-
-
Notifications
You must be signed in to change notification settings - Fork 39
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
[REVIEW]: CSaransh: Software Suite to Study Molecular Dynamics Simulations of Collision Cascades #1461
Comments
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @jmborr, it looks like you're currently assigned as the reviewer for this paper 🎉. ⭐ 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:
For a list of things I can do to help you, just type:
|
|
@katyhuff — have you had any success looking for alternate reviewers? |
I am running the instructions in README.md in a Ubuntu 16.04 box. This I was able to do:
The duplication of this widget within section "View and Compare Cascade Info" is by design? |
Thank you for taking this up. :) Yes, the duplication is meant for comparison. The widget has a lock on top left. With lock open, it will show the stats for currently viewing cascade while once locked the stats get fixed on the current one selected. Thus, one cascade can be fixed on one of the widget and its stats can be compared with others as one views different cascades on the other widget with open lock. By default, the left widget is locked on some arbitrary cascade and right one would change as one selects the cascade from the main table. May be in future we can introduce some better interface to compare figures of two cascades but for now this does the job. Please let me know of any other clarification if needed :) |
The installation went smoothly. I agree with @jmborr that
There are a few dois missing. |
The IAEA challenge shows a need for visualization and analysis tools for collisional cascade molecular dynamics simulation data. Are the results of the challenge available somewhere? I could not find it on their website? |
Thanks @arose for your review! Thank you @jmborr for your review efforts so far. Perhaps the remainder of your review could be revisited at this point (checkboxes at the top of the page). @haptork, can you please respond (with changes to the code, install instructions, etc.) to the requests by the reviewers so far (i.e. the comment regarding adding the npm install command to the instructions, the comment from @rose regarding the dois and the results of the iaea challenge). |
Thank you @arose for reviewing.
Added to the instructions with latest commit (6114548d4da347d386cefa20da28d8db67bea651)
The results were e-mailed to the participants. The results and the software tools of the participants are planned to be put up on the https://cascadesdb.org/ website which is a work in progress as of now. The database that the contest uses and the one which is shown by default in csaransh does have an indirect reference. The database page of the contest is https://www-amdis.iaea.org/CDB/challenge/, for each data point it has a webpage (https://www-amdis.iaea.org/CDB/challenge/data/001.html), which shows the DOI of the publication for the datapoint. The reference publication for the data is http://doi.org/10.1038/s41467-018-03415-5 which we have added as a reference in paper.bib. I don’t think there is any other reference for it now. We can share the mail notifying the results. Also, MoD-PMI presentation participation mentioned in paper, now has a link in the MoD-PMI web page ( http://dpc.nifs.ac.jp/dkato/MoD-PMI2019/ ) . Let me know if anything needs to be done from our side to get the references checked. |
@whedon generate pdf |
|
@whedon check references |
|
|
@katyhuff |
@whedon generate pdf |
|
@katyhuff thanks for your hard work. I feel I have to apologize here because I was very very slow with my review. I was caught at a time where my organization is under pressure to finish a ton of work before some hard deadlines. It was difficult to set aside time for the review 😞 |
@katyhuff The zenodo DOI is: https://doi.org/10.5281/zenodo.3406703. The version number is now 0.3.2. |
@whedon set v0.3.2 as version |
OK. v0.3.2 is the version. |
@whedon set 10.5281/zenodo.3406703 as archive |
OK. 10.5281/zenodo.3406703 is the archive. |
@openjournals/joss-eics : I believe this is ready for your review |
@openjournals/joss-eics : I believe this is ready for your review / cc @kthyng |
Hi @haptork! A few items to wrap up your submission:
Edits for paper:
|
Wow @kthyng sorry I missed all of these things (especially the version -- it's in my checklist, so I'm not at all sure how I missed it!) Thanks for your sharp eyes! |
The zenodo archive version for the DOI I mentioned is 0.3.2 (in its metadata) which corresponds to: https://github.com/haptork/csaransh/releases/tag/v0.3.2. Please ignore the later two versions in the GitHub repo. Sorry for the confusion.
Thank you. Corrected.
Thank you. Added the and removed preprint from the sentence. The paper is in communication in a peer reviewed journal.
Thanks. Corrected.
Corrected. Thanks.
Thanks. It had already been corrected before archiving.
Thanks. Corrected
Thanks. It had already been corrected before archiving. commit for the corrections: d9d3cb9f6e84b737ba22dfd5064d8a545cbb5cc7 Please let me know if anything is to be done. |
@whedon set 10.5281/zenodo.3434635 as archive |
OK. 10.5281/zenodo.3434635 is the archive. |
Great! Thanks @haptork for addressing those items. |
@whedon accept |
|
Check final proof 👉 openjournals/joss-papers#970 If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#970, then you can now move forward with accepting the submission by compiling again with the flag
|
@whedon accept deposit=true |
|
🐦🐦🐦 👉 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... |
🎉🎉🎉 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:
|
Submitting author: @haptork (Utkarsh Bhardwaj)
Repository: https://github.com/haptork/csaransh
Version: v0.3.2
Editor: @katyhuff
Reviewer: @jmborr, @arose
Archive: 10.5281/zenodo.3434635
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
@jmborr & @arose, 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 @katyhuff know.
✨ Please try and complete your review in the next two weeks ✨
Review checklist for @jmborr
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
paper.md
file include a list of authors with their affiliations?Review checklist for @arose
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
paper.md
file include a list of authors with their affiliations?The text was updated successfully, but these errors were encountered: