[REVIEW]: Frackit: a framework for stochastic fracture network generation and analysis

whedon commented 4 years ago

Submitting author: @dglaeser (Dennis Gläser) Repository: https://git.iws.uni-stuttgart.de/tools/frackit Version: v1.2 Editor: @diehlpk Reviewers: @ilyasst, @ctdegroot Archive: 10.5281/zenodo.4315059

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Reviewer instructions & questions

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

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Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

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

Review checklist for @ilyasst

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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] Contribution and authorship: Has the submitting author (@dglaeser) 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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @ilyasst it looks like you're currently assigned to review this paper :tada:.

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whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.18419/opus-289 is OK
- doi.org/10.1016/j.cageo.2015.04.012 is OK
- doi.org/10.1016/j.jhydrol.2015.08.065 is OK
- 10.5194/hess-23-19-2019 is OK
- 10.1016/j.cageo.2017.02.002 is OK
- 10.1016/j.advwatres.2011.03.007 is OK
- doi.org/10.1016/j.advwatres.2017.10.031 is OK
- doi.org/10.1007/s13137-019-0116-8 is OK
- 10.1002/nme.2579 is OK
- 10.1002/nme.6238 is OK
- 10.1016/j.advwatres.2017.10.036 is OK
- doi.org/10.1016/j.petrol.2019.106350 is OK
- 10.1016/j.jcp.2014.12.047 is OK
- 10.1016/j.jcp.2017.07.041 is OK
- doi.org/10.1007/s13137-019-0117-7 is OK
- 10.1016/j.cageo.2019.06.014 is OK
- doi.org/10.1007/s10596-018-9778-9 is OK
- 10.1016/j.jcp.2017.12.003 is OK
- doi.org/10.1007/s12665-014-3211-z is OK
- doi.org/10.1016/j.fuel.2011.08.037 is OK
- 10.1016/j.applthermaleng.2011.01.038 is OK
- 10.1016/j.rser.2014.04.068 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 years ago

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

diehlpk commented 4 years ago

Reviewer instructions & questions

@johntfoster, 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @diehlpk know.

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

Review checklist for @johntfoster

Conflict of interest

[ ] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

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

General checks

[ ] Repository: Is the source code for this software available at the repository url?
[ ] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[ ] Contribution and authorship: Has the submitting author (@dglaeser) 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

[ ] 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)?
[ ] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[ ] 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

[ ] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[ ] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

diehlpk commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

diehlpk commented 4 years ago

@ilyasst and @johntfoster How is your review going?

diehlpk commented 4 years ago

Hi @ilyasst can you estimate when you finish the review?

ilyasst commented 4 years ago

Hopefully in a week or two.

Ilyass

On Jul 20 2020, at 9:48 am, Patrick Diehl notifications@github.com wrote:

Hi @ilyasst (https://github.com/ilyasst) can you estimate when you finish the review? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub (https://github.com/openjournals/joss-reviews/issues/2291#issuecomment-661051101), or unsubscribe (https://github.com/notifications/unsubscribe-auth/AADMMM7N3DFROS6FQHSMJO3R4RDMRANCNFSM4NTSI3MA).

diehlpk commented 4 years ago

Hi @johntfoster can you estimate when you finish the review?

johntfoster commented 4 years ago

I'll also shoot for the end of next week. Sorry for the delay.

On Wed, Jul 22, 2020 at 9:25 AM Patrick Diehl notifications@github.com wrote:

Hi @johntfoster https://github.com/johntfoster can you estimate when you finish the review?

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diehlpk commented 4 years ago

@ilyasst Thanks for finishing the review. You are done with the review. You will get a notification once we paper is published.

diehlpk commented 4 years ago

Hi @johntfoster could you please estimate when you intend to finish the review?

dglaeser commented 4 years ago

Thank you all for your efforts! Let me know if there is anything I can do to help!

diehlpk commented 4 years ago

@dglaeser We are waiting for the review of the second reviewer and as long as he has no remarks you are good.

diehlpk commented 4 years ago

@dglaeser Can you recommend someone on your community as a potential reviewer?

dglaeser commented 4 years ago

I would have one person in mind, do you want me to tag him here or send you an email adress?

diehlpk commented 4 years ago

I would have one person in mind, do you want me to tag him here or send you an email adress?

Put his name here without the @ and I will ask him.

dglaeser commented 4 years ago

I was thinking of Eirik Keilegavlen (keileg on GitHub).

diehlpk commented 4 years ago

Hi @keileg would you be interested to review this paper?

keileg commented 4 years ago

Sure, I can have a look. This looks like an interesting review process, in addition to the paper itself.

diehlpk commented 4 years ago

@whedon add @keileg as reviewer

whedon commented 4 years ago

OK, @keileg is now a reviewer

keileg commented 4 years ago

@diehlpk having read the COI policy, there are one or two things to clarify. Do I write here or in an email?

diehlpk commented 4 years ago

@diehlpk having read the COI policy, there are one or two things to clarify. Do I write here or in an email?

If you feel comfortable, please write them here.

keileg commented 4 years ago

No problem, it is all public:

Over the last 2-3 years I have collaborated with the first and second author of the paper on a benchmarking problem. This has resulted in two manuscripts on arXiv (a benchmark specification and a draft paper), the latter of which is under review in a journal.
The fourth author has an adjoint position in my research group, and will be co-advisor for a new PhD student of mine.

Personally, I am confident I will give an unbiased evaluation of the paper despite the above points, but I don't know what the journal policy is in such cases.

diehlpk commented 4 years ago

No problem, it is all public:

1. Over the last 2-3 years I have collaborated with the first and second author of the paper on a benchmarking problem. This has resulted in two manuscripts on arXiv (a [benchmark specification](https://arxiv.org/abs/1809.06926) and a draft [paper](https://arxiv.org/abs/2002.07005)), the latter of which is under review in a journal.

2. The fourth author has an adjoint position in my research group, and will be co-advisor for a new PhD student of mine.

Personally, I am confident I will give an unbiased evaluation of the paper despite the above points, but I don't know what the journal policy is in such cases.

@keileg I think the recent immediate collaborators results in a conflict. Could you point me to a different reviewer?

diehlpk commented 4 years ago

@whedon remove @keileg as reviewer

whedon commented 4 years ago

OK, @keileg is no longer a reviewer

diehlpk commented 4 years ago

@johntfoster Are you still interested to do the review? If not could you recommend a new reviewer?

keileg commented 4 years ago

No problem, it is all public:
1. Over the last 2-3 years I have collaborated with the first and second author of the paper on a benchmarking problem. This has resulted in two manuscripts on arXiv (a [benchmark specification](https://arxiv.org/abs/1809.06926) and a draft [paper](https://arxiv.org/abs/2002.07005)), the latter of which is under review in a journal.

2. The fourth author has an adjoint position in my research group, and will be co-advisor for a new PhD student of mine.
Personally, I am confident I will give an unbiased evaluation of the paper despite the above points, but I don't know what the journal policy is in such cases.
@keileg I think the recent immediate collaborators results in a conflict. Could you point me to a different reviewer?

Okay.

You may want to try Michael Sargado, GitHub user name jmsargado.

diehlpk commented 4 years ago

Hi @jmsargado would you be interested to review this paper?

diehlpk commented 4 years ago

Hi @katyhuff @Kevin-Mattheus-Moerman @moorepants would you be interested to review this paper?

johntfoster commented 4 years ago

Apologies, I'm trying to get to it. I've been very busy.

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@johntfoster https://github.com/johntfoster Are you still interested to do the review? If not could you recommend a new reviewer?

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katyhuff commented 4 years ago

I'm sorry I won't have the bandwidth or the expertise to do this review.

Kevin-Mattheus-Moerman commented 4 years ago

@diehlpk sorry I cannot review this at this time.

moorepants commented 4 years ago

Hi @katyhuff @Kevin-Mattheus-Moerman @moorepants would you be interested to review this paper?

No, I am already committed to other reviews.

katyhuff commented 4 years ago

@diehlpk I'm sorry, this is not my field.

Looking through the joss reviewer list (and avoiding topic editors, who are usually swamped anyway), I see some candidates with some expertise in fractures, geomechanics, structural mechanics, solid mechanics etc.. Perhaps you have already considered bhajay, whimian, corentin-dev, yangbai90 iagolemos1, thelfer, mattkram?

diehlpk commented 4 years ago

@whedon add @ctdegroot as reviewer

whedon commented 4 years ago

OK, @ctdegroot is now a reviewer

diehlpk commented 4 years ago

Reviewer instructions & questions

@ctdegroot, 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @diehlpk know.

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

Review checklist for @ctdegroot

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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] Contribution and authorship: Has the submitting author (@dglaeser) 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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

diehlpk commented 3 years ago

Hi @ctdegroot and @johntfoster how is your review going?

ctdegroot commented 3 years ago

@diehlpk I am unable to check of items in the list above...

diehlpk commented 3 years ago

@whedon re-invite @ctdegroot as reviewer

whedon commented 3 years ago

The reviewer already has a pending invite.

@ctdegroot please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

diehlpk commented 3 years ago

@diehlpk I am unable to check of items in the list above...

@ctdegroot I invited you again. The invitation expires after two weeks.

diehlpk commented 3 years ago

@ctdegroot Is it working for you ?

diehlpk commented 3 years ago

@johntfoster Would you be fine with removing you from the list of reviewers, since I found a second one?

diehlpk commented 3 years ago

@ctdegroot Could you please tell me your timeline for this review?

johntfoster commented 3 years ago

Yes, please do. And I apologize for not being able to complete a timely review. I really thought I could when I accepted.

On Fri, Oct 30, 2020 at 9:04 AM Patrick Diehl notifications@github.com wrote:

@johntfoster https://github.com/johntfoster Would you be fine with removing you from the list of reviewers, since I found a second one?

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