[REVIEW]: rdbsp: An Open Source Rock Dynamic Behavior Simulation Program

whedon commented 5 years ago

Submitting author: @zhangning737 (Zhang Ning) Repository: https://github.com/zhangning737/rdbsp.git Version: v1.0.0 Editor: @lheagy Reviewers: @dvalters, @srmnitc Archive: 10.5281/zenodo.3335406

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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) 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

@dvalters, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @lheagy know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @dvalters

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[ ] Version: Does the release version given match the GitHub release (v1.0.0)?
[x] Authorship: Has the submitting author (@zhangning737) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[ ] Installation: Does installation proceed as outlined in the documentation?
[ ] Functionality: Have the functional claims of the software been confirmed?
[ ] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[ ] 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)?
[x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
[x] 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

Software paper

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @srmnitc

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Version: Does the release version given match the GitHub release (v1.0.0)?
[x] Authorship: Has the submitting author (@zhangning737) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
[x] 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

Software paper

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

whedon commented 5 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @dvalters it looks like you're currently assigned as the reviewer for this paper :tada:.

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whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

lheagy commented 5 years ago

@dvalters, many thanks for being willing to review! Above there is a checklist to help guide your review. Please let me know if you have any questions or if I can provide any clarification.

lheagy commented 5 years ago

👋 Hi @dvalters, just checking in this review. Please let me know if you have any questions.

lheagy commented 5 years ago

👋 Hi @dvalters, checking in on this - when do you think you will have time to start your review? Thanks!

dvalters commented 5 years ago

Oh sorry @lheagy - totally slipped my mind. Will start tonight 👍

Apologies!

On Tue, 16 Apr 2019, 23:51 Lindsey Heagy, notifications@github.com wrote:

👋 Hi @dvalters https://github.com/dvalters, checking in on this - when do you think you will have time to start your review? Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1328#issuecomment-483872565, or mute the thread https://github.com/notifications/unsubscribe-auth/ACT4WW5PBFYQLXBQHKLUVD3PQZJ5XANCNFSM4G7CQQGA .

lheagy commented 5 years ago

Many thanks @dvalters, please let me know if you have any questions along the way

dvalters commented 5 years ago

Apologies for the delay to my review @lheagy, @zhangning737, this has been due to difficulty in obtaining access to the proprietary Intel compiler required for the installation process.

Can I ask @lheagy, would this requirement be a barrier to acceptance in JOSS?

@zhangning737, is there a way to compile this with an open-source compiler (i.e. gcc) ?

danielskatz commented 5 years ago

👋 @dvalters - you've written to @zhaozhang above, but the software is by @zhangning737

dvalters commented 5 years ago

Apolgies @zhangning737, my question was if there is a way to compile with an open source compiler, or plans to include this functionality in the near future?

lheagy commented 5 years ago

Thanks @dvalters! I have started issue zhangning737/rdbsp#1 to discuss compiler options. @zhangning737: could you please provide some pointers on where to access compilers for the code? It would be preferable if this could be achieved with an open source compiler. If this is not possible, I will check with the editorial board on any concerns for acceptance.

zhangning737 commented 5 years ago

@lheagy @dvalters Actually Intel compiler provide free license to open source contributors. I think just refer this repo could get a free license. Here chooses intel compiler since this software using a mkl subroutine. Of cource it could be compiled with gcc and vc community after minor changes. But I think Intel complier provides long term supports for open source community.

lheagy commented 5 years ago

Thanks @zhangning737. @dvalters: can you give it a try with the link that @zhangning737 provided? If you run into any issues, one option we have is to try installing on mybinder.org

lheagy commented 5 years ago

:wave: Just checking in @dvalters: were you able to get up and running? or would it be beneficial for @zhangning737 to set up a binder-demo?

lheagy commented 5 years ago

Hi @dvalters, would you be willing to take another look at this submission? If so, do you have a time-estimate of when you can get to it? If not, please let me know. Thanks!

lheagy commented 5 years ago

And just a note @zhangning737: if we don't hear back by early next week, I will begin looking for another reviewer to jump in. Thanks for your patience

zhangning737 commented 5 years ago

@lheagy no problem...

lheagy commented 5 years ago

:wave: Hi @jordigh, would you be willing to jump in on this review for JOSS?

lheagy commented 5 years ago

:wave: Hi @danehkar and @srmnitc would you be willing to review this submission for JOSS? The review is already in progress thanks to the help of @dvalters, but we are in need of reviewers to help on the next revision. If you are not able to but have suggestions of other possible reviewers, I would be grateful. Thanks!

srmnitc commented 5 years ago

Hi @lheagy , I think I can help with the review process.

lheagy commented 5 years ago

Many thanks @srmnitc!! I will add you as a reviewer. In the main issue thread above, there will be a checklist that can help guide your review. Please let me know if you have any questions or if I can provide any clarification. And thanks again :)

lheagy commented 5 years ago

@whedon add @srmnitc as reviewer

whedon commented 5 years ago

OK, @srmnitc is now a reviewer

lheagy commented 5 years ago

:wave: @srmnitc, just checking here. Do you think you will have time in the next week to take a look at this submission? Thanks!

srmnitc commented 5 years ago

@lheagy yes definitely. I am currently travelling, but I will definitely be able to take a look in the next few days.

lheagy commented 5 years ago

Many thanks @srmnitc! Safe travels

srmnitc commented 5 years ago

@zhangning737 @lheagy I was finally able to try compiling the code, but I was not successful. I am not sure if its a specific issue with my setup, but in any case, I am of the opinion that there should be more detailed instructions to compile successfully. I have created an issue on the repo

srmnitc commented 5 years ago

@zhangning737 I have also raised an issue with citations and generally citations of books. @lheagy I am reviewing for the first time, so, do I have to take into account typos and other issues in the paper text?

lheagy commented 5 years ago

@srmnitc: If you are willing to point out typos as you spot them (or create a pull request to fix them), that would be much appreciated!

srmnitc commented 5 years ago

@lheagy thanks! Fixed some typos and created a pull request now.

zhangning737 commented 5 years ago

@srmnitc compiling error might relate to the newly update of intel compiler, I'll checking it with the newest version. Thanks.

zhangning737 commented 5 years ago

@lheagy Already pull the request. @srmnitc Please check the configuration model of Intel Compiler. I think I should add that to documentation. If anything else not right, please let me know. Thanks all.

lheagy commented 5 years ago

Thanks @zhangning737. @srmnitc, would you be willing to take a look at the updates?

srmnitc commented 5 years ago

@lheagy just finished looking at it. Most issues are now fixed - installation and tests work perfectly except for some minor changes which I have kept open as an issue. The DOIs on the paper are incomplete, so I have kept the issue open.

srmnitc commented 5 years ago

@lheagy @zhangning737 I still think a better documentation is required - the existing one is complete, but inaccessible from a non specialist perspective. A detailed documentation with example usage would be a recommendation for the future.

srmnitc commented 5 years ago

@lheagy @zhangning737 There are only two issues holding back my review - 1) the DOIs of references are not complete 2) There is no release version of github

zhangning737 commented 5 years ago

@srmnitc Thanks for your advice, the documentation will be improved with more detailed information. @lheagy @srmnitc The DOIs have been added, and removed the debug option and added a tag for release...

srmnitc commented 5 years ago

@lheagy @zhangning737 I think all the points in the checklist are okay now. So, I have finished my review. Thanks for all the quick updates @zhangning737!

lheagy commented 5 years ago

Excellent, many thanks for your review @srmnitc!

lheagy commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

lheagy commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


OK DOIs

- 10.1201/9781315391304 is OK
- 10.1016/j.tust.2015.06.006 is OK
- 10.1007/s002110050020 is OK
- 10.1016/B978-0-08-044606-6.X5000-0 is OK
- 10.1016/C2009-0-24909-9 is OK
- 10.1002/nme.1620170504 is OK
- 10.1016/0749-6419(90)90007-2 is OK
- 10.1002/eqe.4290160314 is OK

MISSING DOIs

- None

INVALID DOIs

- None

lheagy commented 5 years ago

👋 Hi @zhangning737, I started pr zhangning737/rdbsp#6 with a few minor grammatical updates to the paper. Please take a look when you have a chance.

zhangning737 commented 5 years ago

@lheagy Thank you for your revisions. Looks better now... Already pulled...

lheagy commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

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