 as archive |
OK. 10.5281/zenodo.4046260 is the archive. |
@whedon check references |
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@whedon accept |
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👋 @openjournals/joss-eics, this paper is ready to be accepted and published. Check final proof 👉 openjournals/joss-papers#1746 If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1746, then you can now move forward with accepting the submission by compiling again with the flag
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@martin-millon - please make a last check of the PDF proof in openjournals/joss-papers#1746 (I'll do the same). I plan to loop back on this in the morning my time to process/accept this. |
@arfon - I've been through the paper one more time and I don't have anything to change. |
@whedon accept deposit=true |
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🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦 |
🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨 Here's what you must now do:
Any issues? Notify your editorial technical team... |
@danhey, @coljac - many thanks for your reviews here ✨ @martin-millon - your paper is now accepted into JOSS ⚡🚀💥 |
🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉 If you would like to include a link to your paper from your README use the following code snippets:
This is how it will look in your documentation: We need your help! Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:
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@arfon Is there a way with Whedon to get the Latex file from which the paper is generated? I would like to post it on the arXiv. |
@martin-millon - not directly but you can hack it using this script from this issue: openjournals/joss#132 |
Thanks ! |
Submitting author: @martin-millon (Martin Millon)
Repository: https://gitlab.com/cosmograil/PyCS3
Version: v3.0.2
Editor: @arfon
Reviewer: @danhey, @coljac
Archive: 10.5281/zenodo.4046260
Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.
Status
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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
@danhey & @coljac, 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 @arfon 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 ✨
Review checklist for @danhey
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
Review checklist for @coljac
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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