Closed whedon closed 3 years ago
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @JostMigenda, @rafaelab it looks like you're currently assigned to review this paper :tada:.
:warning: JOSS reduced service mode :warning:
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.
:star: Important :star:
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:
For a list of things I can do to help you, just type:
@whedon commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@whedon generate pdf
Software report (experimental):
github.com/AlDanial/cloc v 1.88 T=0.52 s (64.0 files/s, 22191.3 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
HTML 8 729 0 6714
Python 16 499 962 1375
Markdown 4 55 0 278
TeX 1 18 0 239
Jupyter Notebook 2 0 356 162
YAML 2 2 4 42
-------------------------------------------------------------------------------
SUM: 33 1303 1322 8810
-------------------------------------------------------------------------------
Statistical information for the repository '771c9b8052973d42ee3f2975' was
gathered on 2021/04/20.
The following historical commit information, by author, was found:
Author Commits Insertions Deletions % of changes
Alex Pizzuto 29 1291 319 13.88
ChrisCFTung 3 113 32 1.25
Chun Fai Tung 58 1111 267 11.88
Ignacio Taboada 73 1681 2002 31.76
Konstancja Satalecka 3 210 11 1.91
Michael Larson 6 42 26 0.59
René Reimann 71 2876 1615 38.73
Below are the number of rows from each author that have survived and are still
intact in the current revision:
Author Rows Stability Age % in comments
Alex Pizzuto 1139 88.2 1.9 12.20
ChrisCFTung 112 99.1 2.6 13.39
Chun Fai Tung 227 20.4 34.9 14.54
Ignacio Taboada 86 5.1 23.4 12.79
Michael J Larson 35 100.0 1.8 5.71
René Reimann 1237 43.0 37.4 10.02
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.3847/1538-4357/abcaa4 is OK
- 10.1103/PhysRevLett.124.051103 is OK
- 10.1140/epjc/s10052-019-6680-0 is OK
- 10.1126/science.aat1378 is OK
- 10.1126/science.aat2890 is OK
- 10.3847/1538-4357/835/1/45 is OK
- 10.1088/2041-8205/805/1/L5 is OK
- 10.1103/PhysRevD.94.103006 is OK
- 10.1088/1742-6596/632/1/012039 is OK
MISSING DOIs
- 10.22323/1.358.1004 may be a valid DOI for title: Characterization of the Astrophysical Diffuse Neutrino Flux with IceCube High-Energy Starting Events
- 10.22323/1.358.1017 may be a valid DOI for title: Measurement of the diffuse astrophysical muon-neutrino spectrum with ten years of IceCube data
- 10.22323/1.358.1015 may be a valid DOI for title: First Double Cascade Tau Neutrino Candidates in IceCube and a New Measurement of the Flavor Composition
- 10.22323/1.301.0663 may be a valid DOI for title: Constrains on the extragalactic origin of IceCube’s neutrinos using HAWC
- 10.22323/1.358.1017 may be a valid DOI for title: Measurement of the diffuse astrophysical muon-neutrino spectrum with ten years of IceCube data
INVALID DOIs
- None
Hi @ChrisCFTung, thanks for the submission! I’ll install & test the software in a couple of days; for now, just a few initial comments and questions, after looking at the repo and the paper:
Hi @JostMigenda,
Thank you for your comments and questions. Firstly regarding Theo Glauch's contribution, the git history was lost during a migration from Georgia Institute of Technology's git repository to github. In particular, FluxPDF.py
was contributed by Theo.
We have also addressed the other issues you mentioned.
Regarding the comments on the paper:
Regarding init.py and setup.py, version string has been updated.
Regarding the README file, Python3 is now specified in Set-Up.
Hi @ChrisCFTung,
I have read the paper and I am now done testing the software. It looks fine overall, easy to install and easy to use. The examples are very helpful. I will divide my comments in two parts: first about the paper, second about the code.
--> PAPER
Overall I find the paper well-written and I have only minor comments.
FIRESONG was motivated by IceCube, but it clearly has many applications other than neutrino astronomy. For instance, I had to write down a similar code for ultra-high-energy cosmic rays (UHECRs), which turns out to be much slower (~30 times slower) than FIRESONG. It is as useful for neutrinos as it is for UHECRs (and gamma rays). Perhaps these other applications could be briefly mentioned in the paper to reach a broader audience.
The paper refers to cosmolopy, which has now been removed as a dependency, so it should be updated accordingly.
--> CODE
I followed the tutorials and looked into the code to try it out. I had no problems installing nor running it. My comments are more about things that could be useful and some minor suggestions.
Maybe this is me being picky, but I found it annoying that the keyword "Evolution" in firesong_simulation()
is capitalised when all the other keywords are not. I got this wrong twice when trying to run a simple test without copy-pasting. The same goes for "Transient".
When running firesong_simulation()
, I get a dictionary that contains 'sources'. This is also a dictionary containing 'flux', 'z', 'dec'. I tried to write down a function that takes the dictionary and plots the skymap automatically, then I realised 'ra' was missing. I do understand the reason for not including it in the code at first. But I think it would be a useful addition to have this stored in the dictionary for plotting skymaps without having to write down more lines of code. This is very useful for anisotropy analyses.
I am also missing an example with Legend in the notebooks folder.
I have now finished testing the software and have opened issues on the FIRESONG repository where appropriate. These are mostly minor points that shouldn’t take long to resolve, so I hope that we will reach acceptance of this paper before too long.
Apart from the noted issues, the code works well and seems both versatile and useful. It is tested and documented thoroughly. The notebooks give good examples for how to use the code and plot the results; they also nicely illustrate how Firesong and FluxPDF relate to each other. (Like Rafael, I would welcome it if you could add some examples for how to use Legend, too.)
One final point that’s missing right now—as far as I can see— is this one:
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
Just referring people to PRs/Issues on GitHub is perfectly fine, but this should be stated explicitly somewhere; probably in the README file.
Related to community guidelines: I see that the IceCube collaboration has a code of conduct (see Appendix F). Since the FIRESONG repository is under the IceCube organisation on GitHub, I’d assume that it applies to all interactions in this repo as well? If so, that would be good to mention as well; right next to the contribution guidelines.
Interesting! The governance document, including the code of conduct (appendix F) are visible publicly! It's not like that we (IceCube) were hiding the document ... I will need to consult with others if the code of conduct, which was developed for IceCube internal affairs, can or should be applied to non-IceCube people.
Yes—it's linked from IceCube's public web page at https://icecube.wisc.edu/collaboration/institutions/
I noticed that the "Scope" section of the CoC already mentioned the case of "an event participant that is not an IceCube collaborator"; that's why it seemed plausible to me that it could apply here. I understand that this is not what the CoC was originally designed for; on the other hand, having a separate CoC and separate reporting structures may introduce unnecessary confusion, especially since any parties to potential conflicts may likely be IceCube members?
Either way—thanks @itaboada for starting that discussion internally! As far as I understand (@eloisabentivegna, correct me if I'm wrong!), JOSS doesn't require a CoC so while it would be good to clarify this, it shouldn't stop us from proceeding with the review.
:wave: @JostMigenda, please update us on how your review is going (this is an automated reminder).
:wave: @rafaelab, please update us on how your review is going (this is an automated reminder).
Thank you for the comment @rafaelab .
Regarding your comment on the paper, in the paper, we have mentioned publications which applied Firesong on studies of gamma rays in the statement of need section of the paper. Indeed, providing a function to convert Firesong's output to other messengers is one of the open issue for Firesong (#45). However, before that service is mature, we don't want to propose a "standard" way of conversion to the users in this paper, because such conversion is heavily model dependent. We are leaving this up to the users' own capabilities for now.
Regarding the comments for the code
the options will not be changed for the moment, due to possible breakage of existing scripts. However, we will look for a safe way to introduce more coherent option in the future.
Added RA to the output, which is sampled from a uniform distribution. Since we expect the extragalactic sources to be isotropic
Added a notebook as example for Legend.
Hi @ChrisCFTung,
- the options will not be changed for the moment, due to possible breakage of existing scripts. However, we will look for a safe way to introduce more coherent option in the future.
I completely understand that this breaks previous scripts. I saw @JostMigenda's issue and he recommended what I was going to suggest: that these conventions are kept in mind for future releases, if there are any.
- Added RA to the output, which is sampled from a uniform distribution. Since we expect the extragalactic sources to be isotropic
I am aware this is fairly simple, but I think it makes the code more complete and enables easy manipulations of the results as a dictionary.
- Added a notebook as example for Legend.
Having successfully tested this, I have no further comments and I am happy to recommend the paper for publication.
All my comments and issues have been addressed and I'm happy to recommend this paper for publication.
Thanks to @ChrisCFTung and @itaboada for the prompt and helpful responses during the review and congratulations to you and your co-authors!
Thank you @JostMigenda, @rafaelab
(@eloisabentivegna, correct me if I'm wrong!), JOSS doesn't require a CoC so while it would be good to clarify this, it shouldn't stop us from proceeding with the review.
You are correct, @JostMigenda.
Thanks @JostMigenda and @rafaelab for your prompt and thorough reviews. Loads of good points raised and improved. Thanks also to @ChrisCFTung and @itaboada for being so responsive.
I am happy to proceed with prepublication. @ChrisCFTung, could you generate a tagged version and submission archive, as per https://joss.readthedocs.io/en/latest/submitting.html#the-review-process? Please post the details here once you are done.
Hi @eloisabentivegna I have tagged version 1.8 to be the submission version and uploaded the archive to zenodo. The doi of the submission is: 10.5281/zenodo.4744897 It is accessible at https://zenodo.org/record/4744897#.YJiq_GZKjOQ.
Thank you.
@whedon set 1.8 as version
OK. 1.8 is the version.
@whedon set 10.5281/zenodo.4744897 as archive
OK. 10.5281/zenodo.4744897 is the archive.
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@whedon check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.3847/1538-4357/abcaa4 is OK
- 10.1103/PhysRevLett.125.121104 is OK
- 10.1103/PhysRevLett.124.051103 is OK
- 10.22323/1.358.1004 is OK
- 10.22323/1.358.1017 is OK
- 10.22323/1.358.1015 is OK
- 10.1140/epjc/s10052-019-6680-0 is OK
- 10.1126/science.aat1378 is OK
- 10.1126/science.aat2890 is OK
- 10.3847/1538-4357/835/1/45 is OK
- 10.22323/1.301.0663 is OK
- 10.22323/1.358.1017 is OK
- 10.1088/2041-8205/805/1/L5 is OK
- 10.1103/PhysRevD.94.103006 is OK
- 10.1088/1742-6596/632/1/012039 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@ChrisCFTung, it all seems in order, except for two typos in the manuscript:
1) Line 43: "a inverse" -> "an inverse" 2) Line 77: "source distribution" -> "the source distribution"
Could you fix these, regenerate the archive, and post a line once you're done?
@eloisabentivegna
Thank you for spotting the typos. I have updated the archive, and the new DOI is 10.5281/zenodo.4747672
@whedon set 10.5281/zenodo.4747672 as archive
OK. 10.5281/zenodo.4747672 is the archive.
@whedon accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.3847/1538-4357/abcaa4 is OK
- 10.1103/PhysRevLett.125.121104 is OK
- 10.1103/PhysRevLett.124.051103 is OK
- 10.22323/1.358.1004 is OK
- 10.22323/1.358.1017 is OK
- 10.22323/1.358.1015 is OK
- 10.1140/epjc/s10052-019-6680-0 is OK
- 10.1126/science.aat1378 is OK
- 10.1126/science.aat2890 is OK
- 10.3847/1538-4357/835/1/45 is OK
- 10.22323/1.301.0663 is OK
- 10.22323/1.358.1017 is OK
- 10.1088/2041-8205/805/1/L5 is OK
- 10.1103/PhysRevD.94.103006 is OK
- 10.1088/1742-6596/632/1/012039 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.
Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2297
If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2297, then you can now move forward with accepting the submission by compiling again with the flag deposit=true
e.g.
@whedon accept deposit=true
Congratulations to all authors! 🎉
And, of course, thanks to @JostMigenda and @rafaelab for your time and help with the submission. Such an expedited review would have not been possible without your hard work.
@ChrisCFTung - As the AEiC this week, I've proofread your submission in preparation for publication, and found some minor issues, in https://github.com/icecube/FIRESONG/pull/67 - Please either merge this or let me know what you disagree with, then we can proceed to final publication.
@danielskatz Thank you, I have merged the pull request.
@whedon accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.3847/1538-4357/abcaa4 is OK
- 10.1103/PhysRevLett.125.121104 is OK
- 10.1103/PhysRevLett.124.051103 is OK
- 10.22323/1.358.1004 is OK
- 10.22323/1.358.1017 is OK
- 10.22323/1.358.1015 is OK
- 10.1140/epjc/s10052-019-6680-0 is OK
- 10.1126/science.aat1378 is OK
- 10.1126/science.aat2890 is OK
- 10.3847/1538-4357/835/1/45 is OK
- 10.22323/1.301.0663 is OK
- 10.22323/1.358.1017 is OK
- 10.1088/2041-8205/805/1/L5 is OK
- 10.1103/PhysRevD.94.103006 is OK
- 10.1088/1742-6596/632/1/012039 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.
Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2298
If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2298, then you can now move forward with accepting the submission by compiling again with the flag deposit=true
e.g.
@whedon accept deposit=true
@whedon accept deposit=true
Doing it live! Attempting automated processing of paper acceptance...
🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦
🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨
Here's what you must now do:
Party like you just published a paper! 🎉🌈🦄💃👻🤘
Any issues? Notify your editorial technical team...
Congratulations to @ChrisCFTung (Chun Fai Tung) and co-authors!!
And thanks to @JostMigenda and @rafaelab for reviewing, and @eloisabentivegna for editing!
:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:
If you would like to include a link to your paper from your README use the following code snippets:
Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03194/status.svg)](https://doi.org/10.21105/joss.03194)
HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03194">
<img src="https://joss.theoj.org/papers/10.21105/joss.03194/status.svg" alt="DOI badge" >
</a>
reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03194/status.svg
:target: https://doi.org/10.21105/joss.03194
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:
@eloisabentivegna @JostMigenda @rafaelab @danielskatz Thank you, you guys have been great reviewers! I really appreciate this experience.
Submitting author: @ChrisCFTung (Chun Fai Tung) Repository: https://github.com/icecube/FIRESONG Version: 1.8 Editor: @eloisabentivegna Reviewer: @JostMigenda, @rafaelab Archive: 10.5281/zenodo.4747672
:warning: JOSS reduced service mode :warning:
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
Status badge code:
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
@JostMigenda & @rafaelab, 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 @eloisabentivegna 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 @JostMigenda
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
Review checklist for @rafaelab
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper