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[REVIEW]: The Data Behind Dark Matter: Exploring Galactic Rotation #184

Closed whedon closed 1 year ago

whedon commented 2 years ago

Submitting author: !--author-handle-->@villaa<!--end-author-handle-- (Anthony Villano) Repository: https://github.com/villano-lab/galactic-spin-W1 Branch with paper.md (empty if default branch): Version: v3.0.4 Editor: !--editor-->@moorepants<!--end-editor-- Reviewers: @Carreau, @besk467 Archive: 10.5281/zenodo.7951874

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Markdown: [![status](https://jose.theoj.org/papers/9fc3443a7c138ea1a3e1a15f4a3f14df/status.svg)](https://jose.theoj.org/papers/9fc3443a7c138ea1a3e1a15f4a3f14df)

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

@Carreau & @noelstoj, 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/jose-reviews/invitations

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

Conflict of interest

Code of Conduct

General checks

Documentation

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

JOSE paper

Review checklist for @besk467

Conflict of interest

Code of Conduct

General checks

Documentation

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

JOSE paper

whedon commented 2 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @Carreau, @noelstoj 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/jose-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 😿

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whedon commented 2 years ago

Wordcount for paper.md is 1184

whedon commented 2 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.15 s (328.5 files/s, 76011.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           7            943           1844           1230
Jupyter Notebook                10              0           4290            876
TeX                              2             41              0            497
Markdown                        10            133              0            468
YAML                             7             19             48            339
reStructuredText                12            196            271            319
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            50           1344           6461           3764
-------------------------------------------------------------------------------

Statistical information for the repository 'a529a8ff339568830662d8b5' was
gathered on 2022/09/13.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Judit Bergfalk                  37          2449           4400           37.03
Kitt                             7          1314            428            9.42
Kitty                           45          1507           1698           17.33
Kitty Harris                     2             5              5            0.05
Raphael Hatami                  12          5612            281           31.86
nuclearGoblin                    3           360            439            4.32

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
Judit Bergfalk             1138           46.5          3.1               20.30
Kitty                      2285          151.6          0.4               12.52
Raphael Hatami              594           10.6          0.0               20.54
whedon commented 2 years ago

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

whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1086/182804 is OK
- 10.1046/j.1365-8711.2003.06165.x is OK
- 10.3847/0004-6256/152/6/157 is OK
- 10.5281/zenodo.5570790 is OK
- 10.1093/mnras/203.3.735 is OK
- 10.1051/0004-6361/201116634 is OK
- 10.1111/j.1365-2966.2008.12837.x is OK
- 10.1111/j.1365-2966.2007.11532.x is OK
- 10.1093/mnras/stv568 is OK
- 10.1086/318767 is OK
- 10.1051/0004-6361/201425339 is OK
- 10.1111/j.1365-2966.2008.13422.x is OK
- 10.1086/505345 is OK
- 10.1086/527543 is OK
- DOI:10.5281/zenodo.6588350 is OK

MISSING DOIs

- 10.5860/choice.35-2173 may be a valid DOI for title: An Introduction to Error Analysis: The Study of Uncertainties in Physical Measurements

INVALID DOIs

- None
moorepants commented 2 years ago

@Carreau and @noelstoj we will conduct the review in this issue. Please read through the above information and let me know if you have any questions about process. Is it possible for you to review the paper and repository within 4 weeks time?

moorepants commented 2 years ago

The missing DOI leads to a login page: image Is there a way to link to a public version of the paper?

nuclearGoblin commented 2 years ago

That DOI links to a book that does not appear to have a public copy, but it does have a page on the AIP website, would that be an appropriate link?

moorepants commented 2 years ago

I would just cite the book as a traditional citation sans the DOI, as the DOI doesn't seem to lead to the book.

moorepants commented 2 years ago

@whedon set v3.0.0 as version

whedon commented 2 years ago

OK. v3.0.0 is the version.

Carreau commented 2 years ago

Linking to comments in pre-review:

Sérsic bulges(Edo Noordermeer,2008),

Missing space before the opening bracket if we compare to other citations – I don't know if the authors want to fix that.

I also see on the repository that the author have packaged everything to be available on Binder – that I have started to play with and would have love to have 15 years ago in my cosmo classes – maybe the author want to say one or two sentence as to whether they feel it is better to have local install for users to retain their work and. have a working environment, or prefer the ease of use of the an ephemeral binder ?

I finished going through the notebooks and material, and it is a really great content, that show some limitation of Jupyter like having to guide users to "Run all", and sometime the lack of obvious indication that computation is happening, but that is something the jupyter team should fix not the author. I found 1 broken link, for which I sent a PRs.

Carreau commented 2 years ago

I found 1 broken link, for which I sent a PRs.

https://github.com/villano-lab/galactic-spin-W1/pull/32

I actually forgot the press the "Send PR" button...

whedon commented 2 years ago

:wave: @noelstoj, please update us on how your review is going (this is an automated reminder).

villaa commented 2 years ago

@moorepants is there any update from the second reviewer

moorepants commented 2 years ago

No, I've emailed him a couple of times since he agreed to review and have not gotten a response. I need to find another reviewer.

moorepants commented 2 years ago

@villaa Might you have more suggestions for reviewers? I'm not from this field or research/education. Maybe you know more?

villaa commented 2 years ago

@villaa Might you have more suggestions for reviewers? I'm not from this field or research/education. Maybe you know more?

I don't know anyone else on the reviewer list; but I might know some others who have the skills to do it.

I'm not sure if @matthewfeickert would be able to review, but they are very well qualified in all things code and strong overlap with my type of science.

I'll look for others in my field who might be good; shall I send you their emails separately?

matthewfeickert commented 2 years ago

Hi @villaa! :wave: Thanks for thinking of me. I'm unfortunately a bit over committed with work until early December, so I think for the timeline you need I won't be of much help — sorry!

I just wanted to say though that I think that your workshop looks excellent and I think it is fantastic that you're submitting to JOSE! Congratulations in advance on the great work! :rocket:

villaa commented 2 years ago

Thanks @matthewfeickert 👍 -- totally understand about being over-committed!

nuclearGoblin commented 2 years ago

@\villaa Might you have more suggestions for reviewers? I'm not from this field or research/education. Maybe you know more?

(I hope it's okay for me to give some suggestions as well, I can also send a list of a few reviewers if you like.) From the JOSS reviewers list, would @\dpshelio be able to review? It looks like he is familiar with physics programming, python, and astrophysics.

nuclearGoblin commented 1 year ago

@moorepants Is there anything else we can do to help move things forward? We are happy to come up with a new list of reviewers if that would be helpful.

moorepants commented 1 year ago

Yes, please provide a list of reviewers. I have dropped the ball on this (sorry). I tried to search for github users that worked on similar packages and sent a number of email requests for reviewers some time back, but the only hit I got didn't follow through. Ideally we can find an educator in this field that has some software experience. Suggestions are welcome.

moorepants commented 1 year ago

Hi @dpshelio, might you be interested in reviewing this Journal of Open Source Education paper on "The Data Behind Dark Matter: Exploring Galactic Rotation"?

villaa commented 1 year ago

@mattbellis are you willing to review this submission for JOSE--it's a workshop/tutorial on dark matter physics. We've struggled to find a second reviewer so it might even be OK if you can only get to it with a significant delay (say sometime in the new year).

Anyway, it occurred to me you'd be an excellent reviewer here. If you can't, no worries, hope all is well.

mattbellis commented 1 year ago

@villaa Sure thing! I won't be able to really look over anything until mid-Jan, but I will try to move it along once I do. Is that time-frame OK?

villaa commented 1 year ago

@villaa Sure thing! I won't be able to really look over anything until mid-Jan, but I will try to move it along once I do. Is that time-frame OK?

@mattbellis absolutely! Thanks Matt!

mattbellis commented 1 year ago

@villaa You're welcome! What's the next step?

villaa commented 1 year ago

@villaa You're welcome! What's the next step?

probably @moorepants can acknowledge you as a reviewer and put a checklist in this thread. Once you're done with the checklist and if you recommend for publication, the review is finished. @moorepants please confirm.

mattbellis commented 1 year ago

:+1:

labarba commented 1 year ago

@moorepants – Could you pop in this review thread? We have a reviewer who has dropped, but a volunteer who was suggested by the author can replace them. Check it out!

villaa commented 1 year ago

@labarba -- can we add our new reviewer so the thread is ready when he is ready to work on it.

mattbellis commented 1 year ago

I can start looking over this repo / publication whenever I am officially added as a reviewer.

labarba commented 1 year ago

@whedon add @mattbellis as reviewer

whedon commented 1 year ago

OK, @mattbellis is now a reviewer

labarba commented 1 year ago

@whedon remove @noelstoj as reviewer

whedon commented 1 year ago

OK, @noelstoj is no longer a reviewer

moorepants commented 1 year ago

HI @mattbellis. Can you provide some background to you expertise for this review? I wasn't able to quickly find anything online.

mattbellis commented 1 year ago

Sure. I'm an associate professor in the department of physics and astronomy at Siena College. I've been here since 2012.

https://www.siena.edu/faculty-and-staff/person/matthew-bellis/

My primary research is particle physics. I'm currently a member of the CMS and BaBar collaborations and prior to that, I worked with the CLAS and GlueX experiments at Jefferson Lab. I've also collaborated with others and presented posters on work with open data released by the CoGeNT dark matter experiment. Part of my work with CMS involved new dark matter signatures.

I've published work on using GPUs to speed up calculations relevant to large-scale structure in the universe.

I've done a fair amount of work within Siena related to computing in the classroom and I maintain a website with students, Particle Physics Playground that provides simplified data and tutorials for anyone to use.

https://particle-physics-playground.github.io/

I've published in JOSS previously, though never served as a reviewer.

https://joss.theoj.org/papers/10.21105/joss.00384

moorepants commented 1 year ago

Fantastic, thanks for info. That is a perfect fit.

It looks like Lorena made the correct whedon commands, but the reviewer change is not reflected in the opening comments. I'll try it again.

moorepants commented 1 year ago

@whedon remove @noelstoj as reviewer

whedon commented 1 year ago

OK, @noelstoj is no longer a reviewer

moorepants commented 1 year ago

Ok, it looks correct for me now. @mattbellis make sure to read the https://joss.readthedocs.io/en/latest/reviewer_guidelines.html and let me know if you have any questions. Thanks for volunteering.

mattbellis commented 1 year ago

Will do! And you're welcome!

villaa commented 1 year ago

@mattbellis -- just pinging on this review. Thanks again for agreeing to review.

labarba commented 1 year ago

Hi @villaa — could I ask you to address your queries to the handling editor? As you know, everyone is a volunteer here, and we find that being considerate to the different roles is a good idea. Your handling editor also knows if they have have some other thread going with the reviewers (via email or other comms). And thank you for your patience with the review process! 🙏

villaa commented 1 year ago

@moorepants -- can you provide an update on the status of this review?

moorepants commented 1 year ago

I have not heard anything from @mattbellis. @mattbellis can you report in on the status of your review?

mattbellis commented 1 year ago

Thank you for the nudge. I'll be working on this this week. Was actually running it a moment ago after receiving these reminders.

moorepants commented 1 year ago

Hi @mattbellis, have you had a chance to work on this last week?