[REVIEW]: The Basic Model Interface 2.0: A standard interface for coupling numerical models in the geosciences #2317

whedon · 2020-06-09T15:44:37Z

Submitting author: @mdpiper (MARK PIPER)
Repository: https://github.com/csdms/bmi
Version: v2.0
Editor: @diehlpk
Reviewer: @yangbai90, @teuben
Archive: 10.5281/zenodo.3955010

⚠️ JOSS reduced service mode ⚠️

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:

HTML: <a href="https://joss.theoj.org/papers/f0700d419c760b528d79468be4346d4d"><img src="https://joss.theoj.org/papers/f0700d419c760b528d79468be4346d4d/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/f0700d419c760b528d79468be4346d4d/status.svg)](https://joss.theoj.org/papers/f0700d419c760b528d79468be4346d4d)

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

@yangbai90 & @teuben, 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 @yangbai90

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 (@mdpiper) 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?

Review checklist for @teuben

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 (@mdpiper) 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?

The text was updated successfully, but these errors were encountered:

whedon · 2020-06-09T15:44:40Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @yangbai90, @teuben it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

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.

⭐ 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:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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

whedon · 2020-06-09T15:44:59Z

Reference check summary:

OK DOIs

- 10.1029/2018JF004757 is OK

MISSING DOIs

- https://doi.org/10.1177/1094342011414036 may be missing for title: High-performance language interoperability for scientific computing through Babel
- https://doi.org/10.5194/nhess-19-1723-2019 may be missing for title: Evaluating the impact of model complexity on flood wave propagation and inundation extent with a hydrologic-hydrodynamic model coupling framework
- https://doi.org/10.1016/j.cageo.2012.04.002 may be missing for title: A component-based approach to integrated modeling in the geosciences: The design of CSDMS

INVALID DOIs

- None

whedon · 2020-06-09T15:45:07Z

👉 Check article proof 📄 👈

mdpiper · 2020-06-09T19:51:25Z

A quick note: in a pre-submission issue, editors suggested this submission be reviewed in the context of the language specifications and examples derived from the interface defined in the main repository.

yangbai90 · 2020-06-10T12:35:46Z

Hi @mdpiper , I checked your repository. It seems the source code of bmi can't be download via git clone, instead, one can only get the source code from the release page. Is it correct?

mdpiper · 2020-06-10T13:09:01Z

Hi @yangbai90 -- All source is on GitHub, and can be cloned. Note that the only contents of the main repo are documentation and an interface definition file. Source for language specifications derived from the interface are in separate repos listed in the README.

diehlpk · 2020-06-11T14:08:27Z

@mdpiper Are these listed in the JOSS paper as well? If, not would it be possible to add them?

mdpiper · 2020-06-11T14:23:35Z

@diehlpk Yup! See Table 1 in the paper.

diehlpk · 2020-06-12T19:37:57Z

@yangbai90 Can you please confirm that you finished your review? It seems that you have ticked all boxes.

yangbai90 · 2020-06-14T07:37:07Z

Hi @diehlpk, on my side, the paper is ready for publishing.

diehlpk · 2020-06-16T01:38:45Z

Hi @yangbai90 thanks for your effort supporting JOSS :)

diehlpk · 2020-06-26T20:32:08Z

@teuben How is your review going?

teuben · 2020-06-27T14:51:24Z

I hope to finish this by tomorrow.

…

On Fri, Jun 26, 2020, 16:32 Patrick Diehl ***@***.***> wrote: @teuben <https://github.com/teuben> How is your review going? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2317 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAZ4MGODFTEDJ4YX46BLLRTRYUAVLANCNFSM4NZRAPUA> .

diehlpk · 2020-06-29T14:33:45Z

@teuben Thanks for the update.

mdpiper · 2020-07-10T00:45:30Z

Hi @teuben, I think we've addressed your comments in csdms/bmi#68, csdms/bmi#69, and csdms/bmi#70. When you have time, would you please check the open PRs listed under each issue? If they pass muster, I'll merge the PRs and close the issues.

teuben · 2020-07-14T13:17:11Z

so done! I am finished with my review (with my apologies as google decided to count all my joss emails as spam)

diehlpk · 2020-07-14T14:55:08Z

@teuben Thanks.

diehlpk · 2020-07-14T16:13:02Z

@mdpiper I will do the final review on the paper by the end of this week. After that

When a submission is ready to be accepted, we ask that the authors issue a new tagged release of the software (if changed), and archive it (on Zenodo, figshare, or other). The authors then post the version number and archive DOI in the REVIEW issue.

diehlpk · 2020-07-14T17:42:29Z

@mdpiper

State of the field: Do the authors describe how this software compares to other commonly-used packages?

The reviewers agreed on this, however, I am as not as deeply in the topic would prefer if you can highlight this point in the paper a little more. So a broader audience can see this point.

Everything else is fine. After this point is improved, you can start to generate the archive and update the version including the two new pull requests.

mdpiper · 2020-07-14T17:48:05Z

@diehlpk Thanks for your editorial review. I'll add some text to this point. And another thank you--this a good point to make considering model coupling is decades old in, e.g., atmospheric sciences, but still relatively new in the geosciences.

diehlpk · 2020-07-16T13:55:23Z

@whedon generate pdf

whedon · 2020-07-16T13:55:57Z

👉 Check article proof 📄 👈

mdpiper · 2020-07-16T16:18:17Z

@diehlpk Waiting on my coauthors to review my changes...

whedon · 2020-07-21T18:16:52Z

👉 Check article proof 📄 👈

diehlpk · 2020-07-21T18:19:52Z

@mdpiper Can you please check this version of the paper as the final version? After you confirmed I will pass the paper to the EICs. We like to avoid to do some after publication changes.

mdpiper · 2020-07-21T18:55:57Z

@diehlpk The rendered PDF is correct; however, I merged the mdpiper/paper branch into master earlier this morning. (I'm not sure if this is important, but I want to check.)

diehlpk · 2020-07-21T19:23:11Z

@whedon accept

whedon · 2020-07-21T19:23:14Z

Attempting dry run of processing paper acceptance...

whedon · 2020-07-21T19:23:42Z

Reference check summary:

OK DOIs

- 10.1029/2018JF004757 is OK

MISSING DOIs

- https://doi.org/10.1177/1094342005056120 may be missing for title: Design and implementation of components in the Earth System Modeling Framework
- https://doi.org/10.1177/1094342011414036 may be missing for title: High-performance language interoperability for scientific computing through Babel
- https://doi.org/10.5194/nhess-19-1723-2019 may be missing for title: Evaluating the impact of model complexity on flood wave propagation and inundation extent with a hydrologic-hydrodynamic model coupling framework
- https://doi.org/10.1016/j.cageo.2012.04.002 may be missing for title: A component-based approach to integrated modeling in the geosciences: The design of CSDMS

INVALID DOIs

- None

whedon · 2020-07-21T19:23:53Z

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1586

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1586, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

mdpiper · 2020-07-21T19:36:49Z

Thanks, @diehlpk, @yangbai90, and @teuben!

Kevin-Mattheus-Moerman · 2020-07-23T15:30:32Z

@mdpiper I've reviewed your paper. It is ready for acceptance once you make the below change. You can run @whedon generate pdf here to update the paper once you are finished.

Can you add countries to your affiliations?

mdpiper · 2020-07-23T15:42:36Z

@Kevin-Mattheus-Moerman Thank you! Done!

mdpiper · 2020-07-23T15:42:55Z

@whedon generate pdf

whedon · 2020-07-23T15:43:42Z

👉 Check article proof 📄 👈

Kevin-Mattheus-Moerman · 2020-07-23T17:10:00Z

@whedon accept

whedon · 2020-07-23T17:10:03Z

Attempting dry run of processing paper acceptance...

whedon · 2020-07-23T17:10:26Z

Reference check summary:

OK DOIs

- 10.1029/2018JF004757 is OK

MISSING DOIs

- https://doi.org/10.1177/1094342005056120 may be missing for title: Design and implementation of components in the Earth System Modeling Framework
- https://doi.org/10.1177/1094342011414036 may be missing for title: High-performance language interoperability for scientific computing through Babel
- https://doi.org/10.5194/nhess-19-1723-2019 may be missing for title: Evaluating the impact of model complexity on flood wave propagation and inundation extent with a hydrologic-hydrodynamic model coupling framework
- https://doi.org/10.1016/j.cageo.2012.04.002 may be missing for title: A component-based approach to integrated modeling in the geosciences: The design of CSDMS

INVALID DOIs

- None

whedon · 2020-07-23T17:10:37Z

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1587

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1587, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

Kevin-Mattheus-Moerman · 2020-07-23T17:14:59Z

@whedon accept deposit=true

whedon · 2020-07-23T17:15:02Z

Doing it live! Attempting automated processing of paper acceptance...

whedon · 2020-07-23T17:15:45Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2020-07-23T17:15:46Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02317 joss-papers#1588
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02317
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

whedon · 2020-07-23T17:23:56Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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.02317/status.svg)](https://doi.org/10.21105/joss.02317)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02317">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02317/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02317/status.svg
   :target: https://doi.org/10.21105/joss.02317

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:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

mdpiper · 2020-07-23T17:29:55Z

Yay! cc: @mcflugen @gregtucker

mdpiper · 2020-07-28T15:15:22Z

@diehlpk I noticed in the citation string on the sidebar that the volume/issue number on this paper is 1(1), but the papers before/after it are 5(51). (And in the PDF of this paper, the volume/issue are listed as 5(51)) Can you recommend where to check on or report this?

arfon · 2020-07-30T00:52:19Z

@diehlpk I noticed in the citation string on the sidebar that the volume/issue number on this paper is 1(1), but the papers before/after it are 5(51). (And in the PDF of this paper, the volume/issue are listed as 5(51)) Can you recommend where to check on or report this?

I've just fixed this. Not quite sure what happened here...

mdpiper · 2020-07-30T01:36:54Z

@arfon Thank you!

whedon added the review label Jun 9, 2020

whedon assigned diehlpk Jun 9, 2020

whedon mentioned this issue Jun 9, 2020

[PRE REVIEW]: The Basic Model Interface 2.0: A standard interface for coupling numerical models in the geosciences #2280

Closed

whedon assigned teuben and yangbai90 Jun 10, 2020

This was referenced Jun 29, 2020

SIDL reminders in generated files? csdms/bmi#68

Closed

package bmic not found (in a non-standard prefix install) csdms/bmi#69

Closed

whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Jul 21, 2020

whedon added accepted published Papers published in JOSS labels Jul 23, 2020

Kevin-Mattheus-Moerman closed this as completed Jul 23, 2020

editorialbot mentioned this issue Jan 18, 2024

[PRE REVIEW]: SitCoM: Modular framework for the integration of (extreme) events and their impacts in Unity #6239

Closed

[REVIEW]: The Basic Model Interface 2.0: A standard interface for coupling numerical models in the geosciences #2317

[REVIEW]: The Basic Model Interface 2.0: A standard interface for coupling numerical models in the geosciences #2317

Comments

whedon commented Jun 9, 2020 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @yangbai90

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @teuben

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Jun 9, 2020

whedon commented Jun 9, 2020

whedon commented Jun 9, 2020

mdpiper commented Jun 9, 2020

yangbai90 commented Jun 10, 2020

mdpiper commented Jun 10, 2020

diehlpk commented Jun 11, 2020

mdpiper commented Jun 11, 2020

diehlpk commented Jun 12, 2020 • edited Loading

yangbai90 commented Jun 14, 2020

diehlpk commented Jun 16, 2020

diehlpk commented Jun 26, 2020

teuben commented Jun 27, 2020 via email

diehlpk commented Jun 29, 2020

mdpiper commented Jul 10, 2020

teuben commented Jul 14, 2020

diehlpk commented Jul 14, 2020

diehlpk commented Jul 14, 2020

diehlpk commented Jul 14, 2020 • edited Loading

mdpiper commented Jul 14, 2020 • edited Loading

diehlpk commented Jul 16, 2020

whedon commented Jul 16, 2020

mdpiper commented Jul 16, 2020

whedon commented Jul 21, 2020

diehlpk commented Jul 21, 2020

mdpiper commented Jul 21, 2020

diehlpk commented Jul 21, 2020

whedon commented Jul 21, 2020

whedon commented Jul 21, 2020

whedon commented Jul 21, 2020

mdpiper commented Jul 21, 2020

Kevin-Mattheus-Moerman commented Jul 23, 2020 • edited by mdpiper Loading

mdpiper commented Jul 23, 2020

mdpiper commented Jul 23, 2020

whedon commented Jul 23, 2020

Kevin-Mattheus-Moerman commented Jul 23, 2020

whedon commented Jul 23, 2020

whedon commented Jul 23, 2020

whedon commented Jul 23, 2020

Kevin-Mattheus-Moerman commented Jul 23, 2020

whedon commented Jul 23, 2020

whedon commented Jul 23, 2020

whedon commented Jul 23, 2020

whedon commented Jul 23, 2020

mdpiper commented Jul 23, 2020

mdpiper commented Jul 28, 2020

arfon commented Jul 30, 2020

mdpiper commented Jul 30, 2020

whedon commented Jun 9, 2020 •

edited

Loading

diehlpk commented Jun 12, 2020 •

edited

Loading

diehlpk commented Jul 14, 2020 •

edited

Loading

mdpiper commented Jul 14, 2020 •

edited

Loading

Kevin-Mattheus-Moerman commented Jul 23, 2020 •

edited by mdpiper

Loading